diff --git a/.gitmodules b/.gitmodules
deleted file mode 100644
index a6b4e12431a3c6b6994a9066e7cefe8d498c182e..0000000000000000000000000000000000000000
--- a/.gitmodules
+++ /dev/null
@@ -1,3 +0,0 @@
-[submodule "src/sge_modules"]
- path = src/.psmn_modules
- url = gitlab_lbmc:PSMN/modules.git
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 94a42d8af2ed58830fa2be3849124103b1394372..03648b4bcba3a59235e177281406520da2dc4239 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,6 +4,19 @@ All notable changes to this project will be documented in this file.
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+## [0.4.0] - 2019-11-18
+### Added
+- Add new tools (star,...)
+- conda support at the psmn
+
+## Changed
+- configuration simplification
+- docker and singularity image download instead of local build
+- hidden directories in `src` for project clarity (only `nf_modules` is visible)
+
+## Removed
+- conda support at in2p3 with `-profile in2p3_conda`
+
## [0.3.0] - 2019-05-23
### Added
- Add new tools (umi_tools, fastp,...)
diff --git a/README.md b/README.md
index 9fbd72fdc0a3af64ba960e437ac114843a034823..6b234ca424808ecd98e59eab9646e4a073a71dac 100644
--- a/README.md
+++ b/README.md
@@ -8,7 +8,7 @@ To get the last commits from this repository into your fork use the following co
git remote add upstream gitlab_lbmc:pipelines/nextflow.git
git pull upstream master
```
-If you created your `.config` file before version `0.4.0` you need to run the script `src/.update_config.sh` to use the latest docker, singularity and conda configuration (don't forget to check your config files afterward for typos).
+**If you created your `.config` file before version `0.4.0` you need to run the script `src/.update_config.sh` to use the latest docker, singularity and conda configuration (don't forget to check your config files afterward for typos).**
## Getting Started
diff --git a/doc/available_tools.md b/doc/available_tools.md
index 10b97ea32253586727954a4a4019b23a055aa67f..297cc27e9211f15023d415a8e20b13b54c8aac18 100644
--- a/doc/available_tools.md
+++ b/doc/available_tools.md
@@ -34,6 +34,7 @@ sambamba | ok | ok | ok | ok
samblaster | ok | ok | ok | ok
SAMtools | ok | ok | ok | ok
SRAtoolkit | ok | ok | ok | ok
+STAR | ok | ok | ok | ok
subread | **no** | ok | ok | ok
TopHat | **no** | ok | ok | ok
Trimmomatic | **no** | ok | ok | ok
diff --git a/doc/nf_projects.md b/doc/nf_projects.md
index cee6deaffa8033703ac26d7493daad2a7626c2ad..2307ef1cd0df4552620476e510d420cde3e955ec 100644
--- a/doc/nf_projects.md
+++ b/doc/nf_projects.md
@@ -5,6 +5,7 @@
- [https://_https://gitlab.biologie.ens-lyon.fr/gylab/salmoninyeast](https://_https://gitlab.biologie.ens-lyon.fr/gylab/salmoninyeast)
- [https://github.com/LBMC/readthroughpombe](https://github.com/LBMC/readthroughpombe)
- [https://_https://gitlab.biologie.ens-lyon.fr/vvanoost/nextflow](https://_https://gitlab.biologie.ens-lyon.fr/vvanoost/nextflow)
+- [https://gitlab.biologie.ens-lyon.fr/elabaron/HIV_project](https://gitlab.biologie.ens-lyon.fr/elabaron/HIV_project)
### single-cell RNA_-Seq
diff --git a/src/.conda_packages.sh b/src/.conda_packages.sh
index 9ac4dfa7246a8e2c82e3db4edc9cbb49042cafa5..bbf88057d7bff8c04a22c339d78f85fa24c6e4f8 100644
--- a/src/.conda_packages.sh
+++ b/src/.conda_packages.sh
@@ -147,3 +147,12 @@ fi
if [ ! -d ${CONDA_ENVS}star_2.7.3a ]; then
conda create --yes --name star_2.7.3a star=2.7.3a
fi
+if [ ! -d ${CONDA_ENVS}liftover_357 ]; then
+ conda create --yes --name liftover_357 ucsc-liftover==357
+fi
+if [ ! -d ${CONDA_ENVS}axtchain_377 ]; then
+ conda create --yes --name axtchain_377 ucsc-axtchain==377
+fi
+if [ ! -d ${CONDA_ENVS}ribotish_0.2.4 ]; then
+ conda create --name ribotish_0.2.4 ribotish=0.2.4
+fi
diff --git a/src/.docker_modules/bcftools/1.7/docker_init.sh b/src/.docker_modules/bcftools/1.7/docker_init.sh
index 043a63f0e984eb54c108f2baf27ce896dd71dfef..c2bf925159aeb2708d742ff891ff96b5d40bf05a 100755
--- a/src/.docker_modules/bcftools/1.7/docker_init.sh
+++ b/src/.docker_modules/bcftools/1.7/docker_init.sh
@@ -1,2 +1,4 @@
#!/bin/sh
-docker build src/docker_modules/bcftools/1.7 -t 'lbmc/bcftools:1.7'
+docker pull lbmc/bcftools:1.7
+docker build src/.docker_modules/bcftools/1.7 -t 'lbmc/bcftools:1.7'
+docker push lbmc/bcftools:1.7
diff --git a/src/.docker_modules/bedtools/2.25.0/docker_init.sh b/src/.docker_modules/bedtools/2.25.0/docker_init.sh
index 37c05b9d296cb3168afbab20d4ff105ccf3e56c4..e35c4d6aa13c4fd78c4797d68150471af81ef94a 100755
--- a/src/.docker_modules/bedtools/2.25.0/docker_init.sh
+++ b/src/.docker_modules/bedtools/2.25.0/docker_init.sh
@@ -1,2 +1,4 @@
#!/bin/sh
-docker build src/docker_modules/bedtools/2.25.0 -t 'lbmc/bedtools:2.25.0'
+docker pull lbmc/bedtools:2.25.0
+docker build src/.docker_modules/bedtools/2.25.0 -t 'lbmc/bedtools:2.25.0'
+docker push lbmc/bedtools:2.25.0
diff --git a/src/.docker_modules/bioawk/1.0/docker_init.sh b/src/.docker_modules/bioawk/1.0/docker_init.sh
index abbb1e237459d0b8398add029b37de9a1af344b9..8e6d7444062e7368f074f0b80386060e0f0b1a07 100755
--- a/src/.docker_modules/bioawk/1.0/docker_init.sh
+++ b/src/.docker_modules/bioawk/1.0/docker_init.sh
@@ -1,2 +1,4 @@
#!/bin/sh
-docker build src/docker_modules/bioawk/1.0 -t 'lbmc/bioawk:1.0'
+docker pull lbmc/bioawk:1.0
+docker build src/.docker_modules/bioawk/1.0 -t 'lbmc/bioawk:1.0'
+docker push lbmc/bioawk:1.0
diff --git a/src/.docker_modules/bowtie/1.2.2/docker_init.sh b/src/.docker_modules/bowtie/1.2.2/docker_init.sh
index 46f450277569b3d167001c93f43fdd2e57916efa..814a311d967eaf943fd1fa864c8c137ce724c812 100755
--- a/src/.docker_modules/bowtie/1.2.2/docker_init.sh
+++ b/src/.docker_modules/bowtie/1.2.2/docker_init.sh
@@ -1,2 +1,4 @@
#!/bin/sh
-docker build src/docker_modules/bowtie/1.2.2 -t 'lbmc/bowtie:1.2.2'
+docker pull lbmc/bowtie:1.2.2
+docker build src/.docker_modules/bowtie/1.2.2 -t 'lbmc/bowtie:1.2.2'
+docker push lbmc/bowtie:1.2.2
diff --git a/src/.docker_modules/bowtie2/2.3.4.1/docker_init.sh b/src/.docker_modules/bowtie2/2.3.4.1/docker_init.sh
index 83cc97d23b38571387474fee55dc7b7ba06e43aa..bdb93e1663ee77e81a65020a0f25a8df182f9245 100755
--- a/src/.docker_modules/bowtie2/2.3.4.1/docker_init.sh
+++ b/src/.docker_modules/bowtie2/2.3.4.1/docker_init.sh
@@ -1,2 +1,4 @@
#!/bin/sh
-docker build src/docker_modules/bowtie2/2.3.4.1 -t 'lbmc/bowtie2:2.3.4.1'
+docker pull lbmc/bowtie2:2.3.4.1
+docker build src/.docker_modules/bowtie2/2.3.4.1 -t 'lbmc/bowtie2:2.3.4.1'
+docker push lbmc/bowtie2:2.3.4.1
diff --git a/src/.docker_modules/bwa/0.7.17/Dockerfile b/src/.docker_modules/bwa/0.7.17/Dockerfile
index 7a538498bc4a1489f31fe2692224c02203042c44..654cf85e6c005f5be0fbae74fb5624848a367981 100644
--- a/src/.docker_modules/bwa/0.7.17/Dockerfile
+++ b/src/.docker_modules/bwa/0.7.17/Dockerfile
@@ -1,10 +1,10 @@
-FROM sambamba:0.6.7
+FROM lbmc/sambamba:0.6.9
MAINTAINER Laurent Modolo
ENV BWA_VERSION=0.7.17
ENV SAMBLASTER_VERSION=0.1.24
-ENV PACKAGES curl=7.58.0* \
+ENV PACKAGES curl=7.58* \
ca-certificates=20180409 \
build-essential=12.4* \
zlib1g-dev=1:1.2.11*
diff --git a/src/.docker_modules/bwa/0.7.17/docker_init.sh b/src/.docker_modules/bwa/0.7.17/docker_init.sh
index 1b1f27f1a6df201cc8de7ec808f3094574464efb..3cabcbd9adcfdc35d6746a3f56534170a2d1d63a 100755
--- a/src/.docker_modules/bwa/0.7.17/docker_init.sh
+++ b/src/.docker_modules/bwa/0.7.17/docker_init.sh
@@ -1,2 +1,4 @@
#!/bin/sh
-docker build src/docker_modules/bwa/0.7.17 -t 'lbmc/bwa:0.7.17'
+docker pull lbmc/bwa:0.7.17
+docker build src/.docker_modules/bwa/0.7.17 -t 'lbmc/bwa:0.7.17'
+docker push lbmc/bwa:0.7.17
diff --git a/src/.docker_modules/canu/1.6/docker_init.sh b/src/.docker_modules/canu/1.6/docker_init.sh
index 0b96ce1ed5dca35872982c2a8a8d5a93bf111076..b1afabb6dedba67dc9a9537ea570a9c5c62da28f 100755
--- a/src/.docker_modules/canu/1.6/docker_init.sh
+++ b/src/.docker_modules/canu/1.6/docker_init.sh
@@ -1,2 +1,4 @@
#!/bin/sh
-docker build src/docker_modules/canu/1.6 -t 'lbmc/canu:1.6'
+docker pull lbmc/canu:1.6
+docker build src/.docker_modules/canu/1.6 -t 'lbmc/canu:1.6'
+docker push lbmc/canu:1.6
diff --git a/src/.docker_modules/cutadapt/1.14/docker_init.sh b/src/.docker_modules/cutadapt/1.14/docker_init.sh
index 7390c9f69d501317b76197e3d6a72258aa7f4eca..1ba18cb47af7cf8a8c9d4d0fee001f8e2d5747b1 100755
--- a/src/.docker_modules/cutadapt/1.14/docker_init.sh
+++ b/src/.docker_modules/cutadapt/1.14/docker_init.sh
@@ -1,2 +1,4 @@
#!/bin/sh
-docker build src/docker_modules/cutadapt/1.14 -t 'lbmc/cutadapt:1.14'
+docker pull lbmc/cutadapt:1.14
+docker build src/.docker_modules/cutadapt/1.14 -t 'lbmc/cutadapt:1.14'
+docker push lbmc/cutadapt:1.14
diff --git a/src/.docker_modules/cutadapt/1.15/docker_init.sh b/src/.docker_modules/cutadapt/1.15/docker_init.sh
index c5ead618afb680b467044ba43e5c262893a3f5a8..49303006414d8a1ab61bda8da49b850824dde551 100755
--- a/src/.docker_modules/cutadapt/1.15/docker_init.sh
+++ b/src/.docker_modules/cutadapt/1.15/docker_init.sh
@@ -1,2 +1,4 @@
#!/bin/sh
-docker build src/docker_modules/cutadapt/1.15 -t 'lbmc/cutadapt:1.15'
+docker pull lbmc/cutadapt:1.15
+docker build src/.docker_modules/cutadapt/1.15 -t 'lbmc/cutadapt:1.15'
+docker push lbmc/cutadapt:1.15
diff --git a/src/.docker_modules/cutadapt/2.1/docker_init.sh b/src/.docker_modules/cutadapt/2.1/docker_init.sh
index 4b55d68ea92596035f0b8d97dd96b526fefae8b7..cda255f0f22841d3f9cdf61480a053d47c948071 100755
--- a/src/.docker_modules/cutadapt/2.1/docker_init.sh
+++ b/src/.docker_modules/cutadapt/2.1/docker_init.sh
@@ -1,2 +1,4 @@
#!/bin/sh
-docker build src/docker_modules/cutadapt/2.1 -t 'lbmc/cutadapt:2.1'
+docker pull lbmc/cutadapt:2.1
+docker build src/.docker_modules/cutadapt/2.1 -t 'lbmc/cutadapt:2.1'
+docker push lbmc/cutadapt:2.1
diff --git a/src/.docker_modules/deeptools/3.0.2/docker_init.sh b/src/.docker_modules/deeptools/3.0.2/docker_init.sh
index cb392df1f7eaff43aa6d069d500fdd1da92a3ca8..33959edcd7627e94d34d890d875d6cbe0fced74f 100755
--- a/src/.docker_modules/deeptools/3.0.2/docker_init.sh
+++ b/src/.docker_modules/deeptools/3.0.2/docker_init.sh
@@ -1,2 +1,4 @@
#!/bin/sh
-docker build src/docker_modules/deeptools/3.0.2 -t 'lbmc/deeptools:3.0.2'
+docker pull lbmc/deeptools:3.0.2
+docker build src/.docker_modules/deeptools/3.0.2 -t 'lbmc/deeptools:3.0.2'
+docker push lbmc/deeptools:3.0.2
diff --git a/src/.docker_modules/deeptools/3.1.1/docker_init.sh b/src/.docker_modules/deeptools/3.1.1/docker_init.sh
index 7f0e94ff8d6744ec40054797874c33dd82270ba4..06e63a90199385965a012175fe3f448f75539ba4 100755
--- a/src/.docker_modules/deeptools/3.1.1/docker_init.sh
+++ b/src/.docker_modules/deeptools/3.1.1/docker_init.sh
@@ -1,2 +1,4 @@
#!/bin/sh
-docker build src/docker_modules/deeptools/3.1.1 -t 'lbmc/deeptools:3.1.1'
+docker pull lbmc/deeptools:3.1.1
+docker build src/.docker_modules/deeptools/3.1.1 -t 'lbmc/deeptools:3.1.1'
+docker push lbmc/deeptools:3.1.1
diff --git a/src/.docker_modules/docker_push.sh b/src/.docker_modules/docker_push.sh
index 37616d0f9e9c5c34123eb6f81e7c3380134e0809..32e0abc1fac52ceb410b03200b80eea96e9b181a 100755
--- a/src/.docker_modules/docker_push.sh
+++ b/src/.docker_modules/docker_push.sh
@@ -1,2 +1,2 @@
#!/bin/sh
-fd "Dockerfile" src/docke_modules | perl -pe 's|.*docker_modules/(.*)/(.*)/Dockerfile|\1:\2|g' | awk '{system("docker push lbmc/"$0)}'
+fd "Dockerfile" src/.docker_modules | perl -pe 's|.*docker_modules/(.*)/(.*)/Dockerfile|\1:\2|g' | awk '{system("docker push lbmc/"$0)}'
diff --git a/src/.docker_modules/docker_update.sh b/src/.docker_modules/docker_update.sh
index 1ac40cbacd01cdf533dfb0316c19a17037c55bc9..39a729bf3b000647df396663343ac7ef64c30f63 100644
--- a/src/.docker_modules/docker_update.sh
+++ b/src/.docker_modules/docker_update.sh
@@ -1,2 +1,2 @@
#!/bin/sh
-fd "Dockerfile" src/docke_modules | perl -pe 's|.*docker_modules/(.*)/(.*)/Dockerfile|\1:\2|g' | awk '{system("docker tag "$0" lbmc/" $0)}'
+fd "Dockerfile" src/.docke_modules | perl -pe 's|.*docker_modules/(.*)/(.*)/Dockerfile|\1:\2|g' | awk '{system("docker tag "$0" lbmc/" $0)}'
diff --git a/src/.docker_modules/fastp/0.19.7/docker_init.sh b/src/.docker_modules/fastp/0.19.7/docker_init.sh
index 51b7257985e9834345abaffba6681b7913e2b117..1085915c2cfd5caf2599275d8ad50a909704d728 100755
--- a/src/.docker_modules/fastp/0.19.7/docker_init.sh
+++ b/src/.docker_modules/fastp/0.19.7/docker_init.sh
@@ -1,2 +1,4 @@
#!/bin/sh
-docker build src/docker_modules/fastp/0.19.7 -t 'lbmc/fastp:0.19.7'
+docker pull lbmc/fastp:0.19.7
+docker build src/.docker_modules/fastp/0.19.7 -t 'lbmc/fastp:0.19.7'
+docker push lbmc/fastp:0.19.7
diff --git a/src/.docker_modules/fastqc/0.11.5/docker_init.sh b/src/.docker_modules/fastqc/0.11.5/docker_init.sh
index d42d456c49351557ff900ae3b07eace5f9937fea..6b82ff40580dc34b3594278ef2f9c46d36f73560 100755
--- a/src/.docker_modules/fastqc/0.11.5/docker_init.sh
+++ b/src/.docker_modules/fastqc/0.11.5/docker_init.sh
@@ -1,2 +1,4 @@
#!/bin/sh
-docker build src/docker_modules/fastqc/0.11.5 -t 'lbmc/fastqc:0.11.5'
+docker pull lbmc/fastqc:0.11.5
+docker build src/.docker_modules/fastqc/0.11.5 -t 'lbmc/fastqc:0.11.5'
+docker push lbmc/fastqc:0.11.5
diff --git a/src/.docker_modules/file_handle/0.1.1/docker_init.sh b/src/.docker_modules/file_handle/0.1.1/docker_init.sh
index 8fbeec247b4fc96f3c93045d6abf6b304514a4e4..0f1cf512532dc8d72490b9ebb174d90418f4c640 100755
--- a/src/.docker_modules/file_handle/0.1.1/docker_init.sh
+++ b/src/.docker_modules/file_handle/0.1.1/docker_init.sh
@@ -1,2 +1,4 @@
#!/bin/sh
-docker build src/docker_modules/file_handle/0.1.1 -t 'lbmc/file_handle:0.1.1'
+docker pull lbmc/file_handle:0.1.1
+docker build src/.docker_modules/file_handle/0.1.1 -t 'lbmc/file_handle:0.1.1'
+docker push lbmc/file_handle:0.1.1
diff --git a/src/.docker_modules/gatk/4.0.8.1/docker_init.sh b/src/.docker_modules/gatk/4.0.8.1/docker_init.sh
index 5363165595215e90d94fd0bfdea60e0a47aea019..ddfd8ee0205fa9e9af20878ec561821fc4173057 100755
--- a/src/.docker_modules/gatk/4.0.8.1/docker_init.sh
+++ b/src/.docker_modules/gatk/4.0.8.1/docker_init.sh
@@ -1,2 +1,4 @@
#!/bin/sh
-docker build src/docker_modules/gatk/4.0.8.1 -t 'lbmc/gatk:4.0.8.1'
+docker pull lbmc/gatk:4.0.8.1
+docker build src/.docker_modules/gatk/4.0.8.1 -t 'lbmc/gatk:4.0.8.1'
+docker push lbmc/gatk:4.0.8.1
diff --git a/src/.docker_modules/hisat2/2.0.0/Dockerfile b/src/.docker_modules/hisat2/2.0.0/Dockerfile
index 640d69196c2da6ea52e6aeb5fb69cf241e955d44..6da58508779ea3adfa22c26f672040e8f588b85c 100644
--- a/src/.docker_modules/hisat2/2.0.0/Dockerfile
+++ b/src/.docker_modules/hisat2/2.0.0/Dockerfile
@@ -1,4 +1,4 @@
-FROM samtools:1.7
+FROM lbmc/samtools:1.7
MAINTAINER Nicolas Fontrodona
ENV HISAT2_VERSION=2.0.0
diff --git a/src/.docker_modules/hisat2/2.0.0/docker_init.sh b/src/.docker_modules/hisat2/2.0.0/docker_init.sh
index cff5d127d39515485f22b7b8a5db12125ff6c77a..8bfb16363342039e3fff7057259a8e835c2a8c6d 100755
--- a/src/.docker_modules/hisat2/2.0.0/docker_init.sh
+++ b/src/.docker_modules/hisat2/2.0.0/docker_init.sh
@@ -1,2 +1,4 @@
#!/bin/sh
-docker build src/docker_modules/hisat2/2.0.0 -t 'lbmc/hisat2:2.0.0'
+docker pull lbmc/hisat2:2.0.0
+docker build src/.docker_modules/hisat2/2.0.0 -t 'lbmc/hisat2:2.0.0'
+docker push lbmc/hisat2:2.0.0
diff --git a/src/.docker_modules/hisat2/2.1.0/Dockerfile b/src/.docker_modules/hisat2/2.1.0/Dockerfile
index 5f937ce5cbd501ccdbea948dc3f080182f6feb4e..0fc7dacd5984006ac3d0dfebe00dfc42ed050cbd 100644
--- a/src/.docker_modules/hisat2/2.1.0/Dockerfile
+++ b/src/.docker_modules/hisat2/2.1.0/Dockerfile
@@ -1,4 +1,4 @@
-FROM samtools:1.7
+FROM lbmc/samtools:1.7
MAINTAINER Nicolas Fontrodona
ENV HISAT2_VERSION=2.1.0
diff --git a/src/.docker_modules/hisat2/2.1.0/docker_init.sh b/src/.docker_modules/hisat2/2.1.0/docker_init.sh
index bbae87cee302e3603942594aa4aa59e967065f48..55fb191ab23cbe7615f70ba5488a227b0b69580a 100755
--- a/src/.docker_modules/hisat2/2.1.0/docker_init.sh
+++ b/src/.docker_modules/hisat2/2.1.0/docker_init.sh
@@ -1,2 +1,4 @@
#!/bin/sh
-docker build src/docker_modules/hisat2/2.1.0 -t 'lbmc/hisat2:2.1.0'
+docker pull lbmc/hisat2:2.1.0
+docker build src/.docker_modules/hisat2/2.1.0 -t 'lbmc/hisat2:2.1.0'
+docker push lbmc/hisat2:2.1.0
diff --git a/src/.docker_modules/htseq/0.11.2/docker_init.sh b/src/.docker_modules/htseq/0.11.2/docker_init.sh
index f2ead7224e493d65290516a6ef40743a7aece6a6..9bd50893380dc1fb19736559551389934802eade 100755
--- a/src/.docker_modules/htseq/0.11.2/docker_init.sh
+++ b/src/.docker_modules/htseq/0.11.2/docker_init.sh
@@ -1,2 +1,4 @@
#!/bin/sh
-docker build src/docker_modules/htseq/0.11.2 -t 'lbmc/htseq:0.11.2'
+docker pull lbmc/htseq:0.11.2
+docker build src/.docker_modules/htseq/0.11.2 -t 'lbmc/htseq:0.11.2'
+docker push lbmc/htseq:0.11.2
diff --git a/src/.docker_modules/htseq/0.8.0/docker_init.sh b/src/.docker_modules/htseq/0.8.0/docker_init.sh
index 09cf7277aeb245bba90da7a4ea48fb89cbb058fd..e322517cf457f8a8a9041da975a7851caf2ab4ef 100755
--- a/src/.docker_modules/htseq/0.8.0/docker_init.sh
+++ b/src/.docker_modules/htseq/0.8.0/docker_init.sh
@@ -1,2 +1,4 @@
#!/bin/sh
-docker build src/docker_modules/htseq/0.8.0 -t 'lbmc/htseq:0.8.0'
+docker pull lbmc/htseq:0.8.0
+docker build src/.docker_modules/htseq/0.8.0 -t 'lbmc/htseq:0.8.0'
+docker push lbmc/htseq:0.8.0
diff --git a/src/.docker_modules/kallisto/0.43.1/docker_init.sh b/src/.docker_modules/kallisto/0.43.1/docker_init.sh
index 1ff3aca3d1b7e8b34326f44230be85fa5be9c5df..b93c004d24d291b3c92bab0ca7d9ae7c7131cf7a 100755
--- a/src/.docker_modules/kallisto/0.43.1/docker_init.sh
+++ b/src/.docker_modules/kallisto/0.43.1/docker_init.sh
@@ -1,2 +1,4 @@
#!/bin/sh
-docker build src/docker_modules/kallisto/0.43.1 -t 'lbmc/kallisto:0.43.1'
+docker pull lbmc/kallisto:0.43.1
+docker build src/.docker_modules/kallisto/0.43.1 -t 'lbmc/kallisto:0.43.1'
+docker push lbmc/kallisto:0.43.1
diff --git a/src/.docker_modules/kallisto/0.44.0/docker_init.sh b/src/.docker_modules/kallisto/0.44.0/docker_init.sh
index 9e071b69f7892bcb3bc01b0e900a83ccbccc9c35..4fa79008a07f4e9a4afe6c8bb20fb8ca60b98858 100755
--- a/src/.docker_modules/kallisto/0.44.0/docker_init.sh
+++ b/src/.docker_modules/kallisto/0.44.0/docker_init.sh
@@ -1,2 +1,4 @@
#!/bin/sh
-docker build src/docker_modules/kallisto/0.44.0 -t 'lbmc/kallisto:0.44.0'
+docker pull lbmc/kallisto:0.44.0
+docker build src/.docker_modules/kallisto/0.44.0 -t 'lbmc/kallisto:0.44.0'
+docker push lbmc/kallisto:0.44.0
diff --git a/src/.docker_modules/liftover/357/Dockerfile b/src/.docker_modules/liftover/357/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..973a1dc03c9cc8c73209f13f1fecf84906b8be7b
--- /dev/null
+++ b/src/.docker_modules/liftover/357/Dockerfile
@@ -0,0 +1,2 @@
+FROM quay.io/biocontainers/ucsc-liftover:357--1
+MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/liftover/357/docker_init.sh b/src/.docker_modules/liftover/357/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..68bd90585292fb30242e3d2cdd94e3538d277f6f
--- /dev/null
+++ b/src/.docker_modules/liftover/357/docker_init.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+docker pull lbmc/liftover:357
+docker build src/.docker_modules/liftover/357/ -t 'lbmc/liftover:357'
+docker push lbmc/liftover:357
diff --git a/src/.docker_modules/macs2/2.1.2/docker_init.sh b/src/.docker_modules/macs2/2.1.2/docker_init.sh
index 02e9a3825b471442a9b96dfa9a00ddaa44e7f648..8dc7b2483a1aa91f1f637e26812469f861b68f0e 100755
--- a/src/.docker_modules/macs2/2.1.2/docker_init.sh
+++ b/src/.docker_modules/macs2/2.1.2/docker_init.sh
@@ -1,2 +1,4 @@
#!/bin/sh
-docker build src/docker_modules/macs2/2.1.2 -t 'lbmc/macs2:2.1.2'
+docker pull lbmc/macs2:2.1.2
+docker build src/.docker_modules/macs2/2.1.2 -t 'lbmc/macs2:2.1.2'
+docker push lbmc/macs2:2.1.2
diff --git a/src/.docker_modules/multiqc/1.0/docker_init.sh b/src/.docker_modules/multiqc/1.0/docker_init.sh
index 0bab07619a87b9f6df257a649a221b1be7a265e0..1b45ce3e7d6a58c98cf34f7614603dec9ad525fc 100755
--- a/src/.docker_modules/multiqc/1.0/docker_init.sh
+++ b/src/.docker_modules/multiqc/1.0/docker_init.sh
@@ -1,2 +1,4 @@
#!/bin/sh
-docker build src/docker_modules/multiqc/1.0 -t 'lbmc/multiqc:1.0'
+docker pull lbmc/multiqc:1.0
+docker build src/.docker_modules/multiqc/1.0 -t 'lbmc/multiqc:1.0'
+docker push lbmc/multiqc:1.0
diff --git a/src/.docker_modules/multiqc/1.7/docker_init.sh b/src/.docker_modules/multiqc/1.7/docker_init.sh
index fb08cc126bc9a242ca3dde042867ec78a08676bf..e091f04a2752d2fcf2901f580ff8f001c8589df6 100755
--- a/src/.docker_modules/multiqc/1.7/docker_init.sh
+++ b/src/.docker_modules/multiqc/1.7/docker_init.sh
@@ -1,2 +1,4 @@
#!/bin/sh
-docker build src/docker_modules/multiqc/1.7 -t 'lbmc/multiqc:1.7'
+docker pull lbmc/multiqc:1.7
+docker build src/.docker_modules/multiqc/1.7 -t 'lbmc/multiqc:1.7'
+docker push lbmc/multiqc:1.7
diff --git a/src/.docker_modules/music/6613c53/docker_init.sh b/src/.docker_modules/music/6613c53/docker_init.sh
index 3666dfaab151065a918b01dab0b54ffe56094b9c..20e327a97a09ced0c55b16d6a780f35a09e1c881 100755
--- a/src/.docker_modules/music/6613c53/docker_init.sh
+++ b/src/.docker_modules/music/6613c53/docker_init.sh
@@ -1,2 +1,4 @@
#!/bin/sh
-docker build src/docker_modules/music/6613c53 -t 'lbmc/music:6613c53'
+docker pull lbmc/music:6613c53
+docker build src/.docker_modules/music/6613c53 -t 'lbmc/music:6613c53'
+docker push lbmc/music:6613c53
diff --git a/src/.docker_modules/picard/2.18.11/docker_init.sh b/src/.docker_modules/picard/2.18.11/docker_init.sh
index 3dc1585140b5891513796d6c4c891c7103aead8f..82c4cf7d3bdf581587fa7a3345cff9cb465158ae 100755
--- a/src/.docker_modules/picard/2.18.11/docker_init.sh
+++ b/src/.docker_modules/picard/2.18.11/docker_init.sh
@@ -1,2 +1,4 @@
#!/bin/sh
-docker build src/docker_modules/picard/2.18.11 -t 'lbmc/picard:2.18.11'
+docker pull lbmc/picard:2.18.11
+docker build src/.docker_modules/picard/2.18.11 -t 'lbmc/picard:2.18.11'
+docker push lbmc/picard:2.18.11
diff --git a/src/.docker_modules/pigz/2.4/docker_init.sh b/src/.docker_modules/pigz/2.4/docker_init.sh
index 84e508a43ec9dbd99fe61eabc74ee345462c64da..38d7347d72e9345ca69f54c9d8ea2ac3ec0ebbb8 100755
--- a/src/.docker_modules/pigz/2.4/docker_init.sh
+++ b/src/.docker_modules/pigz/2.4/docker_init.sh
@@ -1,2 +1,4 @@
#!/bin/sh
-docker build src/docker_modules/pigz/2.4 -t 'lbmc/pigz:2.4'
+docker pull lbmc/pigz:2.4
+docker build src/.docker_modules/pigz/2.4 -t 'lbmc/pigz:2.4'
+docker push lbmc/pigz:2.4
diff --git a/src/.docker_modules/python/3.8/docker_init.sh b/src/.docker_modules/python/3.8/docker_init.sh
index 18b86e72fade35ff21ce512c4324854ffef60dee..9a1c9b8b04f56586c6fadda16add7af4f66c3454 100755
--- a/src/.docker_modules/python/3.8/docker_init.sh
+++ b/src/.docker_modules/python/3.8/docker_init.sh
@@ -1,2 +1,4 @@
#!/bin/sh
-docker build src/docker_modules/python/3.8 -t 'lbmc/python:3.8'
+docker pull lbmc/python:3.8
+docker build src/.docker_modules/python/3.8 -t 'lbmc/python:3.8'
+docker push lbmc/python:3.8
diff --git a/src/.docker_modules/r/3.5.3/docker_init.sh b/src/.docker_modules/r/3.5.3/docker_init.sh
index e9cb205ec1e58e59e252afedde722ddc8cc8e825..ce78559716b93f92c3c602cf242dd1d42a1e6220 100755
--- a/src/.docker_modules/r/3.5.3/docker_init.sh
+++ b/src/.docker_modules/r/3.5.3/docker_init.sh
@@ -1,2 +1,4 @@
#!/bin/sh
-docker build src/docker_modules/r/3.5.3 -t 'lbmc/r:3.5.3'
+docker pull lbmc/r:3.5.3
+docker build src/.docker_modules/r/3.5.3 -t 'lbmc/r:3.5.3'
+docker push lbmc/r:3.5.3
diff --git a/src/.docker_modules/rsem/1.3.0/docker_init.sh b/src/.docker_modules/rsem/1.3.0/docker_init.sh
index 2907c0ea05d66a5b684c5844bfc3688d8bce2540..aadcb4d8ce01353c3510a6a649d640121865bf8d 100755
--- a/src/.docker_modules/rsem/1.3.0/docker_init.sh
+++ b/src/.docker_modules/rsem/1.3.0/docker_init.sh
@@ -1,2 +1,4 @@
#!/bin/sh
-docker build src/docker_modules/rsem/1.3.0 -t 'lbmc/rsem:1.3.0'
+docker pull lbmc/rsem:1.3.0
+docker build src/.docker_modules/rsem/1.3.0 -t 'lbmc/rsem:1.3.0'
+docker push lbmc/rsem:1.3.0
diff --git a/src/.docker_modules/salmon/0.8.2/docker_init.sh b/src/.docker_modules/salmon/0.8.2/docker_init.sh
index 3a776c0845c5c4cc75e408601af7b22db7108e8f..f44850b49c43ae852f1ef93b88a09f301169f780 100755
--- a/src/.docker_modules/salmon/0.8.2/docker_init.sh
+++ b/src/.docker_modules/salmon/0.8.2/docker_init.sh
@@ -1,2 +1,4 @@
#!/bin/sh
-docker build src/docker_modules/salmon/0.8.2 -t 'lbmc/salmon:0.8.2'
+docker pull lbmc/salmon:0.8.2
+docker build src/.docker_modules/salmon/0.8.2 -t 'lbmc/salmon:0.8.2'
+docker push lbmc/salmon:0.8.2
diff --git a/src/.docker_modules/sambamba/0.6.7/docker_init.sh b/src/.docker_modules/sambamba/0.6.7/docker_init.sh
index d203b20ca443ea044d4c45b69f4f17f9f8cff553..ccedf316633c21653bde1312e1ccd5376b95fafe 100755
--- a/src/.docker_modules/sambamba/0.6.7/docker_init.sh
+++ b/src/.docker_modules/sambamba/0.6.7/docker_init.sh
@@ -1,2 +1,4 @@
#!/bin/sh
-docker build src/docker_modules/sambamba/0.6.7 -t 'lbmc/sambamba:0.6.7'
+docker pull lbmc/sambamba:0.6.7
+docker build src/.docker_modules/sambamba/0.6.7 -t 'lbmc/sambamba:0.6.7'
+docker push lbmc/sambamba:0.6.7
diff --git a/src/.docker_modules/sambamba/0.6.9/Dockerfile b/src/.docker_modules/sambamba/0.6.9/Dockerfile
index 689d0265c734c597a1983491918258909e33c9fe..f45a65412dba77df471e7cd8ee5c79bd2439f1d9 100644
--- a/src/.docker_modules/sambamba/0.6.9/Dockerfile
+++ b/src/.docker_modules/sambamba/0.6.9/Dockerfile
@@ -11,7 +11,6 @@ RUN apt-get update && \
apt-get install -y --no-install-recommends ${PACKAGES} && \
apt-get clean
-RUN curl -k -L https://github.com/biod/sambamba/releases/download/v${SAMBAMBA_VERSION}/sambamba_v${SAMBAMBA_VERSION}_linux.tar.bz2 -o sambamba_v${SAMBAMBA_VERSION}_linux.tar.bz2 && \
-tar xvjf sambamba_v${SAMBAMBA_VERSION}_linux.tar.bz2 && \
-mv sambamba /usr/bin/ && \
-rm -R sambamba_v${SAMBAMBA_VERSION}_linux*
+RUN curl -k -L https://github.com/biod/sambamba/releases/download/v${SAMBAMBA_VERSION}/sambamba-${SAMBAMBA_VERSION}-linux-static.gz -o sambamba_v${SAMBAMBA_VERSION}_linux.gz && \
+gunzip sambamba_v${SAMBAMBA_VERSION}_linux.gz && \
+mv sambamba_v${SAMBAMBA_VERSION}_linux /usr/bin/sambamba
diff --git a/src/.docker_modules/sambamba/0.6.9/docker_init.sh b/src/.docker_modules/sambamba/0.6.9/docker_init.sh
index 7431118e6962e45dcb3fb1e1064c020910a8cfcb..9525b17e688d739198a1421f641c2281b45ade9a 100755
--- a/src/.docker_modules/sambamba/0.6.9/docker_init.sh
+++ b/src/.docker_modules/sambamba/0.6.9/docker_init.sh
@@ -1,2 +1,4 @@
#!/bin/sh
-docker build src/docker_modules/sambamba/0.6.9 -t 'lbmc/sambamba:0.6.9'
+docker pull lbmc/sambamba:0.6.9
+docker build src/.docker_modules/sambamba/0.6.9 -t 'lbmc/sambamba:0.6.9'
+docker push lbmc/sambamba:0.6.9
diff --git a/src/.docker_modules/samblaster/0.1.24/docker_init.sh b/src/.docker_modules/samblaster/0.1.24/docker_init.sh
index 991b92cbacb705e7528f79e153778c51eda8d0b4..0fec5a0782d348935647212a430f9c1efe7d4367 100755
--- a/src/.docker_modules/samblaster/0.1.24/docker_init.sh
+++ b/src/.docker_modules/samblaster/0.1.24/docker_init.sh
@@ -1,2 +1,4 @@
#!/bin/sh
-docker build src/docker_modules/samblaster/0.1.24 -t 'lbmc/samblaster:0.1.24'
+docker pull lbmc/samblaster:0.1.24
+docker build src/.docker_modules/samblaster/0.1.24 -t 'lbmc/samblaster:0.1.24'
+docker push lbmc/samblaster:0.1.24
diff --git a/src/.docker_modules/samtools/1.7/docker_init.sh b/src/.docker_modules/samtools/1.7/docker_init.sh
index 4c47e22b0541c7d7e02a9834e1efd09799ca16f8..83c510a9e6fe22e1c28eac9bed5e44d1c707da15 100755
--- a/src/.docker_modules/samtools/1.7/docker_init.sh
+++ b/src/.docker_modules/samtools/1.7/docker_init.sh
@@ -1,2 +1,4 @@
#!/bin/sh
-docker build src/docker_modules/samtools/1.7 -t 'lbmc/samtools:1.7'
+docker pull lbmc/samtools:1.7
+docker build src/.docker_modules/samtools/1.7 -t 'lbmc/samtools:1.7'
+docker push lbmc/samtools:1.7
diff --git a/src/.docker_modules/sratoolkit/2.8.2/docker_init.sh b/src/.docker_modules/sratoolkit/2.8.2/docker_init.sh
index a7f547e1248b7908dafd47755189d63adde9736e..ce040fcc1b3ed4f7041d01421e7a2031d983ef6f 100755
--- a/src/.docker_modules/sratoolkit/2.8.2/docker_init.sh
+++ b/src/.docker_modules/sratoolkit/2.8.2/docker_init.sh
@@ -1,2 +1,4 @@
#!/bin/sh
-docker build src/docker_modules/sratoolkit/2.8.2 -t 'lbmc/sratoolkit:2.8.2'
+docker pull lbmc/sratoolkit:2.8.2
+docker build src/.docker_modules/sratoolkit/2.8.2 -t 'lbmc/sratoolkit:2.8.2'
+docker push lbmc/sratoolkit:2.8.2
diff --git a/src/.docker_modules/star/2.7.3a/Dockerfile b/src/.docker_modules/star/2.7.3a/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..a045a2352dd59dc8de04e07b233a0399b891cde8
--- /dev/null
+++ b/src/.docker_modules/star/2.7.3a/Dockerfile
@@ -0,0 +1,2 @@
+FROM quay.io/biocontainers/star:2.7.3a--0
+MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/star/2.7.3a/docker_init.sh b/src/.docker_modules/star/2.7.3a/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..50beecfcc7fcb7a9b1943a418651cafb55851495
--- /dev/null
+++ b/src/.docker_modules/star/2.7.3a/docker_init.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+docker pull lbmc/star:2.7.3a
+docker build src/.docker_modules/star/2.7.3a/ -t 'lbmc/star:2.7.3a'
+docker push lbmc/star:2.7.3a
diff --git a/src/.docker_modules/subread/1.6.4/docker_init.sh b/src/.docker_modules/subread/1.6.4/docker_init.sh
index 574c2031d72ff9fd18760ab237dd4496f469a8d2..0dd51ca0dbc45ab1b2c237c1a43c670f14dd184a 100755
--- a/src/.docker_modules/subread/1.6.4/docker_init.sh
+++ b/src/.docker_modules/subread/1.6.4/docker_init.sh
@@ -1,2 +1,4 @@
#!/bin/sh
-docker build src/docker_modules/subread/1.6.4 -t 'lbmc/subread:1.6.4'
+docker pull lbmc/subread:1.6.4
+docker build src/.docker_modules/subread/1.6.4 -t 'lbmc/subread:1.6.4'
+docker push lbmc/subread:1.6.4
diff --git a/src/.docker_modules/tophat/2.1.1/docker_init.sh b/src/.docker_modules/tophat/2.1.1/docker_init.sh
index a6125a865514cedfbb745a2b676d75b3e5cf3c6d..67151131596b2c2dda5e5cc7beadc69dcd64aa6c 100755
--- a/src/.docker_modules/tophat/2.1.1/docker_init.sh
+++ b/src/.docker_modules/tophat/2.1.1/docker_init.sh
@@ -1,2 +1,4 @@
#!/bin/sh
-docker build src/docker_modules/tophat/2.1.1 -t 'lbmc/tophat:2.1.1'
+docker pull lbmc/tophat:2.1.1
+docker build src/.docker_modules/tophat/2.1.1 -t 'lbmc/tophat:2.1.1'
+docker push lbmc/tophat:2.1.1
diff --git a/src/.docker_modules/trimmomatic/0.36/docker_init.sh b/src/.docker_modules/trimmomatic/0.36/docker_init.sh
index 27c970f4c29afb81cf7c079349dc35fe89847110..f054581bde67aff212a04284c5f463f8a6e4ab75 100755
--- a/src/.docker_modules/trimmomatic/0.36/docker_init.sh
+++ b/src/.docker_modules/trimmomatic/0.36/docker_init.sh
@@ -1,2 +1,4 @@
#!/bin/sh
-docker build src/docker_modules/trimmomatic/0.36 -t 'lbmc/trimmomatic:0.36'
+docker pull lbmc/trimmomatic:0.36
+docker build src/.docker_modules/trimmomatic/0.36 -t 'lbmc/trimmomatic:0.36'
+docker push lbmc/trimmomatic:0.36
diff --git a/src/.docker_modules/ucsc/375/Dockerfile b/src/.docker_modules/ucsc/375/Dockerfile
index bd45e0abe38e2aa1736e6b10c6a48a52b1c03569..9365a974bdc86f80897ad97ca8d13436b3bb364d 100644
--- a/src/.docker_modules/ucsc/375/Dockerfile
+++ b/src/.docker_modules/ucsc/375/Dockerfile
@@ -21,6 +21,7 @@ RUN curl -k -L http://hgdownload.soe.ucsc.edu/admin/exe/userApps.v${UCSC_VERSION
tar xvf userApps.v${UCSC_VERSION}.src.tgz &&\
cd userApps/ && \
make &&\
+cd .. &&\
mv userApps/bin/* /usr/bin/ &&\
rm -R userApps.v${UCSC_VERSION}.src.tgz &&\
rm -R userApps
diff --git a/src/.docker_modules/ucsc/375/docker_init.sh b/src/.docker_modules/ucsc/375/docker_init.sh
index 5fd1371ccd03f8c12b515884df3ffeea736250b3..f0cc90565cc1f5583eb0c4303976300f695500e0 100755
--- a/src/.docker_modules/ucsc/375/docker_init.sh
+++ b/src/.docker_modules/ucsc/375/docker_init.sh
@@ -1,2 +1,4 @@
#!/bin/sh
-docker build src/docker_modules/ucsc/375/ -t 'lbmc/ucsc:375'
+docker pull lbmc/ucsc:375
+docker build src/.docker_modules/ucsc/375/ -t 'lbmc/ucsc:375'
+docker push lbmc/ucsc:375
diff --git a/src/.docker_modules/umi_tools/0.5.4/docker_init.sh b/src/.docker_modules/umi_tools/0.5.4/docker_init.sh
index 1b11e25daea666b8e9bf130b6a44530194b5bc1c..200e9c066fe98de8262a48eea0f615b064ff90a4 100755
--- a/src/.docker_modules/umi_tools/0.5.4/docker_init.sh
+++ b/src/.docker_modules/umi_tools/0.5.4/docker_init.sh
@@ -1,2 +1,4 @@
#!/bin/sh
-docker build src/docker_modules/umi_tools/1.0.0/ -t 'lbmc/umi_tools:1.0.0'
+docker pull lbmc/umi_tools:1.0.0
+docker build src/.docker_modules/umi_tools/1.0.0/ -t 'lbmc/umi_tools:1.0.0'
+docker push lbmc/umi_tools:1.0.0
diff --git a/src/.docker_modules/umi_tools/1.0.0/docker_init.sh b/src/.docker_modules/umi_tools/1.0.0/docker_init.sh
index 1b11e25daea666b8e9bf130b6a44530194b5bc1c..200e9c066fe98de8262a48eea0f615b064ff90a4 100755
--- a/src/.docker_modules/umi_tools/1.0.0/docker_init.sh
+++ b/src/.docker_modules/umi_tools/1.0.0/docker_init.sh
@@ -1,2 +1,4 @@
#!/bin/sh
-docker build src/docker_modules/umi_tools/1.0.0/ -t 'lbmc/umi_tools:1.0.0'
+docker pull lbmc/umi_tools:1.0.0
+docker build src/.docker_modules/umi_tools/1.0.0/ -t 'lbmc/umi_tools:1.0.0'
+docker push lbmc/umi_tools:1.0.0
diff --git a/src/.docker_modules/urqt/d62c1f8/docker_init.sh b/src/.docker_modules/urqt/d62c1f8/docker_init.sh
index bb7f161f02ee44fbab80a034fd954a7e1f4b4051..bb3fb4f882ec4f93e4cec643e035fb7d2d7a4963 100755
--- a/src/.docker_modules/urqt/d62c1f8/docker_init.sh
+++ b/src/.docker_modules/urqt/d62c1f8/docker_init.sh
@@ -1,2 +1,4 @@
#!/bin/sh
-docker build src/docker_modules/urqt/d62c1f8 -t 'lbmc/urqt:d62c1f8'
+docker pull lbmc/urqt:d62c1f8
+docker build src/.docker_modules/urqt/d62c1f8 -t 'lbmc/urqt:d62c1f8'
+docker push lbmc/urqt:d62c1f8
diff --git a/src/.psmn_modules b/src/.psmn_modules
deleted file mode 160000
index 8a86db97eb89833a88b1ee876880cb1c07ce8565..0000000000000000000000000000000000000000
--- a/src/.psmn_modules
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 8a86db97eb89833a88b1ee876880cb1c07ce8565
diff --git a/src/.singularity_modules/bcftools/1.7/bcftools b/src/.singularity_modules/bcftools/1.7/bcftools
deleted file mode 100644
index 0b6dd7dd2c3fcf8e4d37bdf285bb4caefa1aaf51..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/bcftools/1.7/bcftools
+++ /dev/null
@@ -1,2 +0,0 @@
-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/bcftools:1.7.img bcftools $@
diff --git a/src/.singularity_modules/bcftools/1.7/bcftools.def b/src/.singularity_modules/bcftools/1.7/bcftools.def
deleted file mode 100644
index be53f0798df70ab4eac22fbadc1ccfd482a5f669..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/bcftools/1.7/bcftools.def
+++ /dev/null
@@ -1,20 +0,0 @@
-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-BCFTOOLS_VERSION=1.7
-PACKAGES=bcftools=${BCFTOOLS_VERSION}*
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-%environment
-export BCFTOOLS_VERSION=1.7
-
-%runscript
-exec /bin/bash "$@"
diff --git a/src/.singularity_modules/bcftools/1.7/build.sh b/src/.singularity_modules/bcftools/1.7/build.sh
deleted file mode 100755
index 96ecae5578d87feea685b260167cfeb1056989e4..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/bcftools/1.7/build.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#/bin/sh
-sudo singularity build --force bin/bcftools:1.7.img src/singularity_modules/bcftools/1.7/bcftools.def && \
-singularity sign bin/bcftools:1.7.img
diff --git a/src/.singularity_modules/bedtools/2.25.0/bedtools b/src/.singularity_modules/bedtools/2.25.0/bedtools
deleted file mode 100644
index 33f7309a610e53d7db01ae2f14ecae3f7b5b9756..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/bedtools/2.25.0/bedtools
+++ /dev/null
@@ -1,2 +0,0 @@
-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/bedtools:2.25.0.img bedtools $@
diff --git a/src/.singularity_modules/bedtools/2.25.0/bedtools.def b/src/.singularity_modules/bedtools/2.25.0/bedtools.def
deleted file mode 100644
index 4078e8efc50126f874e0c97349e3130e66fa164a..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/bedtools/2.25.0/bedtools.def
+++ /dev/null
@@ -1,20 +0,0 @@
-Bootstrap: docker
-From: ubuntu:16.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-BEDTOOLS_VERSION=2.25.0
-PACKAGES=bedtools=${BEDTOOLS_VERSION}*
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-%environment
-export BEDTOOLS_VERSION=2.25.0
-
-%runscript
-exec /bin/bash "$@"
diff --git a/src/.singularity_modules/bedtools/2.25.0/build.sh b/src/.singularity_modules/bedtools/2.25.0/build.sh
deleted file mode 100755
index 936a71be2f68a8f06061216dad3f2448f38f596e..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/bedtools/2.25.0/build.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#/bin/sh
-sudo singularity build --force bin/bedtools:2.25.0.img src/singularity_modules/bedtools/2.25.0/bedtools.def && \
-singularity sign bin/bedtools:2.25.0.img
diff --git a/src/.singularity_modules/bioawk/1.0/bioawk b/src/.singularity_modules/bioawk/1.0/bioawk
deleted file mode 100644
index af1106ffe9bca165c12eb784b570d5eb736a4ac3..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/bioawk/1.0/bioawk
+++ /dev/null
@@ -1,2 +0,0 @@
-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/bioawk:1.0.img bioawk $@
diff --git a/src/.singularity_modules/bioawk/1.0/bioawk.def b/src/.singularity_modules/bioawk/1.0/bioawk.def
deleted file mode 100644
index 9bb6946ed551c03e758c5d31f11cbc1a860ce58e..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/bioawk/1.0/bioawk.def
+++ /dev/null
@@ -1,32 +0,0 @@
-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-BIOAWK_VERSION=1.0
-PACKAGES="git \
- build-essential \
- ca-certificates \
- zlib1g-dev \
- byacc"
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-git clone https://github.com/lh3/bioawk.git && \
- cd bioawk && \
- git checkout tags/v${BIOAWK_VERSION} && \
- make && \
- cd .. && \
- mv bioawk/bioawk /usr/bin/ && \
- rm -Rf bioawk
-
-%environment
-export BIOAWK_VERSION=1.0
-
-%runscript
-exec /bin/bash "$@"
diff --git a/src/.singularity_modules/bioawk/1.0/build.sh b/src/.singularity_modules/bioawk/1.0/build.sh
deleted file mode 100755
index be5a5098f61c617db40b2e9f5bacb7299a9fafcd..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/bioawk/1.0/build.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#/bin/sh
-sudo singularity build --force bin/bioawk:1.0.img src/singularity_modules/bioawk/1.0/bioawk.def && \
-singularity sign bin/bioawk:1.0.img
diff --git a/src/.singularity_modules/bowtie/1.2.2/bowtie b/src/.singularity_modules/bowtie/1.2.2/bowtie
deleted file mode 100644
index 9b4503234b30626d0668bfd619d9243e0814a103..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/bowtie/1.2.2/bowtie
+++ /dev/null
@@ -1,2 +0,0 @@
-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/bowtie:1.2.2.img bowtie $@
diff --git a/src/.singularity_modules/bowtie/1.2.2/bowtie.def b/src/.singularity_modules/bowtie/1.2.2/bowtie.def
deleted file mode 100644
index 4d6def9a67fd08b27c6a2951cbeab061b3b8f874..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/bowtie/1.2.2/bowtie.def
+++ /dev/null
@@ -1,23 +0,0 @@
-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-BOWTIE_VERSION=1.2.2
-SAMTOOLS_VERSION=1.7
-PACKAGES="bowtie=${BOWTIE_VERSION}* \
-samtools=${SAMTOOLS_VERSION}*"
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-%environment
-export BOWTIE_VERSION=1.2.2
-export SAMTOOLS_VERSION=1.7
-
-%runscript
-exec /bin/bash "$@"
diff --git a/src/.singularity_modules/bowtie/1.2.2/build.sh b/src/.singularity_modules/bowtie/1.2.2/build.sh
deleted file mode 100755
index a5a5c54de96ed09e45b17b33ee218a906483b192..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/bowtie/1.2.2/build.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#/bin/sh
-sudo singularity build --force bin/bowtie:1.2.2.img src/singularity_modules/bowtie/1.2.2/bowtie.def && \
-singularity sign bin/bowtie:1.2.2.img
diff --git a/src/.singularity_modules/bowtie2/2.3.4.1/bowtie2 b/src/.singularity_modules/bowtie2/2.3.4.1/bowtie2
deleted file mode 100644
index e8c41bdc8af82fee3cce41f0f6496f21b55704be..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/bowtie2/2.3.4.1/bowtie2
+++ /dev/null
@@ -1,2 +0,0 @@
-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/bowtie2:2.3.4.1.img bowtie2 $@
diff --git a/src/.singularity_modules/bowtie2/2.3.4.1/bowtie2.def b/src/.singularity_modules/bowtie2/2.3.4.1/bowtie2.def
deleted file mode 100644
index adf38167caca9b37c07a1e7d4857a2dcacfe399d..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/bowtie2/2.3.4.1/bowtie2.def
+++ /dev/null
@@ -1,24 +0,0 @@
-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-BOWTIE2_VERSION=2.3.4.1
-SAMTOOLS_VERSION=1.7
-PACKAGES="bowtie2=${BOWTIE2_VERSION}* \
-samtools=${SAMTOOLS_VERSION}* \
-perl=5.26.1*"
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-%environment
-export BOWTIE2_VERSION=2.3.4.1
-export SAMTOOLS_VERSION=1.7
-
-%runscript
-exec /bin/bash "$@"
diff --git a/src/.singularity_modules/bowtie2/2.3.4.1/build.sh b/src/.singularity_modules/bowtie2/2.3.4.1/build.sh
deleted file mode 100755
index c01beabb54124f4b9f5d79a8410330e8206e56b5..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/bowtie2/2.3.4.1/build.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#/bin/sh
-sudo singularity build --force bin/bowtie2:2.3.4.1.img src/singularity_modules/bowtie2/2.3.4.1/bowtie2.def && \
-singularity sign bin/bowtie2:2.3.4.1.img
diff --git a/src/.singularity_modules/bwa/0.7.17/build.sh b/src/.singularity_modules/bwa/0.7.17/build.sh
deleted file mode 100755
index 0392a0c13c69399a0c95f8e838dc2114113a27f7..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/bwa/0.7.17/build.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#/bin/sh
-sudo singularity build --force bin/bwa:0.7.17.img src/singularity_modules/bwa/0.7.17/bwa.def && \
-singularity sign bin/bwa:0.7.17.img
diff --git a/src/.singularity_modules/bwa/0.7.17/bwa b/src/.singularity_modules/bwa/0.7.17/bwa
deleted file mode 100644
index cf69e9236b4760843073281fc4311a1507a3201a..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/bwa/0.7.17/bwa
+++ /dev/null
@@ -1,2 +0,0 @@
-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/bwa:0.7.17.img bwa $@
diff --git a/src/.singularity_modules/bwa/0.7.17/bwa.def b/src/.singularity_modules/bwa/0.7.17/bwa.def
deleted file mode 100644
index 074892f8e986740b3fca75043733adee23987dc4..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/bwa/0.7.17/bwa.def
+++ /dev/null
@@ -1,47 +0,0 @@
-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-BWA_VERSION=0.7.17
-SAMBLASTER_VERSION=0.1.24
-
-PACKAGES=curl="7.58.0* \
-ca-certificates=20180409 \
-build-essential=12.4* \
-zlib1g-dev=1:1.2.11*"
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-curl -k -L https://github.com/biod/sambamba/releases/download/v${SAMBAMBA_VERSION}/sambamba_v${SAMBAMBA_VERSION}_linux.tar.bz2 -o sambamba_v${SAMBAMBA_VERSION}_linux.tar.bz2 && \
-tar xvjf sambamba_v${SAMBAMBA_VERSION}_linux.tar.bz2 && \
-mv sambamba /usr/bin/ && \
-rm -R sambamba_v${SAMBAMBA_VERSION}_linux*
-
-curl -k -L https://github.com/lh3/bwa/releases/download/v${BWA_VERSION}/bwa-${BWA_VERSION}.tar.bz2 -o bwa-v${BWA_VERSION}.tar.bz2 && \
-tar xjf bwa-v${BWA_VERSION}.tar.bz2 && \
-cd bwa-${BWA_VERSION}/ && \
-make && \
-cp bwa /usr/bin && \
-cd .. && \
-rm -R bwa-${BWA_VERSION}/
-
-curl -k -L https://github.com/GregoryFaust/samblaster/releases/download/v.${SAMBLASTER_VERSION}/samblaster-v.${SAMBLASTER_VERSION}.tar.gz -o samblaster-v.${SAMBLASTER_VERSION}.tar.gz && \
-tar xvf samblaster-v.${SAMBLASTER_VERSION}.tar.gz && \
-cd samblaster-v.${SAMBLASTER_VERSION}/ && \
-make && \
-cp samblaster /usr/bin && \
-cd .. && \
-rm -R samblaster-v.${SAMBLASTER_VERSION}/
-
-%environment
-export BWA_VERSION=0.7.17
-export SAMBLASTER_VERSION=0.1.24
-
-%runscript
-exec /bin/bash "$@"
diff --git a/src/.singularity_modules/canu/1.6/build.sh b/src/.singularity_modules/canu/1.6/build.sh
deleted file mode 100755
index 78805dac402711a96131cffef808fb01d3e63b70..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/canu/1.6/build.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#/bin/sh
-sudo singularity build --force bin/canu:1.6.img src/singularity_modules/canu/1.6/canu.def && \
-singularity sign bin/canu:1.6.img
diff --git a/src/.singularity_modules/canu/1.6/canu b/src/.singularity_modules/canu/1.6/canu
deleted file mode 100644
index fa7348ae17fe786286fc0be73d3c3faf6604d932..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/canu/1.6/canu
+++ /dev/null
@@ -1,2 +0,0 @@
-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/canu:1.6.img canu $@
diff --git a/src/.singularity_modules/canu/1.6/canu.def b/src/.singularity_modules/canu/1.6/canu.def
deleted file mode 100644
index 3b0e23e7824e95b3e20b90b1c206785545d064af..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/canu/1.6/canu.def
+++ /dev/null
@@ -1,20 +0,0 @@
-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-CANU_VERSION=1.6
-PACKAGES=canu=${CANU_VERSION}*
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-%environment
-export CANU_VERSION=1.6
-
-%runscript
-exec /bin/bash "$@"
diff --git a/src/.singularity_modules/cutadapt/1.14/build.sh b/src/.singularity_modules/cutadapt/1.14/build.sh
deleted file mode 100755
index 0369e0dfd33740fd7c6ad99eda36ac3bb9f5ec16..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/cutadapt/1.14/build.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#/bin/sh
-sudo singularity build --force bin/cutadapt:1.14.img src/singularity_modules/cutadapt/1.14/cutadapt.def && \
-singularity sign bin/cutadapt:1.14.img
diff --git a/src/.singularity_modules/cutadapt/1.14/cutadapt b/src/.singularity_modules/cutadapt/1.14/cutadapt
deleted file mode 100644
index 362bda98bd24973e0a517e9baed1a4c3b3505945..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/cutadapt/1.14/cutadapt
+++ /dev/null
@@ -1,2 +0,0 @@
-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/cutadapt:1.14.img cutadapt $@
diff --git a/src/.singularity_modules/cutadapt/1.14/cutadapt.def b/src/.singularity_modules/cutadapt/1.14/cutadapt.def
deleted file mode 100644
index 152cf71bee0a67e6cdef586296994ee512e6911f..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/cutadapt/1.14/cutadapt.def
+++ /dev/null
@@ -1,28 +0,0 @@
-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-CUTADAPT_VERSION=1.14
-PACKAGES="bash \
- python3 \
- python3-dev \
- musl-dev \
- python3-pip \
- gcc"
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-pip3 install setuptools
-pip3 install cutadapt==${CUTADAPT_VERSION}
-
-%environment
-export CUTADAPT_VERSION=1.14
-
-%runscript
-exec /bin/bash "$@"
diff --git a/src/.singularity_modules/cutadapt/1.15/build.sh b/src/.singularity_modules/cutadapt/1.15/build.sh
deleted file mode 100755
index 95883b041fe741e6482d3dbaec4078b7b453046c..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/cutadapt/1.15/build.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#/bin/sh
-sudo singularity build --force bin/cutadapt:1.15.img src/singularity_modules/cutadapt/1.15/cutadapt.def && \
-singularity sign bin/cutadapt:1.15.img
diff --git a/src/.singularity_modules/cutadapt/1.15/cutadapt b/src/.singularity_modules/cutadapt/1.15/cutadapt
deleted file mode 100644
index 71f969248e0aa79fb0cea9dc24eb756aae1acaee..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/cutadapt/1.15/cutadapt
+++ /dev/null
@@ -1,2 +0,0 @@
-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/cutadapt:1.15.img cutadapt $@
diff --git a/src/.singularity_modules/cutadapt/1.15/cutadapt.def b/src/.singularity_modules/cutadapt/1.15/cutadapt.def
deleted file mode 100644
index 27e284c17c54f2fd38aa3fc9bc9b43f93a9a3383..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/cutadapt/1.15/cutadapt.def
+++ /dev/null
@@ -1,29 +0,0 @@
-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-CUTADAPT_VERSION=1.15
-PACKAGES="bash \
- python3 \
- python3-dev \
- musl-dev \
- python3-pip \
- gcc"
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-pip3 install setuptools
-pip3 install cutadapt==${CUTADAPT_VERSION}
-
-%environment
-export CUTADAPT_VERSION=1.14
-
-%runscript
-exec /bin/bash "$@"
-xec /bin/bash "$@"
diff --git a/src/.singularity_modules/cutadapt/2.1/build.sh b/src/.singularity_modules/cutadapt/2.1/build.sh
deleted file mode 100755
index 5a7070ec2e72a3cae9276d8a208dcba1dcd7a0eb..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/cutadapt/2.1/build.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#/bin/sh
-sudo singularity build --force bin/cutadapt:2.1.img src/singularity_modules/cutadapt/2.1/cutadapt.def && \
-singularity sign bin/cutadapt:2.1.img
diff --git a/src/.singularity_modules/cutadapt/2.1/cutadapt b/src/.singularity_modules/cutadapt/2.1/cutadapt
deleted file mode 100644
index e653e488281d4a0c0f556ba672e159d4aa3a5dcd..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/cutadapt/2.1/cutadapt
+++ /dev/null
@@ -1,2 +0,0 @@
-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/cutadapt:2.1.img cutadapt $@
diff --git a/src/.singularity_modules/cutadapt/2.1/cutadapt.def b/src/.singularity_modules/cutadapt/2.1/cutadapt.def
deleted file mode 100644
index 0223799c03b416d530ee7da41040b377ccf8297f..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/cutadapt/2.1/cutadapt.def
+++ /dev/null
@@ -1,28 +0,0 @@
-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-CUTADAPT_VERSION=2.1
-PACKAGES="bash \
- python3 \
- python3-dev \
- musl-dev \
- python3-pip \
- gcc"
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-pip3 install setuptools
-pip3 install cutadapt==${CUTADAPT_VERSION}
-
-%environment
-export CUTADAPT_VERSION=2.1
-
-%runscript
-exec /bin/bash "$@"
diff --git a/src/.singularity_modules/deeptools/3.0.2/build.sh b/src/.singularity_modules/deeptools/3.0.2/build.sh
deleted file mode 100755
index 2ffc99376f780286b44fc2ad5015cb7da14dc5ad..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/deeptools/3.0.2/build.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#/bin/sh
-sudo singularity build --force bin/deeptools:3.0.2.img src/singularity_modules/deeptools/3.0.2/deeptools.def && \
-singularity sign bin/deeptools:3.0.2.img
diff --git a/src/.singularity_modules/deeptools/3.0.2/deeptools b/src/.singularity_modules/deeptools/3.0.2/deeptools
deleted file mode 100644
index 4053b759aaa1bc3b33fe0ab5ceef1b1c32f440dd..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/deeptools/3.0.2/deeptools
+++ /dev/null
@@ -1,2 +0,0 @@
-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/deeptools:3.0.2.img deeptools $@
diff --git a/src/.singularity_modules/deeptools/3.0.2/deeptools.def b/src/.singularity_modules/deeptools/3.0.2/deeptools.def
deleted file mode 100644
index e108aa37a3d41a2264bbc672419a42de4262a0c2..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/deeptools/3.0.2/deeptools.def
+++ /dev/null
@@ -1,29 +0,0 @@
-Bootstrap: docker
-From: debian:stretch
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-DEEPTOOLS_VERSION=3.0.2
-PACKAGES="build-essential \
- python3-pip \
- python3-setuptools \
- python3-dev \
- python3-wheel \
- zlib1g-dev \
- procps \
- libcurl4-gnutls-dev"
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-pip3 install deeptools==${DEEPTOOLS_VERSION}
-
-%environment
-export DEEPTOOLS_VERSION=3.0.2
-
-%runscript
-exec /bin/bash "$@"
diff --git a/src/.singularity_modules/deeptools/3.1.1/build.sh b/src/.singularity_modules/deeptools/3.1.1/build.sh
deleted file mode 100755
index 78304343c115bb7eaa3773e1ee16eea3de700bf0..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/deeptools/3.1.1/build.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#/bin/sh
-sudo singularity build --force bin/deeptools:3.1.1.img src/singularity_modules/deeptools/3.1.1/deeptools.def && \
-singularity sign bin/deeptools:3.1.1.img
diff --git a/src/.singularity_modules/deeptools/3.1.1/deeptools b/src/.singularity_modules/deeptools/3.1.1/deeptools
deleted file mode 100644
index ffecc35fed3de3dd88832fc1f621898ccd957c01..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/deeptools/3.1.1/deeptools
+++ /dev/null
@@ -1,2 +0,0 @@
-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/deeptools:3.1.1.img deeptools $@
diff --git a/src/.singularity_modules/deeptools/3.1.1/deeptools.def b/src/.singularity_modules/deeptools/3.1.1/deeptools.def
deleted file mode 100644
index 8bae622c762882f3e84198ab078de67c45b76531..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/deeptools/3.1.1/deeptools.def
+++ /dev/null
@@ -1,29 +0,0 @@
-Bootstrap: docker
-From: debian:stretch
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-DEEPTOOLS_VERSION=3.1.1
-PACKAGES="build-essential \
- python3-pip \
- python3-setuptools \
- python3-dev \
- python3-wheel \
- zlib1g-dev \
- procps \
- libcurl4-gnutls-dev"
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-pip3 install deeptools==${DEEPTOOLS_VERSION}
-
-%environment
-export DEEPTOOLS_VERSION=3.0.2
-
-%runscript
-exec /bin/bash "$@"
diff --git a/src/.singularity_modules/docker_to_singularity.sh b/src/.singularity_modules/docker_to_singularity.sh
deleted file mode 100644
index 0a71bfbccb414bbd3b24bc98612321200ca8b4c8..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/docker_to_singularity.sh
+++ /dev/null
@@ -1,13 +0,0 @@
-# install spython
-# sudo pip3 install spython
-
-find src/docker_modules/ -name "Dockerfile" | \
- perl -pe "s/docker/singularity/g" | \
- perl -pe "s/Dockerfile//g" | \
- awk '{system("mkdir -p " $0)}'
-
-find src/docker_modules/ -name "Dockerfile" | \
- perl -pe "s/(^.*$)/spython recipe \1 > \1/g" | \
- perl -pe "s/(^.*)docker_modules(.*$)/\1singularity_modules\2/g" | \
- perl -pe "s/(^.*\/([^\/]*)\/[^\/]*\/)Dockerfile$/\1\2.def/g" | \
- awk '{system($0)}'
diff --git a/src/.singularity_modules/fastp/0.19.7/build.sh b/src/.singularity_modules/fastp/0.19.7/build.sh
deleted file mode 100755
index be161e19b88586b1469fdfd4c21c87f690cdd669..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/fastp/0.19.7/build.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#/bin/sh
-sudo singularity build --force bin/fastp:0.19.7.img src/singularity_modules/fastp/0.19.7/fastp.def && \
-singularity sign bin/fastp:0.19.7.img
diff --git a/src/.singularity_modules/fastp/0.19.7/fastp b/src/.singularity_modules/fastp/0.19.7/fastp
deleted file mode 100644
index cc0d2213cbf7e723bcf76d788c5e6d617e6317d6..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/fastp/0.19.7/fastp
+++ /dev/null
@@ -1,2 +0,0 @@
-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/fastp:0.19.7.img fastp $@
diff --git a/src/.singularity_modules/fastp/0.19.7/fastp.def b/src/.singularity_modules/fastp/0.19.7/fastp.def
deleted file mode 100644
index eca9d45fae1debeb34329064e731376f42e5e69c..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/fastp/0.19.7/fastp.def
+++ /dev/null
@@ -1,15 +0,0 @@
-Bootstrap: docker
-From: docker://quay.io/biocontainers/fastp:0.19.7--hdbcaa40_0
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-FASTP_VERSION=0.19.7
-
-%environment
-export FASTP_VERSION=0.19.7
-
-%runscript
-exec /bin/bash "$@"
diff --git a/src/.singularity_modules/fastqc/0.11.5/build.sh b/src/.singularity_modules/fastqc/0.11.5/build.sh
deleted file mode 100755
index ef313d4e3bd1a19519227c5677c8bfa7ca4bf927..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/fastqc/0.11.5/build.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#/bin/sh
-sudo singularity build --force bin/fastqc:0.11.5.img src/singularity_modules/fastqc/0.11.5/fastqc.def && \
-singularity sign bin/fastqc:0.11.5.img
diff --git a/src/.singularity_modules/fastqc/0.11.5/fastqc b/src/.singularity_modules/fastqc/0.11.5/fastqc
deleted file mode 100644
index 1da370ad5ecf6eabaa3321ff8b4bee5d3cfd909e..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/fastqc/0.11.5/fastqc
+++ /dev/null
@@ -1,2 +0,0 @@
-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/fastqc:0.11.5.img fastqc $@
diff --git a/src/.singularity_modules/fastqc/0.11.5/fastqc.def b/src/.singularity_modules/fastqc/0.11.5/fastqc.def
deleted file mode 100644
index 11d529d19d815904e9106c272cfee06023cf30db..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/fastqc/0.11.5/fastqc.def
+++ /dev/null
@@ -1,22 +0,0 @@
-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-FASTQC_VERSION=0.11.5
-PACKAGES="fastqc=${FASTQC_VERSION}* \
-perl=5.26*"
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-%environment
-export FASTQC_VERSION=0.11.5
-export PACKAGES=fastqc=${FASTQC_VERSION}*
-
-%runscript
-exec /bin/bash "$@"
diff --git a/src/.singularity_modules/file_handle/0.1.1/build.sh b/src/.singularity_modules/file_handle/0.1.1/build.sh
deleted file mode 100755
index b48ae449778ba2afe084269b3eb50e645f5067f2..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/file_handle/0.1.1/build.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#/bin/sh
-sudo singularity build --force bin/file_handle:0.1.1.img src/singularity_modules/file_handle/0.1.1/file_handle.def && \
-singularity sign bin/file_handle:0.1.1.img
diff --git a/src/.singularity_modules/file_handle/0.1.1/file_handle b/src/.singularity_modules/file_handle/0.1.1/file_handle
deleted file mode 100644
index 2eccd8be1780e951ed61ebfb2e294dc596336cf6..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/file_handle/0.1.1/file_handle
+++ /dev/null
@@ -1,2 +0,0 @@
-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/file_handle:0.1.1.img file_handle $@
diff --git a/src/.singularity_modules/file_handle/0.1.1/file_handle.def b/src/.singularity_modules/file_handle/0.1.1/file_handle.def
deleted file mode 100644
index 240f876443215b94fdde20f6ada761999fd466e6..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/file_handle/0.1.1/file_handle.def
+++ /dev/null
@@ -1,28 +0,0 @@
-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-
-FILE_HANDLE_VERSION=0.1.1
-PACKAGES="git \
-ca-certificates "
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-git clone https://github.com/LBMC/file_handle.git && \
-cd file_handle && \
-git checkout tags/v${FILE_HANDLE_VERSION} && \
-cp src/file_handle.py /usr/bin/file_handle.py && \
-chmod +x /usr/bin/file_handle.py
-
-%environment
-export FILE_HANDLE_VERSION=0.1.1
-
-%runscript
-exec /bin/bash "$@"
diff --git a/src/.singularity_modules/gatk/4.0.8.1/build.sh b/src/.singularity_modules/gatk/4.0.8.1/build.sh
deleted file mode 100755
index 87e095b7ad5eba073b4b5d92ad50f865889a7df8..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/gatk/4.0.8.1/build.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#/bin/sh
-sudo singularity build --force bin/gatk:4.0.8.1.img src/singularity_modules/gatk/4.0.8.1/gatk.def && \
-singularity sign bin/gatk:4.0.8.1.img
diff --git a/src/.singularity_modules/gatk/4.0.8.1/gatk b/src/.singularity_modules/gatk/4.0.8.1/gatk
deleted file mode 100644
index d16d21b6cca2901f323af7a57e6f96394c2c75a3..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/gatk/4.0.8.1/gatk
+++ /dev/null
@@ -1,2 +0,0 @@
-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/gatk:4.0.8.1.img gatk $@
diff --git a/src/.singularity_modules/gatk/4.0.8.1/gatk.def b/src/.singularity_modules/gatk/4.0.8.1/gatk.def
deleted file mode 100644
index c87b5be2e5030c4d06993536bcd30f08eff3c73b..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/gatk/4.0.8.1/gatk.def
+++ /dev/null
@@ -1,17 +0,0 @@
-Bootstrap: docker
-From: broadinstitute/gatk:4.0.8.1
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-
-GATK_VERSION=4.0.8.1
-cp gatk/gatk /usr/bin/
-
-%environment
-export GATK_VERSION=4.0.8.1
-
-%runscript
-exec /bin/bash "$@"
diff --git a/src/.singularity_modules/hisat2/2.0.0/build.sh b/src/.singularity_modules/hisat2/2.0.0/build.sh
deleted file mode 100755
index 4ba74ed48f773c6cd96c580e5d0031e6f33af320..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/hisat2/2.0.0/build.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#/bin/sh
-sudo singularity build --force bin/hisat2:2.0.0.img src/singularity_modules/hisat2/2.0.0/hisat2.def && \
-singularity sign bin/hisat2:2.0.0.img
diff --git a/src/.singularity_modules/hisat2/2.0.0/hisat2 b/src/.singularity_modules/hisat2/2.0.0/hisat2
deleted file mode 100644
index e8282a1ee8d4eab71440c2943f4d1876b1012c2d..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/hisat2/2.0.0/hisat2
+++ /dev/null
@@ -1,2 +0,0 @@
-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/hisat2:2.0.0.img hisat2 $@
diff --git a/src/.singularity_modules/hisat2/2.0.0/hisat2.def b/src/.singularity_modules/hisat2/2.0.0/hisat2.def
deleted file mode 100644
index a4ea94d63f024b8b4b48a402db2041d947e8f642..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/hisat2/2.0.0/hisat2.def
+++ /dev/null
@@ -1,51 +0,0 @@
-Bootstrap: docker
-From: alpine:3.8
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-SAMTOOLS_VERSION=1.7
-HISAT2_VERSION=2.0.0
-PACKAGES="git \
- make \
- gcc \
- musl-dev \
- zlib-dev \
- ncurses-dev \
- bzip2-dev \
- xz-dev \
- bash \
- curl \
- zip \
- g++ \
- perl \
- python"
-apk update && \
-apk add ${PACKAGES}
-
-git clone https://github.com/samtools/htslib.git && \
-cd htslib && \
-git checkout ${SAMTOOLS_VERSION} && \
-cd .. && \
-git clone https://github.com/samtools/samtools.git && \
-cd samtools && \
-git checkout ${SAMTOOLS_VERSION} && \
-make && \
-cp samtools /usr/bin/
-
-curl -k -L http://ccb.jhu.edu/software/hisat2/downloads/hisat2-${HISAT2_VERSION}-beta-source.zip -o hisat2_linux-v${HISAT2_VERSION}.zip && \
-unzip hisat2_linux-v${HISAT2_VERSION}.zip && \
-cd hisat2-${HISAT2_VERSION}-beta && \
-make && \
-cp hisat2 /usr/bin && \
-cp hisat2-* /usr/bin && \
-rm -Rf hisat2-${HISAT2_VERSION}-beta
-
-%environment
-export SAMTOOLS_VERSION=1.7
-export HISAT2_VERSION=2.0.0
-
-%runscript
-exec /bin/bash "$@"
diff --git a/src/.singularity_modules/hisat2/2.1.0/build.sh b/src/.singularity_modules/hisat2/2.1.0/build.sh
deleted file mode 100755
index 5a23a14463d2463fc2f8bd6a52330468daecfa55..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/hisat2/2.1.0/build.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#/bin/sh
-sudo singularity build --force bin/hisat2:2.1.0.img src/singularity_modules/hisat2/2.1.0/hisat2.def && \
-singularity sign bin/hisat2:2.1.0.img
diff --git a/src/.singularity_modules/hisat2/2.1.0/hisat2 b/src/.singularity_modules/hisat2/2.1.0/hisat2
deleted file mode 100644
index 0c4ab6f90b1cc818b8b12a4fbf8b77b8051a07be..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/hisat2/2.1.0/hisat2
+++ /dev/null
@@ -1,2 +0,0 @@
-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/hisat2:2.1.0.img hisat2 $@
diff --git a/src/.singularity_modules/hisat2/2.1.0/hisat2.def b/src/.singularity_modules/hisat2/2.1.0/hisat2.def
deleted file mode 100644
index 092d3f0bf0a7cecd31cb2d4f5a86d733a3c1a6fb..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/hisat2/2.1.0/hisat2.def
+++ /dev/null
@@ -1,51 +0,0 @@
-Bootstrap: docker
-From: alpine:3.8
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-SAMTOOLS_VERSION=1.7
-HISAT2_VERSION=2.1.0
-PACKAGES="git \
- make \
- gcc \
- musl-dev \
- zlib-dev \
- ncurses-dev \
- bzip2-dev \
- xz-dev \
- bash \
- curl \
- zip \
- g++ \
- perl \
- python"
-apk update && \
-apk add ${PACKAGES}
-
-git clone https://github.com/samtools/htslib.git && \
-cd htslib && \
-git checkout ${SAMTOOLS_VERSION} && \
-cd .. && \
-git clone https://github.com/samtools/samtools.git && \
-cd samtools && \
-git checkout ${SAMTOOLS_VERSION} && \
-make && \
-cp samtools /usr/bin/
-
-curl -k -L http://ccb.jhu.edu/software/hisat2/dl/hisat2-${HISAT2_VERSION}-source.zip -o hisat2_linux-v${HISAT2_VERSION}.zip && \
-unzip hisat2_linux-v${HISAT2_VERSION}.zip && \
-cd hisat2-${HISAT2_VERSION} && \
-make && \
-cp hisat2 /usr/bin && \
-cp hisat2-* /usr/bin && \
-rm -Rf hisat2-${HISAT2_VERSION}
-
-%environment
-export SAMTOOLS_VERSION=1.7
-export HISAT2_VERSION=2.1.0
-
-%runscript
-exec /bin/bash "$@"
diff --git a/src/.singularity_modules/htseq/0.11.2/build.sh b/src/.singularity_modules/htseq/0.11.2/build.sh
deleted file mode 100755
index 116d41a811b1dfc384b65e146c50ec91f0a2eae5..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/htseq/0.11.2/build.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#/bin/sh
-sudo singularity build --force bin/htseq:0.11.2.img src/singularity_modules/htseq/0.11.2/htseq.def && \
-singularity sign bin/htseq:0.11.2.img
diff --git a/src/.singularity_modules/htseq/0.11.2/htseq b/src/.singularity_modules/htseq/0.11.2/htseq
deleted file mode 100644
index df87417d41360cd13c6adcaf02ef91ca81978ad6..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/htseq/0.11.2/htseq
+++ /dev/null
@@ -1,2 +0,0 @@
-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/htseq:0.11.2.img htseq $@
diff --git a/src/.singularity_modules/htseq/0.11.2/htseq.def b/src/.singularity_modules/htseq/0.11.2/htseq.def
deleted file mode 100644
index 76ab6c32f498541e10afcd3bba3064575e974d5c..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/htseq/0.11.2/htseq.def
+++ /dev/null
@@ -1,28 +0,0 @@
-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-HTSEQ_VERSION=0.11.2
-PACKAGES="build-essential \
-python3-pip \
-python3-setuptools \
-python3-dev \
-python3-wheel"
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-pip3 install numpy==1.14.3
-pip3 install pysam==0.15.0
-pip3 install HTSeq==${HTSEQ_VERSION}
-
-%environment
-export HTSEQ_VERSION=0.11.2
-
-%runscript
-exec /bin/bash "$@"
diff --git a/src/.singularity_modules/htseq/0.8.0/build.sh b/src/.singularity_modules/htseq/0.8.0/build.sh
deleted file mode 100755
index 19aed8a6cbf1be1e9534ca2344a9462e012f87fe..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/htseq/0.8.0/build.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#/bin/sh
-sudo singularity build --force bin/htseq:0.8.0.img src/singularity_modules/htseq/0.8.0/htseq.def && \
-singularity sign bin/htseq:0.8.0.img
diff --git a/src/.singularity_modules/htseq/0.8.0/htseq b/src/.singularity_modules/htseq/0.8.0/htseq
deleted file mode 100644
index f7be0c13925dfbe3ac6560ad27d53f6d837b3cc5..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/htseq/0.8.0/htseq
+++ /dev/null
@@ -1,2 +0,0 @@
-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/htseq:0.8.0.img htseq $@
diff --git a/src/.singularity_modules/htseq/0.8.0/htseq.def b/src/.singularity_modules/htseq/0.8.0/htseq.def
deleted file mode 100644
index a96643a583ea107ec654438d4485e6e57268bc07..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/htseq/0.8.0/htseq.def
+++ /dev/null
@@ -1,28 +0,0 @@
-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-HTSEQ_VERSION=0.8.0
-PACKAGES="build-essential \
-python3-pip \
-python3-setuptools \
-python3-dev \
-python3-wheel"
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-pip3 install numpy==1.14.3
-pip3 install pysam==0.15.0
-pip3 install HTSeq==${HTSEQ_VERSION}
-
-%environment
-export HTSEQ_VERSION=0.8.0
-
-%runscript
-exec /bin/bash "$@"
diff --git a/src/.singularity_modules/kallisto/0.43.1/build.sh b/src/.singularity_modules/kallisto/0.43.1/build.sh
deleted file mode 100755
index 1a83c7c621874535db355448941b98710cad8d97..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/kallisto/0.43.1/build.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#/bin/sh
-sudo singularity build --force bin/kallisto:0.43.1.img src/singularity_modules/kallisto/0.43.1/kallisto.def && \
-singularity sign bin/kallisto:0.43.1.img
diff --git a/src/.singularity_modules/kallisto/0.43.1/kallisto b/src/.singularity_modules/kallisto/0.43.1/kallisto
deleted file mode 100644
index 27ad1732154be9cf7b44d6a7881e704d88c0907f..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/kallisto/0.43.1/kallisto
+++ /dev/null
@@ -1,2 +0,0 @@
-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/kallisto:0.43.1.img kallisto $@
diff --git a/src/.singularity_modules/kallisto/0.43.1/kallisto.def b/src/.singularity_modules/kallisto/0.43.1/kallisto.def
deleted file mode 100644
index 84a452f9a47d7776662f536440bf97e124976411..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/kallisto/0.43.1/kallisto.def
+++ /dev/null
@@ -1,26 +0,0 @@
-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-KALLISTO_VERSION=0.43.1
-PACKAGES="curl \
-ca-certificates"
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-curl -k -L https://github.com/pachterlab/kallisto/releases/download/v${KALLISTO_VERSION}/kallisto_linux-v${KALLISTO_VERSION}.tar.gz -o kallisto_linux-v${KALLISTO_VERSION}.tar.gz && \
-tar xzf kallisto_linux-v${KALLISTO_VERSION}.tar.gz && \
-cp kallisto_linux-v${KALLISTO_VERSION}/kallisto /usr/bin && \
-rm -Rf kallisto_linux-v${KALLISTO_VERSION}*
-
-%environment
-export KALLISTO_VERSION=0.44.0
-
-%runscript
-exec /bin/bash "$@"
diff --git a/src/.singularity_modules/kallisto/0.44.0/build.sh b/src/.singularity_modules/kallisto/0.44.0/build.sh
deleted file mode 100755
index bf884fb987b05902e653cde3a4e119c3d5f1d0a0..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/kallisto/0.44.0/build.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#/bin/sh
-sudo singularity build --force bin/kallisto:0.44.0.img src/singularity_modules/kallisto/0.44.0/kallisto.def && \
-singularity sign bin/kallisto:0.44.0.img
diff --git a/src/.singularity_modules/kallisto/0.44.0/kallisto b/src/.singularity_modules/kallisto/0.44.0/kallisto
deleted file mode 100755
index c5d5177fad1a9ad70886eb849c1cf57f71f7bbd2..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/kallisto/0.44.0/kallisto
+++ /dev/null
@@ -1,2 +0,0 @@
-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/kallisto:0.44.0.img kallisto $@
diff --git a/src/.singularity_modules/kallisto/0.44.0/kallisto.def b/src/.singularity_modules/kallisto/0.44.0/kallisto.def
deleted file mode 100644
index 74ead1bfe67fe4b50cc1c58d5e6ebdc458b3ba30..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/kallisto/0.44.0/kallisto.def
+++ /dev/null
@@ -1,28 +0,0 @@
-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-
-KALLISTO_VERSION=0.44.0
-PACKAGES="curl \
-ca-certificates"
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-curl -k -L https://github.com/pachterlab/kallisto/releases/download/v${KALLISTO_VERSION}/kallisto_linux-v${KALLISTO_VERSION}.tar.gz -o kallisto_linux-v${KALLISTO_VERSION}.tar.gz && \
-tar xzf kallisto_linux-v${KALLISTO_VERSION}.tar.gz && \
-cp kallisto_linux-v${KALLISTO_VERSION}/kallisto /usr/bin && \
-rm -Rf kallisto_linux-v${KALLISTO_VERSION}*
-
-
-%environment
-export KALLISTO_VERSION=0.44.0
-
-%runscript
-exec /bin/bash "$@"
diff --git a/src/.singularity_modules/macs2/2.1.2/build.sh b/src/.singularity_modules/macs2/2.1.2/build.sh
deleted file mode 100755
index 260c2fef9d41210d65221c8eaf6931aed1e04569..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/macs2/2.1.2/build.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#/bin/sh
-sudo singularity build --force bin/macs2:2.1.2.img docker://quay.io/biocontainers/macs2:2.1.2--py27r351h14c3975_1 && \
-singularity sign bin/macs2:2.1.2.img
diff --git a/src/.singularity_modules/macs2/2.1.2/macs2 b/src/.singularity_modules/macs2/2.1.2/macs2
deleted file mode 100644
index b6f899fb77933047db8f2ae06cf5c8aeea4b8fc7..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/macs2/2.1.2/macs2
+++ /dev/null
@@ -1,2 +0,0 @@
-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/macs2:2.1.2.img macs2 $@
diff --git a/src/.singularity_modules/macs2/2.1.2/macs2.def b/src/.singularity_modules/macs2/2.1.2/macs2.def
deleted file mode 100644
index 05003a38d7ccb6f4fb0e3e0f997208d2ba95b0a4..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/macs2/2.1.2/macs2.def
+++ /dev/null
@@ -1,29 +0,0 @@
-Bootstrap: docker
-From: ubuntu:18.04
-%labels
-MAINTAINER Laurent Modolo
-%post
-mkdir -p /sps /pbs /scratch
-
-MACS_VERSION=2.1.2
-PACKAGES="git \
-build-essential \
-python-pip \
-ca-certificates \
-python-setuptools \
-python-dev \
-python-numpy \
-python-wheel \
-zlib1g-dev"
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-pip install MACS2==${MACS_VERSION}
-
-%environment
-export MACS_VERSION=2.1.1.20160309
-
-%runscript
-exec /bin/bash "$@"
diff --git a/src/.singularity_modules/multiqc/1.0/build.sh b/src/.singularity_modules/multiqc/1.0/build.sh
deleted file mode 100755
index 4622469f01cc28bbf86a3003d9035c71e407b71f..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/multiqc/1.0/build.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#/bin/sh
-sudo singularity build --force bin/multiqc:1.0.img src/singularity_modules/multiqc/1.0/multiqc.def && \
-singularity sign bin/multiqc:1.0.img
diff --git a/src/.singularity_modules/multiqc/1.0/multiqc b/src/.singularity_modules/multiqc/1.0/multiqc
deleted file mode 100644
index 230104ddcb6a688d962fb1aa1bc0309202a06652..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/multiqc/1.0/multiqc
+++ /dev/null
@@ -1,2 +0,0 @@
-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/multiqc:1.0.img multiqc $@
diff --git a/src/.singularity_modules/multiqc/1.0/multiqc.def b/src/.singularity_modules/multiqc/1.0/multiqc.def
deleted file mode 100644
index 21feeaf227806ac7762df91292a551227abb4139..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/multiqc/1.0/multiqc.def
+++ /dev/null
@@ -1,39 +0,0 @@
-Bootstrap: docker
-From: debian:stretch
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-MULTIQC_VERSION=1.0
-PACKAGES="build-essential \
- python3-pip \
- python3-setuptools \
- python3-dev \
- python3-wheel \
- procps \
- locales"
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-locale-gen en_US.UTF-8
-LC_ALL=en_US.utf-8
-LANG=en_US.utf-8
-LC_ALL=C.UTF-8
-LANG=C.UTF-8
-
-pip3 install multiqc==${MULTIQC_VERSION}
-
-%environment
-export KALLISTO_VERSION=0.44.0
-export LC_ALL=en_US.utf-8
-export LANG=en_US.utf-8
-export LC_ALL=C.UTF-8
-export LANG=C.UTF-8
-
-%runscript
-exec /bin/bash "$@"
-
diff --git a/src/.singularity_modules/multiqc/1.7/build.sh b/src/.singularity_modules/multiqc/1.7/build.sh
deleted file mode 100755
index 89176b32c0ceb1dd974c5445d3988bfadecf4ff0..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/multiqc/1.7/build.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#/bin/sh
-sudo singularity build --force bin/multiqc:1.7.img src/singularity_modules/multiqc/1.7/multiqc.def && \
-singularity sign bin/multiqc:1.7.img
diff --git a/src/.singularity_modules/multiqc/1.7/multiqc b/src/.singularity_modules/multiqc/1.7/multiqc
deleted file mode 100644
index 00743e8cd8a4fcf679d8138897c76da601ccae34..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/multiqc/1.7/multiqc
+++ /dev/null
@@ -1,2 +0,0 @@
-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/multiqc:1.7.img multiqc $@
diff --git a/src/.singularity_modules/multiqc/1.7/multiqc.def b/src/.singularity_modules/multiqc/1.7/multiqc.def
deleted file mode 100644
index fe7710f76efea82d347586042795d8bb2ec8fc46..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/multiqc/1.7/multiqc.def
+++ /dev/null
@@ -1,39 +0,0 @@
-Bootstrap: docker
-From: debian:stretch
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-MULTIQC_VERSION=1.7
-PACKAGES="build-essential \
- python3-pip \
- python3-setuptools \
- python3-dev \
- python3-wheel \
- procps \
- locales"
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-locale-gen en_US.UTF-8
-LC_ALL=en_US.utf-8
-LANG=en_US.utf-8
-LC_ALL=C.UTF-8
-LANG=C.UTF-8
-
-pip3 install multiqc==${MULTIQC_VERSION}
-
-%environment
-export KALLISTO_VERSION=0.44.0
-export LC_ALL=en_US.utf-8
-export LANG=en_US.utf-8
-export LC_ALL=C.UTF-8
-export LANG=C.UTF-8
-
-%runscript
-exec /bin/bash "$@"
-
diff --git a/src/.singularity_modules/music/6613c53/build.sh b/src/.singularity_modules/music/6613c53/build.sh
deleted file mode 100755
index 49d7d42e6eb9491f31be809f6cf1db63454efda1..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/music/6613c53/build.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#/bin/sh
-sudo singularity build --force bin/music:6613c53.img src/singularity_modules/music/6613c53/music.def && \
-singularity sign bin/music:6613c53.img
diff --git a/src/.singularity_modules/music/6613c53/music b/src/.singularity_modules/music/6613c53/music
deleted file mode 100644
index fe772f25e652e7694adf8bc618a81d1832a20ade..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/music/6613c53/music
+++ /dev/null
@@ -1,2 +0,0 @@
-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/music:6613c53.img music $@
diff --git a/src/.singularity_modules/music/6613c53/music.def b/src/.singularity_modules/music/6613c53/music.def
deleted file mode 100644
index 2d16c135d2213d9ab999fcefbb7c075c82195c58..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/music/6613c53/music.def
+++ /dev/null
@@ -1,51 +0,0 @@
-Bootstrap: docker
-From: alpine:3.8
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-MUSIC_VERSION=6613c53
-SAMTOOLS_VERSION=1.7
-PACKAGES="git \
- make \
- gcc \
- g++ \
- musl-dev \
- zlib-dev \
- ncurses-dev \
- bzip2-dev \
- xz-dev \
- ca-certificates \
- bash"
-
-apk update && \
-apk add ${PACKAGES}
-
-curl -L -o samtools-${SAMTOOLS_VERSION}.tar.bz2 \
- http://jaist.dl.sourceforge.net/project/samtools/samtools/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2 \
- && tar jxvf samtools-${SAMTOOLS_VERSION}.tar.bz2 \
- && cd samtools-${SAMTOOLS_VERSION}/ \
- && ./configure --without-curses \
- && make \
- && make install
-
-git clone https://github.com/gersteinlab/MUSIC.git && \
-cd MUSIC && \
-git checkout ${MUSIC_VERSION} && \
-make clean && \
-make && \
-cd .. && \
-mv MUSIC/bin/MUSIC /usr/bin/ && \
-mv MUSIC/bin/generate_multimappability_signal.csh /usr/bin/ && \
-mv MUSIC/bin/run_MUSIC.csh /usr/bin/ && \
-rm -Rf MUSIC
-
-chmod +x /usr/bin/*
-
-%environment
-export MUSIC_VERSION=6613c53
-
-%runscript
-exec /bin/bash "$@"
diff --git a/src/.singularity_modules/picard/2.18.11/PicardCommandLine b/src/.singularity_modules/picard/2.18.11/PicardCommandLine
deleted file mode 100644
index ce067365785f2f03c722668eff8d80a94b9b34d3..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/picard/2.18.11/PicardCommandLine
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/bin/sh
-set -eu
-PRG="$(basename -- "$0")"
-case "$PRG" in
-picard-tools)
- echo 1>&2 'Warning: picard-tools is deprecated and should be replaced by PicardCommandLine'
- ;;
-PicardCommandLine)
- ;;
-*)
- set -- "$PRG" "$@"
- ;;
-esac
-
-exec java ${JAVA_OPTIONS-} -jar /usr/share/java/picard.jar "$@"
diff --git a/src/.singularity_modules/picard/2.18.11/build.sh b/src/.singularity_modules/picard/2.18.11/build.sh
deleted file mode 100755
index e6752395713ba40fbefc0b54b7fed9e78512a7b9..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/picard/2.18.11/build.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#/bin/sh
-sudo singularity build --force bin/picard:2.18.11.img src/singularity_modules/picard/2.18.11/picard.def && \
-singularity sign bin/picard:2.18.11.img
diff --git a/src/.singularity_modules/picard/2.18.11/picard b/src/.singularity_modules/picard/2.18.11/picard
deleted file mode 100644
index 19b4bb3baa30d87651716fbd07d05b5f35dd8359..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/picard/2.18.11/picard
+++ /dev/null
@@ -1,2 +0,0 @@
-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/picard:2.18.11.img picard $@
diff --git a/src/.singularity_modules/picard/2.18.11/picard.def b/src/.singularity_modules/picard/2.18.11/picard.def
deleted file mode 100644
index 3ee5418db399b6042da94d158b266d478f0d0dd0..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/picard/2.18.11/picard.def
+++ /dev/null
@@ -1,31 +0,0 @@
-Bootstrap: docker
-From: ubuntu:18.04
-
-%files
-src/singularity_modules/picard/2.18.11/PicardCommandLine /usr/bin/
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-PICARD_VERSION=2.18.11
-PACKAGES="default-jre \
-curl \
-ca-certificates"
-
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-curl -k -L https://github.com/broadinstitute/picard/releases/download/${PICARD_VERSION}/picard.jar -o picard.jar && \
-mkdir -p /usr/share/java/ && \
-mv picard.jar /usr/share/java/
-chmod +x /usr/bin/PicardCommandLine
-
-%environment
-export PICARD_VERSION=2.18.11
-
-%runscript
-exec /bin/bash "$@"
diff --git a/src/.singularity_modules/pigz/2.4/build.sh b/src/.singularity_modules/pigz/2.4/build.sh
deleted file mode 100755
index d5cb798fc49422c3d53b8609131884c7eabf3eb7..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/pigz/2.4/build.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#/bin/sh
-sudo singularity build --force bin/pigz:2.4.img src/singularity_modules/pigz/2.4/pigz.def && \
-singularity sign bin/pigz:2.4.img
diff --git a/src/.singularity_modules/pigz/2.4/pigz b/src/.singularity_modules/pigz/2.4/pigz
deleted file mode 100644
index 47d5cd4cc118d198b7d619670114a3f376100812..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/pigz/2.4/pigz
+++ /dev/null
@@ -1,2 +0,0 @@
-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/pigz:2.4.img pigz $@
diff --git a/src/.singularity_modules/pigz/2.4/pigz.def b/src/.singularity_modules/pigz/2.4/pigz.def
deleted file mode 100644
index 6a757e2952fa15d72ad6a34230524c5abb526e70..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/pigz/2.4/pigz.def
+++ /dev/null
@@ -1,21 +0,0 @@
-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-PIGZ_VERSION=2.4
-PACKAGES=pigz=${PIGZ_VERSION}*
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-%environment
-export PIGZ_VERSION=2.4
-export PACKAGES=pigz=${PIGZ_VERSION}*
-
-%runscript
-exec /bin/bash "$@"
diff --git a/src/.singularity_modules/r/3.5.3/build.sh b/src/.singularity_modules/r/3.5.3/build.sh
deleted file mode 100755
index 2d0d3ab946095ed3be03c1d641f464ef5e3981c8..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/r/3.5.3/build.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#/bin/sh
-sudo singularity build --force bin/r:3.5.3.img src/singularity_modules/r/3.5.3/r.def && \
-singularity sign bin/r:3.5.3.img
diff --git a/src/.singularity_modules/r/3.5.3/r b/src/.singularity_modules/r/3.5.3/r
deleted file mode 100644
index f9cc35225b0b714b46fd6f74b0ddb89dba8a392a..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/r/3.5.3/r
+++ /dev/null
@@ -1,2 +0,0 @@
-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/r:3.5.3.img R $@
diff --git a/src/.singularity_modules/r/3.5.3/r.def b/src/.singularity_modules/r/3.5.3/r.def
deleted file mode 100644
index 7575d9692cec418097a5f260cae1d76d3c803595..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/r/3.5.3/r.def
+++ /dev/null
@@ -1,26 +0,0 @@
-Bootstrap: docker
-From: rocker/r-ver:3.5.3
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-PACKAGES="libssl-dev \
-libcurl4-openssl-dev \
-libxml2-dev \
-zlib1g-dev \
-procps \
-git"
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-R -e "install.packages('tidyverse', dependencies=TRUE, repos='https://cran.rstudio.com/')"
-
-%environment
-export R_VERSION=3.5.3
-
-%runscript
-exec /bin/bash "$@"
diff --git a/src/.singularity_modules/rsem/1.3.0/build.sh b/src/.singularity_modules/rsem/1.3.0/build.sh
deleted file mode 100755
index 841decceb4c7e47c070373d5d878b264a0d3a751..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/rsem/1.3.0/build.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#/bin/sh
-sudo singularity build --force bin/rsem:1.3.0.img src/singularity_modules/rsem/1.3.0/rsem.def && \
-singularity sign bin/rsem:1.3.0.img
diff --git a/src/.singularity_modules/rsem/1.3.0/rsem b/src/.singularity_modules/rsem/1.3.0/rsem
deleted file mode 100644
index 8578c72689205a3ddb9cd95d73be23f4ca0ce31e..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/rsem/1.3.0/rsem
+++ /dev/null
@@ -1,2 +0,0 @@
-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/rsem:1.3.0.img rsem $@
diff --git a/src/.singularity_modules/rsem/1.3.0/rsem.def b/src/.singularity_modules/rsem/1.3.0/rsem.def
deleted file mode 100644
index 4aecc678e137dbefec1d15c83255bca7adbec044..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/rsem/1.3.0/rsem.def
+++ /dev/null
@@ -1,37 +0,0 @@
-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-RSEM_VERSION=1.3.0
-BOWTIE2_VERSION=2.3.4.1
-SAMTOOLS_VERSION=1.7
-PACKAGES="git \
-build-essential \
-ca-certificates \
-zlib1g-dev \
-bowtie2=${BOWTIE2_VERSION}* \
-samtools=${SAMTOOLS_VERSION}*"
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-git clone https://github.com/deweylab/RSEM.git RSEM_${RSEM_VERSION} && \
-cd RSEM_${RSEM_VERSION} && \
-git checkout tags/v${RSEM_VERSION} && \
-make && \
-cd .. && \
-mv RSEM_${RSEM_VERSION}/rsem-* RSEM_${RSEM_VERSION}/rsem_* RSEM_${RSEM_VERSION}/convert-* RSEM_${RSEM_VERSION}/extract-* /usr/bin/ && \
-rm -Rf RSEM_${RSEM_VERSION}
-
-%environment
-export RSEM_VERSION=1.3.0
-export BOWTIE2_VERSION=2.3.4.1
-export SAMTOOLS_VERSION=1.7
-
-%runscript
-exec /bin/bash "$@"
diff --git a/src/.singularity_modules/salmon/0.8.2/build.sh b/src/.singularity_modules/salmon/0.8.2/build.sh
deleted file mode 100755
index a87d021ad9a5a2d29ec522aef105b907f7243b7e..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/salmon/0.8.2/build.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#/bin/sh
-sudo singularity build --force bin/salmon:0.8.2.img src/singularity_modules/salmon/0.8.2/salmon.def && \
-singularity sign bin/salmon:0.8.2.img
diff --git a/src/.singularity_modules/salmon/0.8.2/salmon b/src/.singularity_modules/salmon/0.8.2/salmon
deleted file mode 100644
index e7321e510b98ddd1aced59ce5841f3dd10e8a086..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/salmon/0.8.2/salmon
+++ /dev/null
@@ -1,2 +0,0 @@
-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/salmon:0.8.2.img salmon $@
diff --git a/src/.singularity_modules/salmon/0.8.2/salmon.def b/src/.singularity_modules/salmon/0.8.2/salmon.def
deleted file mode 100644
index ef56bebdeaa239c7f8f827cfac0e97add7e3b5d9..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/salmon/0.8.2/salmon.def
+++ /dev/null
@@ -1,26 +0,0 @@
-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-SALMON_VERSION=0.8.2
-PACKAGES="curl \
-ca-certificates"
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-curl -k -L https://github.com/COMBINE-lab/salmon/releases/download/v${SALMON_VERSION}/Salmon-${SALMON_VERSION}_linux_x86_64.tar.gz -o Salmon-${SALMON_VERSION}_linux_x86_64.tar.gz && \
-tar xzf Salmon-${SALMON_VERSION}_linux_x86_64.tar.gz && \
-mv Salmon-${SALMON_VERSION}_linux_x86_64/bin/* /usr/bin/ && \
-rm -Rf Salmon-${SALMON_VERSION}*
-
-%environment
-export SALMON_VERSION=0.8.2
-
-%runscript
-exec /bin/bash "$@"
diff --git a/src/.singularity_modules/sambamba/0.6.7/build.sh b/src/.singularity_modules/sambamba/0.6.7/build.sh
deleted file mode 100755
index d70f385c79942e53bf9bee5ca40bac87469b994c..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/sambamba/0.6.7/build.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#/bin/sh
-sudo singularity build --force bin/sambamba:0.6.7.img src/singularity_modules/sambamba/0.6.7/sambamba.def && \
-singularity sign bin/sambamba:0.6.7.img
diff --git a/src/.singularity_modules/sambamba/0.6.7/sambamba b/src/.singularity_modules/sambamba/0.6.7/sambamba
deleted file mode 100644
index 35b6aa7294bf723e51c477d4b4d23b1b80a249a0..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/sambamba/0.6.7/sambamba
+++ /dev/null
@@ -1,2 +0,0 @@
-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/sambamba:0.6.7.img sambamba $@
diff --git a/src/.singularity_modules/sambamba/0.6.7/sambamba.def b/src/.singularity_modules/sambamba/0.6.7/sambamba.def
deleted file mode 100644
index 7ec23567569e49992ebd25e6e2e79eb779ec6994..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/sambamba/0.6.7/sambamba.def
+++ /dev/null
@@ -1,28 +0,0 @@
-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-SAMBAMBA_VERSION=0.6.7
-PACKAGES="curl=7.58.0* \
-ca-certificates=20180409 \
-build-essential=12.4* \
-zlib1g-dev=1:1.2.11*"
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-curl -k -L https://github.com/biod/sambamba/releases/download/v${SAMBAMBA_VERSION}/sambamba_v${SAMBAMBA_VERSION}_linux.tar.bz2 -o sambamba_v${SAMBAMBA_VERSION}_linux.tar.bz2 && \
-tar xvjf sambamba_v${SAMBAMBA_VERSION}_linux.tar.bz2 && \
-mv sambamba /usr/bin/ && \
-rm -R sambamba_v${SAMBAMBA_VERSION}_linux*
-
-%environment
-export SAMBAMBA_VERSION=0.6.7
-
-%runscript
-exec /bin/bash "$@"
diff --git a/src/.singularity_modules/sambamba/0.6.9/build.sh b/src/.singularity_modules/sambamba/0.6.9/build.sh
deleted file mode 100755
index 4976ecc20944982a7ac5f1e708568e8f763c1334..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/sambamba/0.6.9/build.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#/bin/sh
-sudo singularity build --force bin/sambamba:0.6.9.img src/singularity_modules/sambamba/0.6.9/sambamba.def && \
-singularity sign bin/sambamba:0.6.9.img
diff --git a/src/.singularity_modules/sambamba/0.6.9/sambamba b/src/.singularity_modules/sambamba/0.6.9/sambamba
deleted file mode 100644
index 35b6aa7294bf723e51c477d4b4d23b1b80a249a0..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/sambamba/0.6.9/sambamba
+++ /dev/null
@@ -1,2 +0,0 @@
-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/sambamba:0.6.7.img sambamba $@
diff --git a/src/.singularity_modules/sambamba/0.6.9/sambamba.def b/src/.singularity_modules/sambamba/0.6.9/sambamba.def
deleted file mode 100644
index 3222c744f2a06e8a435406229e0843f813c15607..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/sambamba/0.6.9/sambamba.def
+++ /dev/null
@@ -1,28 +0,0 @@
-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-SAMBAMBA_VERSION=0.6.9
-PACKAGES="curl=7.58.0* \
-ca-certificates=20180409 \
-build-essential=12.4* \
-zlib1g-dev=1:1.2.11*"
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-curl -k -L https://github.com/biod/sambamba/releases/download/v${SAMBAMBA_VERSION}/sambamba_v${SAMBAMBA_VERSION}_linux.tar.bz2 -o sambamba_v${SAMBAMBA_VERSION}_linux.tar.bz2 && \
-tar xvjf sambamba_v${SAMBAMBA_VERSION}_linux.tar.bz2 && \
-mv sambamba /usr/bin/ && \
-rm -R sambamba_v${SAMBAMBA_VERSION}_linux*
-
-%environment
-export SAMBAMBA_VERSION=0.6.9
-
-%runscript
-exec /bin/bash "$@"
diff --git a/src/.singularity_modules/samblaster/0.1.24/build.sh b/src/.singularity_modules/samblaster/0.1.24/build.sh
deleted file mode 100755
index 6761f50108b43bace04b6d1a11a0b8cb74ef6e70..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/samblaster/0.1.24/build.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#/bin/sh
-sudo singularity build --force bin/samblaster:0.1.24.img src/singularity_modules/samblaster/0.1.24/samblaster.def && \
-singularity sign bin/samblaster:0.1.24.img
diff --git a/src/.singularity_modules/samblaster/0.1.24/samblaster b/src/.singularity_modules/samblaster/0.1.24/samblaster
deleted file mode 100644
index 57100d993e0cd5737be2ddfb4412296c4b2e9077..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/samblaster/0.1.24/samblaster
+++ /dev/null
@@ -1,2 +0,0 @@
-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/samblaster:0.1.24.img samblaster $@
diff --git a/src/.singularity_modules/samblaster/0.1.24/samblaster.def b/src/.singularity_modules/samblaster/0.1.24/samblaster.def
deleted file mode 100644
index 57f7c415bf1ec006551db245250ed2a7aa24f47c..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/samblaster/0.1.24/samblaster.def
+++ /dev/null
@@ -1,31 +0,0 @@
-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-SAMBLASTER_VERSION=0.1.24
-PACKAGES="curl \
-ca-certificates \
-build-essential \
-zlib1g-dev"
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-curl -k -L https://github.com/GregoryFaust/samblaster/releases/download/v.${SAMBLASTER_VERSION}/samblaster-v.${SAMBLASTER_VERSION}.tar.gz -o samblaster-v.${SAMBLASTER_VERSION}.tar.gz && \
-tar xvf samblaster-v.${SAMBLASTER_VERSION}.tar.gz && \
-cd samblaster-v.${SAMBLASTER_VERSION}/ && \
-make && \
-cp samblaster /usr/bin && \
-cd .. && \
-rm -R samblaster-v.${SAMBLASTER_VERSION}/
-
-%environment
-export SAMBLASTER_VERSION=0.1.24
-
-%runscript
-exec /bin/bash "$@"
diff --git a/src/.singularity_modules/samtools/1.7/build.sh b/src/.singularity_modules/samtools/1.7/build.sh
deleted file mode 100755
index 7121a402411b0375e2f0074bb61e07ddc45bae8e..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/samtools/1.7/build.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#/bin/sh
-sudo singularity build --force bin/samtools:1.7.img src/singularity_modules/samtools/1.7/samtools.def && \
-singularity sign bin/samtools:1.7.img
diff --git a/src/.singularity_modules/samtools/1.7/samtools b/src/.singularity_modules/samtools/1.7/samtools
deleted file mode 100644
index d811b276612bd32babbdca75c57b1fd769f7b7ba..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/samtools/1.7/samtools
+++ /dev/null
@@ -1,2 +0,0 @@
-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/samtools:1.7.img samtools $@
diff --git a/src/.singularity_modules/samtools/1.7/samtools.def b/src/.singularity_modules/samtools/1.7/samtools.def
deleted file mode 100644
index ea295f0e026a42f2825d64bd28a8d7ba3d27fb72..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/samtools/1.7/samtools.def
+++ /dev/null
@@ -1,36 +0,0 @@
-Bootstrap: docker
-From: alpine:3.8
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-SAMTOOLS_VERSION=1.7
-PACKAGES="git \
- make \
- gcc \
- musl-dev \
- zlib-dev \
- ncurses-dev \
- bzip2-dev \
- xz-dev \
- bash"
-apk update && \
-apk add ${PACKAGES}
-
-git clone https://github.com/samtools/htslib.git && \
-cd htslib && \
-git checkout ${SAMTOOLS_VERSION} && \
-cd .. && \
-git clone https://github.com/samtools/samtools.git && \
-cd samtools && \
-git checkout ${SAMTOOLS_VERSION} && \
-make && \
-cp samtools /usr/bin/
-
-%environment
-export SAMTOOLS_VERSION=1.7
-
-%runscript
-exec /bin/bash "$@"
diff --git a/src/.singularity_modules/sratoolkit/2.8.2/build.sh b/src/.singularity_modules/sratoolkit/2.8.2/build.sh
deleted file mode 100755
index c71c8a5f7da1f911f602d849b4f9cdd112c00421..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/sratoolkit/2.8.2/build.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#/bin/sh
-sudo singularity build --force bin/sratoolkit:2.8.2.img src/singularity_modules/sratoolkit/2.8.2/sratoolkit.def && \
-singularity sign bin/sratoolkit:2.8.2.img
diff --git a/src/.singularity_modules/sratoolkit/2.8.2/sratoolkit b/src/.singularity_modules/sratoolkit/2.8.2/sratoolkit
deleted file mode 100644
index 6f87648a9109a83560c6182e72223d587b64a767..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/sratoolkit/2.8.2/sratoolkit
+++ /dev/null
@@ -1,2 +0,0 @@
-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/sratoolkit:2.8.2.img sratoolkit $@
diff --git a/src/.singularity_modules/sratoolkit/2.8.2/sratoolkit.def b/src/.singularity_modules/sratoolkit/2.8.2/sratoolkit.def
deleted file mode 100644
index c7c3e50c32c93b0ed493098eb8d4fb2c23a47c0b..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/sratoolkit/2.8.2/sratoolkit.def
+++ /dev/null
@@ -1,20 +0,0 @@
-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-SRATOOLKIT_VERSION=2.8.2
-PACKAGES=sra-toolkit=${SRATOOLKIT_VERSION}*
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-%environment
-export SRATOOLKIT_VERSION=2.8.2
-
-%runscript
-exec /bin/bash "$@"
diff --git a/src/.singularity_modules/subread/1.6.4/build.sh b/src/.singularity_modules/subread/1.6.4/build.sh
deleted file mode 100755
index 4a758ee573f93415c63ce5a5b76c48f08571d4ad..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/subread/1.6.4/build.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#/bin/sh
-sudo singularity build --force bin/subread:1.6.4.img src/singularity_modules/subread/1.6.4/subread.def && \
-singularity sign bin/subread:1.6.4.img
diff --git a/src/.singularity_modules/subread/1.6.4/subread b/src/.singularity_modules/subread/1.6.4/subread
deleted file mode 100644
index 382bf0440aae90eccd045fc7b07a27af6ba6743c..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/subread/1.6.4/subread
+++ /dev/null
@@ -1,2 +0,0 @@
-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/subread:1.6.4.img subread $@
diff --git a/src/.singularity_modules/subread/1.6.4/subread.def b/src/.singularity_modules/subread/1.6.4/subread.def
deleted file mode 100644
index db8f00c2d69c767cf1568302e2efabde5c4d6ce9..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/subread/1.6.4/subread.def
+++ /dev/null
@@ -1,15 +0,0 @@
-Bootstrap: docker
-From: quay.io/biocontainers/subread:1.6.4--h84994c4_1
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-SUBREF_VERSION=1.6.4
-
-%environment
-export SUBREF_VERSION=1.6.4
-
-%runscript
-exec /bin/bash "$@"
diff --git a/src/.singularity_modules/tophat/2.1.1/build.sh b/src/.singularity_modules/tophat/2.1.1/build.sh
deleted file mode 100755
index 002911a76f89fc08aed5d83f6f62d3eb0b95f5ad..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/tophat/2.1.1/build.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#/bin/sh
-sudo singularity build --force bin/tophat:2.1.1.img src/singularity_modules/tophat/2.1.1/tophat.def && \
-singularity sign bin/tophat:2.1.1.img
diff --git a/src/.singularity_modules/tophat/2.1.1/tophat b/src/.singularity_modules/tophat/2.1.1/tophat
deleted file mode 100644
index 44bb8bb85f9bd3162dde41d25f1f80fa9c5c94b3..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/tophat/2.1.1/tophat
+++ /dev/null
@@ -1,2 +0,0 @@
-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/tophat:2.1.1.img tophat $@
diff --git a/src/.singularity_modules/tophat/2.1.1/tophat.def b/src/.singularity_modules/tophat/2.1.1/tophat.def
deleted file mode 100644
index e4697b9cffff4db2fd2118c5f48badb1f8066743..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/tophat/2.1.1/tophat.def
+++ /dev/null
@@ -1,20 +0,0 @@
-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-TOPHAT_VERSION=2.1.1
-PACKAGES=tophat=${BOWTIE2_VERSION}*
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-%environment
-export TOPHAT_VERSION=2.1.1
-
-%runscript
-exec /bin/bash "$@"
diff --git a/src/.singularity_modules/trimmomatic/0.36/build.sh b/src/.singularity_modules/trimmomatic/0.36/build.sh
deleted file mode 100755
index e911a1c2d30b59da8274ef0fd7217c709864880a..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/trimmomatic/0.36/build.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#/bin/sh
-sudo singularity build --force bin/trimmomatic:0.36.img src/singularity_modules/trimmomatic/0.36/trimmomatic.def && \
-singularity sign bin/trimmomatic:0.36.img
diff --git a/src/.singularity_modules/trimmomatic/0.36/trimmomatic b/src/.singularity_modules/trimmomatic/0.36/trimmomatic
deleted file mode 100644
index 8511bddfaa7faba56d022d33dbeedeca5058198d..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/trimmomatic/0.36/trimmomatic
+++ /dev/null
@@ -1,2 +0,0 @@
-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/trimmomatic:0.36.img trimmomatic $@
diff --git a/src/.singularity_modules/trimmomatic/0.36/trimmomatic.def b/src/.singularity_modules/trimmomatic/0.36/trimmomatic.def
deleted file mode 100644
index 3281905754bc088110e56806fd1db222e91f7585..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/trimmomatic/0.36/trimmomatic.def
+++ /dev/null
@@ -1,20 +0,0 @@
-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-TRIMMOMATIC_VERSION=0.36
-PACKAGES=trimmomatic=${TRIMMOMATIC_VERSION}*
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-%environment
-export TRIMMOMATIC_VERSION=0.36
-
-%runscript
-exec /bin/bash "$@"
diff --git a/src/.singularity_modules/ucsc/375/build.sh b/src/.singularity_modules/ucsc/375/build.sh
deleted file mode 100755
index 9546fa685da95b8d6fe7090cedb2173fdb9669dd..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/ucsc/375/build.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#/bin/sh
-sudo singularity build --force bin/ucsc:375.img src/singularity_modules/ucsc/375/ucsc.def && \
-singularity sign bin/ucsc:375.img
diff --git a/src/.singularity_modules/ucsc/375/ucsc b/src/.singularity_modules/ucsc/375/ucsc
deleted file mode 100644
index 344b13431f15bb2d11dbf9a7d69321bb9890412f..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/ucsc/375/ucsc
+++ /dev/null
@@ -1,2 +0,0 @@
-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/ucsc:375.img ucsc $@
diff --git a/src/.singularity_modules/ucsc/375/ucsc.def b/src/.singularity_modules/ucsc/375/ucsc.def
deleted file mode 100644
index 7dd798897d4a7aa9134109317a762d9b46cc30c8..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/ucsc/375/ucsc.def
+++ /dev/null
@@ -1,38 +0,0 @@
-Bootstrap: docker
-From: debian:jessie
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-UCSC_VERSION=375
-PACKAGES="apt-utils \
- curl \
- build-essential \
- libssl-dev \
- libpng-dev \
- uuid-dev \
- procps \
- libmysqlclient-dev \
- rsync"
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-curl -k -L http://hgdownload.soe.ucsc.edu/admin/exe/userApps.v${UCSC_VERSION}.src.tgz -o userApps.v${UCSC_VERSION}.src.tgz &&\
-tar xvf userApps.v${UCSC_VERSION}.src.tgz &&\
-cd userApps/ && \
-make &&\
-cd .. &&\
-mv userApps/bin/* /usr/bin/ &&\
-rm -R userApps.v${UCSC_VERSION}.src.tgz &&\
-rm -R userApps
-
-%environment
-export UCSC_VERSION=375
-
-%runscript
-exec /bin/bash "$@"
-
diff --git a/src/.singularity_modules/umi_tools/1.0.0/build.sh b/src/.singularity_modules/umi_tools/1.0.0/build.sh
deleted file mode 100755
index 011337df0d6dd979474c65a8aab271e1dda8dc64..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/umi_tools/1.0.0/build.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#/bin/sh
-sudo singularity build --force bin/umi_tools:1.0.0.img src/singularity_modules/umi_tools/1.0.0/umi_tools.def && \
-singularity sign bin/umi_tools:1.0.0.img
diff --git a/src/.singularity_modules/umi_tools/1.0.0/umi_tools b/src/.singularity_modules/umi_tools/1.0.0/umi_tools
deleted file mode 100644
index 673c53e23a82eacd1aeeed2dfef8be2ad0fd7949..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/umi_tools/1.0.0/umi_tools
+++ /dev/null
@@ -1,2 +0,0 @@
-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/umi_tools:1.0.0.img umi_tools $@
diff --git a/src/.singularity_modules/umi_tools/1.0.0/umi_tools.def b/src/.singularity_modules/umi_tools/1.0.0/umi_tools.def
deleted file mode 100644
index 0eb75622cbcb60990e554cb4fb2572aaeaf0a9fb..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/umi_tools/1.0.0/umi_tools.def
+++ /dev/null
@@ -1,28 +0,0 @@
-Bootstrap: docker
-From: debian:stretch
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-UMI_TOOLS_VERSION=1.0.0
-PACKAGES="bash \
- python3 \
- python3-dev \
- python3-pip \
- procps \
- gcc"
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-pip3 install setuptools
-pip3 install umi_tools==${UMI_TOOLS_VERSION}
-
-%environment
-export UMI_TOOLS_VERSION=1.0.0
-
-%runscript
-exec /bin/bash "$@"
diff --git a/src/.singularity_modules/urqt/d62c1f8/build.sh b/src/.singularity_modules/urqt/d62c1f8/build.sh
deleted file mode 100755
index 7d8d0a1c2e292a545166c04207d4b59c3669861d..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/urqt/d62c1f8/build.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#/bin/sh
-sudo singularity build --force bin/urqt:d62c1f8.img src/singularity_modules/urqt/d62c1f8/urqt.def && \
-singularity sign bin/urqt:d62c1f8.img
diff --git a/src/.singularity_modules/urqt/d62c1f8/urqt b/src/.singularity_modules/urqt/d62c1f8/urqt
deleted file mode 100644
index 924beee1d8a6cd0c432b1c6a791fb87123cd3697..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/urqt/d62c1f8/urqt
+++ /dev/null
@@ -1,2 +0,0 @@
-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/urqt:d62c1f8.img urqt $@
diff --git a/src/.singularity_modules/urqt/d62c1f8/urqt.def b/src/.singularity_modules/urqt/d62c1f8/urqt.def
deleted file mode 100644
index eba8af974d834d0dcb350200df805595d8118fda..0000000000000000000000000000000000000000
--- a/src/.singularity_modules/urqt/d62c1f8/urqt.def
+++ /dev/null
@@ -1,33 +0,0 @@
-Bootstrap: docker
-From: debian:9
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-URQT_VERSION=d62c1f8
-PACKAGES="git \
-g++ \
-make \
-ca-certificates \
-procps \
-zlib1g-dev"
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-git clone https://github.com/l-modolo/UrQt.git && \
-cd UrQt && \
-git checkout ${URQT_VERSION} && \
-make && \
-cd .. && \
-mv UrQt/UrQt /usr/bin/ && \
-rm -Rf UrQt
-
-%environment
-export URQT_VERSION=d62c1f8
-
-%runscript
-exec /bin/bash "$@"
diff --git a/src/.update_config.sh b/src/.update_config.sh
index 8d66be127de642ba1b3a4075d14cb12574e40cad..ffb76502cdf7a5a035dcd98809401ca8591201ff 100644
--- a/src/.update_config.sh
+++ b/src/.update_config.sh
@@ -5,7 +5,7 @@ fd ".*config" -E "nf_modules" src/ -x perl -0777pe 's|container = "|container =
fd ".*config" -E "nf_modules" src/ -x perl -pe 's|container = "lbmc/file://bin/(.*).img"|container = "lbmc/\1"|g' -i {}
# update singularity config
-fd ".*config" -E "nf_modules" src/ -x perl -0777pe 's|\n\s*singularity {\n\s*singularity.enabled = true|\n singularity {\n singularity.enabled = true\n singularity.cacheDir = "./bin/"|mg' -i {}
+fd ".*config" -E "nf_modules" src/ -x perl -0776pe 's|\n\s*singularity {\n\s*singularity.enabled = true|\n singularity {\n singularity.enabled = true\n singularity.cacheDir = "./bin/"|mg' -i {}
# update in2p3 config
fd ".*config" -E "nf_modules" src/ -x perl -0777pe 's|\n\s*ccin2p3 {\n\s*singularity.enabled = true|\n ccin2p3 {\n singularity.enabled = true\n singularity.cacheDir = "/sps/lbmc/common/singularity/"|mg' -i {}
diff --git a/src/nextflow.pbs b/src/nextflow.pbs
deleted file mode 100644
index e89d8599f10aeac03270e3b1b26d9a376edf7a15..0000000000000000000000000000000000000000
--- a/src/nextflow.pbs
+++ /dev/null
@@ -1,39 +0,0 @@
-#! /usr/local/bin/bash -l
-#####################################
-# job script example with GE options
-#####################################
-#$ -q demon
-#$ -l demon=1
-#$ -P P_lbmc
-#$ -N nf_pipe
-#$ -o /sps/lbmc/<user>/logs/ # change to your username !
-#$ -e /sps/lbmc/<user>/logs/ # change to your username !
-#$ -r n # relaunch y/n
-#$ -M <email>@ens-lyon.fr # change to your mail !
-#$ -m be ## send an email when the job starts and ends
-#$ -l os=cl7 ## choose OS
-#$ -l sps=1 ## acces /sps directory
-#####################################
-
-# change to your username !
-SCRATCH=/sps/lbmc/<user>/
-# change to your project name !
-PROJECT=<project>
-#change to your project version !
-PIPELINE=<pipeline_name>
-#NF version to user
-NF_VERSION=19.04
-
-
-NEXTFLOW=/pbs/throng/lbmc/cl7/nextflow/${NF_VERSION}/nextflow
-NF=${SCRATCH}/${PROJECT}/src/${PIPELINE}.nf
-CONFIG=${SCRATCH}/${PROJECT}/src/${PIPELINE}.config
-DATA=${SCRATCH}/${PROJECT}/data
-NF_OPTIONS="-w \"${SCRATCH}/${PROJECT}/work/\" \
--with-report \"${SCRATCH}/${PROJECT}/results/${PIPELINE}_report.html\" \
--with-timeline \"${SCRATCH}/${PROJECT}/results/${PIPELINE}_timeline.html\" \
--with-dag \"${SCRATCH}/${PROJECT}/results/${PIPELINE}_dag.html\""
-
-${NEXTFLOW} ${NF} -c ${CONFIG} -profile ccin2p3 ${NF_OPTIONS} \
---fasta "${DATA}/fasta" \
---results "${SCRATCH}/${PROJECT}/results/"
diff --git a/src/nf_modules/star/indexing.config b/src/nf_modules/star/indexing.config
new file mode 100644
index 0000000000000000000000000000000000000000..3e4017b92dc87fa553c890055f1769beef836468
--- /dev/null
+++ b/src/nf_modules/star/indexing.config
@@ -0,0 +1,54 @@
+profiles {
+ docker {
+ docker.temp = 'auto'
+ docker.enabled = true
+ process {
+ withName: index_fasta {
+ container = "lbmc/star:2.7.3a"
+ cpus = 4
+ }
+ }
+ }
+ singularity {
+ singularity.enabled = true
+ singularity.cacheDir = "./bin/"
+ process {
+ withName: index_fasta {
+ container = "lbmc/star:2.7.3a"
+ cpus = 4
+ }
+ }
+ }
+ psmn{
+ process{
+ withName: index_fasta {
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/star_2.7.3a"
+ executor = "sge"
+ clusterOptions = "-cwd -V"
+ cpus = 16
+ memory = "20GB"
+ time = "12h"
+ queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+ penv = 'openmp16'
+ }
+ }
+ }
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.cacheDir = "/sps/lbmc/common/singularity/"
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withName: index_fasta {
+ container = "lbmc/star:2.7.3a"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ cpus = 1
+ queue = 'huge'
+ }
+ }
+ }
+}
diff --git a/src/nf_modules/star/indexing.nf b/src/nf_modules/star/indexing.nf
new file mode 100644
index 0000000000000000000000000000000000000000..0f340b2d3d11ff5fd79d6b1e5e3f8c56d35f2154
--- /dev/null
+++ b/src/nf_modules/star/indexing.nf
@@ -0,0 +1,36 @@
+params.fasta = "$baseDir/data/bam/*.fasta"
+params.annotation = "$baseDir/data/bam/*.gtf"
+
+log.info "fasta files : ${params.fasta}"
+
+Channel
+ .fromPath( params.fasta )
+ .ifEmpty { error "Cannot find any fasta files matching: ${params.fasta}" }
+ .set { fasta_file }
+Channel
+ .fromPath( params.annotation )
+ .ifEmpty { error "Cannot find any annotation files matching: ${params.annotation}" }
+ .set { annotation_file }
+
+process index_fasta {
+ tag "$fasta.baseName"
+ publishDir "results/mapping/index/", mode: 'copy'
+
+ input:
+ file fasta from fasta_file
+ file annotation from annotation_file
+
+ output:
+ file "*" into index_files
+
+ script:
+"""
+STAR --runThreadN ${task.cpus} --runMode genomeGenerate \
+--genomeDir ./ \
+--genomeFastaFiles ${fasta} \
+--sjdbGTFfile ${annotation} \
+--genomeSAindexNbases 3 # min(14, log2(GenomeLength)/2 - 1)
+"""
+}
+
+
diff --git a/src/nf_modules/star/mapping_paired.config b/src/nf_modules/star/mapping_paired.config
new file mode 100644
index 0000000000000000000000000000000000000000..c2de5c50997fa856cf9923522ca2cd54f6313a29
--- /dev/null
+++ b/src/nf_modules/star/mapping_paired.config
@@ -0,0 +1,54 @@
+profiles {
+ docker {
+ docker.temp = 'auto'
+ docker.enabled = true
+ process {
+ withName: mapping_fastq {
+ container = "lbmc/star:2.7.3a"
+ cpus = 4
+ }
+ }
+ }
+ singularity {
+ singularity.enabled = true
+ singularity.cacheDir = "./bin/"
+ process {
+ withName: mapping_fastq {
+ container = "lbmc/star:2.7.3a"
+ cpus = 4
+ }
+ }
+ }
+ psmn{
+ process{
+ withName: mapping_fastq {
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/star_2.7.3a"
+ executor = "sge"
+ clusterOptions = "-cwd -V"
+ cpus = 16
+ memory = "30GB"
+ time = "24h"
+ queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+ penv = 'openmp16'
+ }
+ }
+ }
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.cacheDir = "/sps/lbmc/common/singularity/"
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withName: mapping_fastq {
+ container = "lbmc/star:2.7.3a"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ cpus = 1
+ queue = 'huge'
+ }
+ }
+ }
+}
diff --git a/src/nf_modules/star/mapping_paired.nf b/src/nf_modules/star/mapping_paired.nf
new file mode 100644
index 0000000000000000000000000000000000000000..9ea901751da50944d23327f47bc3813ff3a49859
--- /dev/null
+++ b/src/nf_modules/star/mapping_paired.nf
@@ -0,0 +1,40 @@
+params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
+params.index = "$baseDir/data/index/*.index.*"
+
+log.info "fastq files : ${params.fastq}"
+log.info "index files : ${params.index}"
+
+Channel
+ .fromFilePairs( params.fastq )
+ .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
+ .set { fastq_files }
+Channel
+ .fromPath( params.index )
+ .ifEmpty { error "Cannot find any index files matching: ${params.index}" }
+ .set { index_files }
+
+process mapping_fastq {
+ tag "$pair_id"
+ publishDir "results/mapping/bams/", mode: 'copy'
+
+ input:
+ set pair_id, file(reads) from fastq_files
+ file index from index_files.collect()
+
+ output:
+ set pair_id, "*.bam" into bam_files
+ file "*.out" into mapping_report
+
+ script:
+"""
+mkdir -p index
+mv ${index} index/
+STAR --runThreadN ${task.cpus} \
+--genomeDir index/ \
+--readFilesIn ${reads[0]} ${reads[1]} \
+--outFileNamePrefix ${pair_id} \
+--outSAMmapqUnique 0 \
+--outSAMtype BAM SortedByCoordinate
+"""
+}
+
diff --git a/src/nf_modules/star/mapping_single.config b/src/nf_modules/star/mapping_single.config
new file mode 100644
index 0000000000000000000000000000000000000000..c2de5c50997fa856cf9923522ca2cd54f6313a29
--- /dev/null
+++ b/src/nf_modules/star/mapping_single.config
@@ -0,0 +1,54 @@
+profiles {
+ docker {
+ docker.temp = 'auto'
+ docker.enabled = true
+ process {
+ withName: mapping_fastq {
+ container = "lbmc/star:2.7.3a"
+ cpus = 4
+ }
+ }
+ }
+ singularity {
+ singularity.enabled = true
+ singularity.cacheDir = "./bin/"
+ process {
+ withName: mapping_fastq {
+ container = "lbmc/star:2.7.3a"
+ cpus = 4
+ }
+ }
+ }
+ psmn{
+ process{
+ withName: mapping_fastq {
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/star_2.7.3a"
+ executor = "sge"
+ clusterOptions = "-cwd -V"
+ cpus = 16
+ memory = "30GB"
+ time = "24h"
+ queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+ penv = 'openmp16'
+ }
+ }
+ }
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.cacheDir = "/sps/lbmc/common/singularity/"
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withName: mapping_fastq {
+ container = "lbmc/star:2.7.3a"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ cpus = 1
+ queue = 'huge'
+ }
+ }
+ }
+}
diff --git a/src/nf_modules/star/mapping_single.nf b/src/nf_modules/star/mapping_single.nf
new file mode 100644
index 0000000000000000000000000000000000000000..9d3d51b38da6cc7cf7dff985e5c0052b2924168a
--- /dev/null
+++ b/src/nf_modules/star/mapping_single.nf
@@ -0,0 +1,39 @@
+params.fastq = "$baseDir/data/fastq/*.fastq"
+
+log.info "fastq files : ${params.fastq}"
+log.info "index files : ${params.index}"
+
+Channel
+ .fromPath( params.fastq )
+ .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
+ .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
+ .set { fastq_files }
+Channel
+ .fromPath( params.index )
+ .ifEmpty { error "Cannot find any index files matching: ${params.index}" }
+ .set { index_files }
+
+process mapping_fastq {
+ tag "$file_id"
+ publishDir "results/mapping/bams/", mode: 'copy'
+
+ input:
+ set file_id, file(reads) from fastq_files
+ file index from index_files.collect()
+
+ output:
+ set file_id, "*.bam" into bam_files
+ file "*.out" into mapping_report
+
+ script:
+"""
+mkdir -p index
+mv ${index} index/
+STAR --runThreadN ${task.cpus} \
+--genomeDir index/ \
+--readFilesIn ${reads} \
+--outFileNamePrefix ${file_id} \
+--outSAMmapqUnique 0 \
+--outSAMtype BAM SortedByCoordinate
+"""
+}
diff --git a/src/nf_modules/star/tests.sh b/src/nf_modules/star/tests.sh
new file mode 100755
index 0000000000000000000000000000000000000000..046ffe4f32bc78467a61440774553335f888b288
--- /dev/null
+++ b/src/nf_modules/star/tests.sh
@@ -0,0 +1,43 @@
+./nextflow src/nf_modules/star/indexing.nf \
+ -c src/nf_modules/star/indexing.config \
+ -profile docker \
+ --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
+ --annotation "data/tiny_dataset/annot/tiny.gtf" \
+ -resume
+
+./nextflow src/nf_modules/star/mapping_single.nf \
+ -c src/nf_modules/star/mapping_single.config \
+ -profile docker \
+ --index "results/mapping/index/*" \
+ --fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
+ -resume
+
+./nextflow src/nf_modules/star/mapping_paired.nf \
+ -c src/nf_modules/star/mapping_paired.config \
+ -profile docker \
+ --index "results/mapping/index/*" \
+ --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
+ -resume
+
+if [ -x "$(command -v singularity)" ]; then
+./nextflow src/nf_modules/star/indexing.nf \
+ -c src/nf_modules/star/indexing.config \
+ -profile singularity \
+ --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
+ --annotation "data/tiny_dataset/annot/tiny.gtf" \
+ -resume
+
+./nextflow src/nf_modules/star/mapping_single.nf \
+ -c src/nf_modules/star/mapping_single.config \
+ -profile singularity \
+ --index "results/mapping/index/*" \
+ --fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
+ -resume
+
+./nextflow src/nf_modules/star/mapping_paired.nf \
+ -c src/nf_modules/star/mapping_paired.config \
+ -profile singularity \
+ --index "results/mapping/index/*" \
+ --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
+ -resume
+fi