From e4c29f64ee9cb01442042c5e4a94ca7a8eaf4480 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Wed, 20 Nov 2019 16:16:46 +0100
Subject: [PATCH] singularity: remove module as they are pulled from docker
since 0.4.0
---
.../bcftools/1.7/bcftools | 2 -
.../bcftools/1.7/bcftools.def | 20 --------
.../bcftools/1.7/build.sh | 3 --
.../bedtools/2.25.0/bedtools | 2 -
.../bedtools/2.25.0/bedtools.def | 20 --------
.../bedtools/2.25.0/build.sh | 3 --
src/.singularity_modules/bioawk/1.0/bioawk | 2 -
.../bioawk/1.0/bioawk.def | 32 ------------
src/.singularity_modules/bioawk/1.0/build.sh | 3 --
src/.singularity_modules/bowtie/1.2.2/bowtie | 2 -
.../bowtie/1.2.2/bowtie.def | 23 ---------
.../bowtie/1.2.2/build.sh | 3 --
.../bowtie2/2.3.4.1/bowtie2 | 2 -
.../bowtie2/2.3.4.1/bowtie2.def | 24 ---------
.../bowtie2/2.3.4.1/build.sh | 3 --
src/.singularity_modules/bwa/0.7.17/build.sh | 3 --
src/.singularity_modules/bwa/0.7.17/bwa | 2 -
src/.singularity_modules/bwa/0.7.17/bwa.def | 47 -----------------
src/.singularity_modules/canu/1.6/build.sh | 3 --
src/.singularity_modules/canu/1.6/canu | 2 -
src/.singularity_modules/canu/1.6/canu.def | 20 --------
.../cutadapt/1.14/build.sh | 3 --
.../cutadapt/1.14/cutadapt | 2 -
.../cutadapt/1.14/cutadapt.def | 28 ----------
.../cutadapt/1.15/build.sh | 3 --
.../cutadapt/1.15/cutadapt | 2 -
.../cutadapt/1.15/cutadapt.def | 29 -----------
.../cutadapt/2.1/build.sh | 3 --
.../cutadapt/2.1/cutadapt | 2 -
.../cutadapt/2.1/cutadapt.def | 28 ----------
.../deeptools/3.0.2/build.sh | 3 --
.../deeptools/3.0.2/deeptools | 2 -
.../deeptools/3.0.2/deeptools.def | 29 -----------
.../deeptools/3.1.1/build.sh | 3 --
.../deeptools/3.1.1/deeptools | 2 -
.../deeptools/3.1.1/deeptools.def | 29 -----------
.../docker_to_singularity.sh | 13 -----
.../fastp/0.19.7/build.sh | 3 --
src/.singularity_modules/fastp/0.19.7/fastp | 2 -
.../fastp/0.19.7/fastp.def | 15 ------
.../fastqc/0.11.5/build.sh | 3 --
src/.singularity_modules/fastqc/0.11.5/fastqc | 2 -
.../fastqc/0.11.5/fastqc.def | 22 --------
.../file_handle/0.1.1/build.sh | 3 --
.../file_handle/0.1.1/file_handle | 2 -
.../file_handle/0.1.1/file_handle.def | 28 ----------
.../gatk/4.0.8.1/build.sh | 3 --
src/.singularity_modules/gatk/4.0.8.1/gatk | 2 -
.../gatk/4.0.8.1/gatk.def | 17 -------
.../hisat2/2.0.0/build.sh | 3 --
src/.singularity_modules/hisat2/2.0.0/hisat2 | 2 -
.../hisat2/2.0.0/hisat2.def | 51 -------------------
.../hisat2/2.1.0/build.sh | 3 --
src/.singularity_modules/hisat2/2.1.0/hisat2 | 2 -
.../hisat2/2.1.0/hisat2.def | 51 -------------------
.../htseq/0.11.2/build.sh | 3 --
src/.singularity_modules/htseq/0.11.2/htseq | 2 -
.../htseq/0.11.2/htseq.def | 28 ----------
src/.singularity_modules/htseq/0.8.0/build.sh | 3 --
src/.singularity_modules/htseq/0.8.0/htseq | 2 -
.../htseq/0.8.0/htseq.def | 28 ----------
.../kallisto/0.43.1/build.sh | 3 --
.../kallisto/0.43.1/kallisto | 2 -
.../kallisto/0.43.1/kallisto.def | 26 ----------
.../kallisto/0.44.0/build.sh | 3 --
.../kallisto/0.44.0/kallisto | 2 -
.../kallisto/0.44.0/kallisto.def | 28 ----------
src/.singularity_modules/macs2/2.1.2/build.sh | 3 --
src/.singularity_modules/macs2/2.1.2/macs2 | 2 -
.../macs2/2.1.2/macs2.def | 29 -----------
src/.singularity_modules/multiqc/1.0/build.sh | 3 --
src/.singularity_modules/multiqc/1.0/multiqc | 2 -
.../multiqc/1.0/multiqc.def | 39 --------------
src/.singularity_modules/multiqc/1.7/build.sh | 3 --
src/.singularity_modules/multiqc/1.7/multiqc | 2 -
.../multiqc/1.7/multiqc.def | 39 --------------
.../music/6613c53/build.sh | 3 --
src/.singularity_modules/music/6613c53/music | 2 -
.../music/6613c53/music.def | 51 -------------------
.../picard/2.18.11/PicardCommandLine | 15 ------
.../picard/2.18.11/build.sh | 3 --
.../picard/2.18.11/picard | 2 -
.../picard/2.18.11/picard.def | 31 -----------
src/.singularity_modules/pigz/2.4/build.sh | 3 --
src/.singularity_modules/pigz/2.4/pigz | 2 -
src/.singularity_modules/pigz/2.4/pigz.def | 21 --------
src/.singularity_modules/r/3.5.3/build.sh | 3 --
src/.singularity_modules/r/3.5.3/r | 2 -
src/.singularity_modules/r/3.5.3/r.def | 26 ----------
src/.singularity_modules/rsem/1.3.0/build.sh | 3 --
src/.singularity_modules/rsem/1.3.0/rsem | 2 -
src/.singularity_modules/rsem/1.3.0/rsem.def | 37 --------------
.../salmon/0.8.2/build.sh | 3 --
src/.singularity_modules/salmon/0.8.2/salmon | 2 -
.../salmon/0.8.2/salmon.def | 26 ----------
.../sambamba/0.6.7/build.sh | 3 --
.../sambamba/0.6.7/sambamba | 2 -
.../sambamba/0.6.7/sambamba.def | 28 ----------
.../sambamba/0.6.9/build.sh | 3 --
.../sambamba/0.6.9/sambamba | 2 -
.../sambamba/0.6.9/sambamba.def | 28 ----------
.../samblaster/0.1.24/build.sh | 3 --
.../samblaster/0.1.24/samblaster | 2 -
.../samblaster/0.1.24/samblaster.def | 31 -----------
.../samtools/1.7/build.sh | 3 --
.../samtools/1.7/samtools | 2 -
.../samtools/1.7/samtools.def | 36 -------------
.../sratoolkit/2.8.2/build.sh | 3 --
.../sratoolkit/2.8.2/sratoolkit | 2 -
.../sratoolkit/2.8.2/sratoolkit.def | 20 --------
.../subread/1.6.4/build.sh | 3 --
.../subread/1.6.4/subread | 2 -
.../subread/1.6.4/subread.def | 15 ------
.../tophat/2.1.1/build.sh | 3 --
src/.singularity_modules/tophat/2.1.1/tophat | 2 -
.../tophat/2.1.1/tophat.def | 20 --------
.../trimmomatic/0.36/build.sh | 3 --
.../trimmomatic/0.36/trimmomatic | 2 -
.../trimmomatic/0.36/trimmomatic.def | 20 --------
src/.singularity_modules/ucsc/375/build.sh | 3 --
src/.singularity_modules/ucsc/375/ucsc | 2 -
src/.singularity_modules/ucsc/375/ucsc.def | 38 --------------
.../umi_tools/1.0.0/build.sh | 3 --
.../umi_tools/1.0.0/umi_tools | 2 -
.../umi_tools/1.0.0/umi_tools.def | 28 ----------
.../urqt/d62c1f8/build.sh | 3 --
src/.singularity_modules/urqt/d62c1f8/urqt | 2 -
.../urqt/d62c1f8/urqt.def | 33 ------------
128 files changed, 1457 deletions(-)
delete mode 100644 src/.singularity_modules/bcftools/1.7/bcftools
delete mode 100644 src/.singularity_modules/bcftools/1.7/bcftools.def
delete mode 100755 src/.singularity_modules/bcftools/1.7/build.sh
delete mode 100644 src/.singularity_modules/bedtools/2.25.0/bedtools
delete mode 100644 src/.singularity_modules/bedtools/2.25.0/bedtools.def
delete mode 100755 src/.singularity_modules/bedtools/2.25.0/build.sh
delete mode 100644 src/.singularity_modules/bioawk/1.0/bioawk
delete mode 100644 src/.singularity_modules/bioawk/1.0/bioawk.def
delete mode 100755 src/.singularity_modules/bioawk/1.0/build.sh
delete mode 100644 src/.singularity_modules/bowtie/1.2.2/bowtie
delete mode 100644 src/.singularity_modules/bowtie/1.2.2/bowtie.def
delete mode 100755 src/.singularity_modules/bowtie/1.2.2/build.sh
delete mode 100644 src/.singularity_modules/bowtie2/2.3.4.1/bowtie2
delete mode 100644 src/.singularity_modules/bowtie2/2.3.4.1/bowtie2.def
delete mode 100755 src/.singularity_modules/bowtie2/2.3.4.1/build.sh
delete mode 100755 src/.singularity_modules/bwa/0.7.17/build.sh
delete mode 100644 src/.singularity_modules/bwa/0.7.17/bwa
delete mode 100644 src/.singularity_modules/bwa/0.7.17/bwa.def
delete mode 100755 src/.singularity_modules/canu/1.6/build.sh
delete mode 100644 src/.singularity_modules/canu/1.6/canu
delete mode 100644 src/.singularity_modules/canu/1.6/canu.def
delete mode 100755 src/.singularity_modules/cutadapt/1.14/build.sh
delete mode 100644 src/.singularity_modules/cutadapt/1.14/cutadapt
delete mode 100644 src/.singularity_modules/cutadapt/1.14/cutadapt.def
delete mode 100755 src/.singularity_modules/cutadapt/1.15/build.sh
delete mode 100644 src/.singularity_modules/cutadapt/1.15/cutadapt
delete mode 100644 src/.singularity_modules/cutadapt/1.15/cutadapt.def
delete mode 100755 src/.singularity_modules/cutadapt/2.1/build.sh
delete mode 100644 src/.singularity_modules/cutadapt/2.1/cutadapt
delete mode 100644 src/.singularity_modules/cutadapt/2.1/cutadapt.def
delete mode 100755 src/.singularity_modules/deeptools/3.0.2/build.sh
delete mode 100644 src/.singularity_modules/deeptools/3.0.2/deeptools
delete mode 100644 src/.singularity_modules/deeptools/3.0.2/deeptools.def
delete mode 100755 src/.singularity_modules/deeptools/3.1.1/build.sh
delete mode 100644 src/.singularity_modules/deeptools/3.1.1/deeptools
delete mode 100644 src/.singularity_modules/deeptools/3.1.1/deeptools.def
delete mode 100644 src/.singularity_modules/docker_to_singularity.sh
delete mode 100755 src/.singularity_modules/fastp/0.19.7/build.sh
delete mode 100644 src/.singularity_modules/fastp/0.19.7/fastp
delete mode 100644 src/.singularity_modules/fastp/0.19.7/fastp.def
delete mode 100755 src/.singularity_modules/fastqc/0.11.5/build.sh
delete mode 100644 src/.singularity_modules/fastqc/0.11.5/fastqc
delete mode 100644 src/.singularity_modules/fastqc/0.11.5/fastqc.def
delete mode 100755 src/.singularity_modules/file_handle/0.1.1/build.sh
delete mode 100644 src/.singularity_modules/file_handle/0.1.1/file_handle
delete mode 100644 src/.singularity_modules/file_handle/0.1.1/file_handle.def
delete mode 100755 src/.singularity_modules/gatk/4.0.8.1/build.sh
delete mode 100644 src/.singularity_modules/gatk/4.0.8.1/gatk
delete mode 100644 src/.singularity_modules/gatk/4.0.8.1/gatk.def
delete mode 100755 src/.singularity_modules/hisat2/2.0.0/build.sh
delete mode 100644 src/.singularity_modules/hisat2/2.0.0/hisat2
delete mode 100644 src/.singularity_modules/hisat2/2.0.0/hisat2.def
delete mode 100755 src/.singularity_modules/hisat2/2.1.0/build.sh
delete mode 100644 src/.singularity_modules/hisat2/2.1.0/hisat2
delete mode 100644 src/.singularity_modules/hisat2/2.1.0/hisat2.def
delete mode 100755 src/.singularity_modules/htseq/0.11.2/build.sh
delete mode 100644 src/.singularity_modules/htseq/0.11.2/htseq
delete mode 100644 src/.singularity_modules/htseq/0.11.2/htseq.def
delete mode 100755 src/.singularity_modules/htseq/0.8.0/build.sh
delete mode 100644 src/.singularity_modules/htseq/0.8.0/htseq
delete mode 100644 src/.singularity_modules/htseq/0.8.0/htseq.def
delete mode 100755 src/.singularity_modules/kallisto/0.43.1/build.sh
delete mode 100644 src/.singularity_modules/kallisto/0.43.1/kallisto
delete mode 100644 src/.singularity_modules/kallisto/0.43.1/kallisto.def
delete mode 100755 src/.singularity_modules/kallisto/0.44.0/build.sh
delete mode 100755 src/.singularity_modules/kallisto/0.44.0/kallisto
delete mode 100644 src/.singularity_modules/kallisto/0.44.0/kallisto.def
delete mode 100755 src/.singularity_modules/macs2/2.1.2/build.sh
delete mode 100644 src/.singularity_modules/macs2/2.1.2/macs2
delete mode 100644 src/.singularity_modules/macs2/2.1.2/macs2.def
delete mode 100755 src/.singularity_modules/multiqc/1.0/build.sh
delete mode 100644 src/.singularity_modules/multiqc/1.0/multiqc
delete mode 100644 src/.singularity_modules/multiqc/1.0/multiqc.def
delete mode 100755 src/.singularity_modules/multiqc/1.7/build.sh
delete mode 100644 src/.singularity_modules/multiqc/1.7/multiqc
delete mode 100644 src/.singularity_modules/multiqc/1.7/multiqc.def
delete mode 100755 src/.singularity_modules/music/6613c53/build.sh
delete mode 100644 src/.singularity_modules/music/6613c53/music
delete mode 100644 src/.singularity_modules/music/6613c53/music.def
delete mode 100644 src/.singularity_modules/picard/2.18.11/PicardCommandLine
delete mode 100755 src/.singularity_modules/picard/2.18.11/build.sh
delete mode 100644 src/.singularity_modules/picard/2.18.11/picard
delete mode 100644 src/.singularity_modules/picard/2.18.11/picard.def
delete mode 100755 src/.singularity_modules/pigz/2.4/build.sh
delete mode 100644 src/.singularity_modules/pigz/2.4/pigz
delete mode 100644 src/.singularity_modules/pigz/2.4/pigz.def
delete mode 100755 src/.singularity_modules/r/3.5.3/build.sh
delete mode 100644 src/.singularity_modules/r/3.5.3/r
delete mode 100644 src/.singularity_modules/r/3.5.3/r.def
delete mode 100755 src/.singularity_modules/rsem/1.3.0/build.sh
delete mode 100644 src/.singularity_modules/rsem/1.3.0/rsem
delete mode 100644 src/.singularity_modules/rsem/1.3.0/rsem.def
delete mode 100755 src/.singularity_modules/salmon/0.8.2/build.sh
delete mode 100644 src/.singularity_modules/salmon/0.8.2/salmon
delete mode 100644 src/.singularity_modules/salmon/0.8.2/salmon.def
delete mode 100755 src/.singularity_modules/sambamba/0.6.7/build.sh
delete mode 100644 src/.singularity_modules/sambamba/0.6.7/sambamba
delete mode 100644 src/.singularity_modules/sambamba/0.6.7/sambamba.def
delete mode 100755 src/.singularity_modules/sambamba/0.6.9/build.sh
delete mode 100644 src/.singularity_modules/sambamba/0.6.9/sambamba
delete mode 100644 src/.singularity_modules/sambamba/0.6.9/sambamba.def
delete mode 100755 src/.singularity_modules/samblaster/0.1.24/build.sh
delete mode 100644 src/.singularity_modules/samblaster/0.1.24/samblaster
delete mode 100644 src/.singularity_modules/samblaster/0.1.24/samblaster.def
delete mode 100755 src/.singularity_modules/samtools/1.7/build.sh
delete mode 100644 src/.singularity_modules/samtools/1.7/samtools
delete mode 100644 src/.singularity_modules/samtools/1.7/samtools.def
delete mode 100755 src/.singularity_modules/sratoolkit/2.8.2/build.sh
delete mode 100644 src/.singularity_modules/sratoolkit/2.8.2/sratoolkit
delete mode 100644 src/.singularity_modules/sratoolkit/2.8.2/sratoolkit.def
delete mode 100755 src/.singularity_modules/subread/1.6.4/build.sh
delete mode 100644 src/.singularity_modules/subread/1.6.4/subread
delete mode 100644 src/.singularity_modules/subread/1.6.4/subread.def
delete mode 100755 src/.singularity_modules/tophat/2.1.1/build.sh
delete mode 100644 src/.singularity_modules/tophat/2.1.1/tophat
delete mode 100644 src/.singularity_modules/tophat/2.1.1/tophat.def
delete mode 100755 src/.singularity_modules/trimmomatic/0.36/build.sh
delete mode 100644 src/.singularity_modules/trimmomatic/0.36/trimmomatic
delete mode 100644 src/.singularity_modules/trimmomatic/0.36/trimmomatic.def
delete mode 100755 src/.singularity_modules/ucsc/375/build.sh
delete mode 100644 src/.singularity_modules/ucsc/375/ucsc
delete mode 100644 src/.singularity_modules/ucsc/375/ucsc.def
delete mode 100755 src/.singularity_modules/umi_tools/1.0.0/build.sh
delete mode 100644 src/.singularity_modules/umi_tools/1.0.0/umi_tools
delete mode 100644 src/.singularity_modules/umi_tools/1.0.0/umi_tools.def
delete mode 100755 src/.singularity_modules/urqt/d62c1f8/build.sh
delete mode 100644 src/.singularity_modules/urqt/d62c1f8/urqt
delete mode 100644 src/.singularity_modules/urqt/d62c1f8/urqt.def
diff --git a/src/.singularity_modules/bcftools/1.7/bcftools b/src/.singularity_modules/bcftools/1.7/bcftools
deleted file mode 100644
index 0b6dd7dd..00000000
--- 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 $@
diff --git a/src/.singularity_modules/bcftools/1.7/bcftools.def b/src/.singularity_modules/bcftools/1.7/bcftools.def
deleted file mode 100644
index be53f079..00000000
--- a/src/.singularity_modules/bcftools/1.7/bcftools.def
+++ /dev/null
@@ -1,20 +0,0 @@
-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-BCFTOOLS_VERSION=1.7
-PACKAGES=bcftools=${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 96ecae55..00000000
--- 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 33f7309a..00000000
--- 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 $@
diff --git a/src/.singularity_modules/bedtools/2.25.0/bedtools.def b/src/.singularity_modules/bedtools/2.25.0/bedtools.def
deleted file mode 100644
index 4078e8ef..00000000
--- a/src/.singularity_modules/bedtools/2.25.0/bedtools.def
+++ /dev/null
@@ -1,20 +0,0 @@
-Bootstrap: docker
-From: ubuntu:16.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-BEDTOOLS_VERSION=2.25.0
-PACKAGES=bedtools=${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 936a71be..00000000
--- 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 af1106ff..00000000
--- 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 9bb6946e..00000000
--- 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 be5a5098..00000000
--- 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 9b450323..00000000
--- 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 $@
diff --git a/src/.singularity_modules/bowtie/1.2.2/bowtie.def b/src/.singularity_modules/bowtie/1.2.2/bowtie.def
deleted file mode 100644
index 4d6def9a..00000000
--- a/src/.singularity_modules/bowtie/1.2.2/bowtie.def
+++ /dev/null
@@ -1,23 +0,0 @@
-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-BOWTIE_VERSION=1.2.2
-SAMTOOLS_VERSION=1.7
-PACKAGES="bowtie=${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 a5a5c54d..00000000
--- 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 e8c41bdc..00000000
--- 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 $@
diff --git a/src/.singularity_modules/bowtie2/2.3.4.1/bowtie2.def b/src/.singularity_modules/bowtie2/2.3.4.1/bowtie2.def
deleted file mode 100644
index adf38167..00000000
--- a/src/.singularity_modules/bowtie2/2.3.4.1/bowtie2.def
+++ /dev/null
@@ -1,24 +0,0 @@
-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-BOWTIE2_VERSION=2.3.4.1
-SAMTOOLS_VERSION=1.7
-PACKAGES="bowtie2=${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 c01beabb..00000000
--- 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 0392a0c1..00000000
--- 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 cf69e923..00000000
--- 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 074892f8..00000000
--- 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 78805dac..00000000
--- 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 fa7348ae..00000000
--- 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 $@
diff --git a/src/.singularity_modules/canu/1.6/canu.def b/src/.singularity_modules/canu/1.6/canu.def
deleted file mode 100644
index 3b0e23e7..00000000
--- a/src/.singularity_modules/canu/1.6/canu.def
+++ /dev/null
@@ -1,20 +0,0 @@
-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-CANU_VERSION=1.6
-PACKAGES=canu=${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 0369e0df..00000000
--- 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 362bda98..00000000
--- 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 152cf71b..00000000
--- 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 95883b04..00000000
--- 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 71f96924..00000000
--- 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 27e284c1..00000000
--- 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 5a7070ec..00000000
--- 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 e653e488..00000000
--- 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 0223799c..00000000
--- 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 2ffc9937..00000000
--- 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 4053b759..00000000
--- 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 e108aa37..00000000
--- 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 78304343..00000000
--- 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 ffecc35f..00000000
--- 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 8bae622c..00000000
--- 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 0a71bfbc..00000000
--- 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 be161e19..00000000
--- 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 cc0d2213..00000000
--- 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 $@
diff --git a/src/.singularity_modules/fastp/0.19.7/fastp.def b/src/.singularity_modules/fastp/0.19.7/fastp.def
deleted file mode 100644
index eca9d45f..00000000
--- a/src/.singularity_modules/fastp/0.19.7/fastp.def
+++ /dev/null
@@ -1,15 +0,0 @@
-Bootstrap: docker
-From: docker://quay.io/biocontainers/fastp:0.19.7--hdbcaa40_0
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-FASTP_VERSION=0.19.7
-
-%environment
-export FASTP_VERSION=0.19.7
-
-%runscript
-exec /bin/bash "$@"
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 ef313d4e..00000000
--- 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 1da370ad..00000000
--- 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 $@
diff --git a/src/.singularity_modules/fastqc/0.11.5/fastqc.def b/src/.singularity_modules/fastqc/0.11.5/fastqc.def
deleted file mode 100644
index 11d529d1..00000000
--- a/src/.singularity_modules/fastqc/0.11.5/fastqc.def
+++ /dev/null
@@ -1,22 +0,0 @@
-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-FASTQC_VERSION=0.11.5
-PACKAGES="fastqc=${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 b48ae449..00000000
--- 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 2eccd8be..00000000
--- 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 240f8764..00000000
--- 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 87e095b7..00000000
--- 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 d16d21b6..00000000
--- 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 $@
diff --git a/src/.singularity_modules/gatk/4.0.8.1/gatk.def b/src/.singularity_modules/gatk/4.0.8.1/gatk.def
deleted file mode 100644
index c87b5be2..00000000
--- a/src/.singularity_modules/gatk/4.0.8.1/gatk.def
+++ /dev/null
@@ -1,17 +0,0 @@
-Bootstrap: docker
-From: broadinstitute/gatk:4.0.8.1
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-
-GATK_VERSION=4.0.8.1
-cp gatk/gatk /usr/bin/
-
-%environment
-export GATK_VERSION=4.0.8.1
-
-%runscript
-exec /bin/bash "$@"
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 4ba74ed4..00000000
--- 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 e8282a1e..00000000
--- 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 a4ea94d6..00000000
--- 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 5a23a144..00000000
--- 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 0c4ab6f9..00000000
--- 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 092d3f0b..00000000
--- 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 116d41a8..00000000
--- 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 df87417d..00000000
--- 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 76ab6c32..00000000
--- 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 19aed8a6..00000000
--- 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 f7be0c13..00000000
--- 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 a96643a5..00000000
--- 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 1a83c7c6..00000000
--- 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 27ad1732..00000000
--- 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 84a452f9..00000000
--- 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 bf884fb9..00000000
--- 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 c5d5177f..00000000
--- 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 74ead1bf..00000000
--- 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 260c2fef..00000000
--- 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 b6f899fb..00000000
--- 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 05003a38..00000000
--- 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 4622469f..00000000
--- 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 230104dd..00000000
--- 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 21feeaf2..00000000
--- 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 89176b32..00000000
--- 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 00743e8c..00000000
--- 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 fe7710f7..00000000
--- 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 49d7d42e..00000000
--- 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 fe772f25..00000000
--- 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 2d16c135..00000000
--- 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 ce067365..00000000
--- 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 e6752395..00000000
--- 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 19b4bb3b..00000000
--- 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 3ee5418d..00000000
--- 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 d5cb798f..00000000
--- 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 47d5cd4c..00000000
--- 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 $@
diff --git a/src/.singularity_modules/pigz/2.4/pigz.def b/src/.singularity_modules/pigz/2.4/pigz.def
deleted file mode 100644
index 6a757e29..00000000
--- a/src/.singularity_modules/pigz/2.4/pigz.def
+++ /dev/null
@@ -1,21 +0,0 @@
-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-PIGZ_VERSION=2.4
-PACKAGES=pigz=${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 2d0d3ab9..00000000
--- 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 f9cc3522..00000000
--- 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 7575d969..00000000
--- 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 841decce..00000000
--- 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 8578c726..00000000
--- 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 $@
diff --git a/src/.singularity_modules/rsem/1.3.0/rsem.def b/src/.singularity_modules/rsem/1.3.0/rsem.def
deleted file mode 100644
index 4aecc678..00000000
--- a/src/.singularity_modules/rsem/1.3.0/rsem.def
+++ /dev/null
@@ -1,37 +0,0 @@
-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-RSEM_VERSION=1.3.0
-BOWTIE2_VERSION=2.3.4.1
-SAMTOOLS_VERSION=1.7
-PACKAGES="git \
-build-essential \
-ca-certificates \
-zlib1g-dev \
-bowtie2=${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 a87d021a..00000000
--- 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 e7321e51..00000000
--- 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 ef56bebd..00000000
--- 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 d70f385c..00000000
--- 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 35b6aa72..00000000
--- 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 7ec23567..00000000
--- 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 4976ecc2..00000000
--- 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 35b6aa72..00000000
--- 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 3222c744..00000000
--- 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 6761f501..00000000
--- 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 57100d99..00000000
--- 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 57f7c415..00000000
--- 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 7121a402..00000000
--- 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 d811b276..00000000
--- 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 ea295f0e..00000000
--- 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 c71c8a5f..00000000
--- 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 6f87648a..00000000
--- 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 $@
diff --git a/src/.singularity_modules/sratoolkit/2.8.2/sratoolkit.def b/src/.singularity_modules/sratoolkit/2.8.2/sratoolkit.def
deleted file mode 100644
index c7c3e50c..00000000
--- a/src/.singularity_modules/sratoolkit/2.8.2/sratoolkit.def
+++ /dev/null
@@ -1,20 +0,0 @@
-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-SRATOOLKIT_VERSION=2.8.2
-PACKAGES=sra-toolkit=${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 4a758ee5..00000000
--- 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 382bf044..00000000
--- 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 $@
diff --git a/src/.singularity_modules/subread/1.6.4/subread.def b/src/.singularity_modules/subread/1.6.4/subread.def
deleted file mode 100644
index db8f00c2..00000000
--- a/src/.singularity_modules/subread/1.6.4/subread.def
+++ /dev/null
@@ -1,15 +0,0 @@
-Bootstrap: docker
-From: quay.io/biocontainers/subread:1.6.4--h84994c4_1
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-SUBREF_VERSION=1.6.4
-
-%environment
-export SUBREF_VERSION=1.6.4
-
-%runscript
-exec /bin/bash "$@"
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 002911a7..00000000
--- 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 44bb8bb8..00000000
--- 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 $@
diff --git a/src/.singularity_modules/tophat/2.1.1/tophat.def b/src/.singularity_modules/tophat/2.1.1/tophat.def
deleted file mode 100644
index e4697b9c..00000000
--- a/src/.singularity_modules/tophat/2.1.1/tophat.def
+++ /dev/null
@@ -1,20 +0,0 @@
-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-TOPHAT_VERSION=2.1.1
-PACKAGES=tophat=${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 e911a1c2..00000000
--- 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 8511bddf..00000000
--- 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 $@
diff --git a/src/.singularity_modules/trimmomatic/0.36/trimmomatic.def b/src/.singularity_modules/trimmomatic/0.36/trimmomatic.def
deleted file mode 100644
index 32819057..00000000
--- a/src/.singularity_modules/trimmomatic/0.36/trimmomatic.def
+++ /dev/null
@@ -1,20 +0,0 @@
-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-TRIMMOMATIC_VERSION=0.36
-PACKAGES=trimmomatic=${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 9546fa68..00000000
--- 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 344b1343..00000000
--- 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 7dd79889..00000000
--- 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 011337df..00000000
--- 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 673c53e2..00000000
--- 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 0eb75622..00000000
--- 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 7d8d0a1c..00000000
--- 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 924beee1..00000000
--- 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 eba8af97..00000000
--- 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 ${URQT_VERSION} && \
-make && \
-cd .. && \
-mv UrQt/UrQt /usr/bin/ && \
-rm -Rf UrQt
-
-%environment
-export URQT_VERSION=d62c1f8
-
-%runscript
-exec /bin/bash "$@"
--
GitLab