version 0.4.0

.gitmodules

-[submodule "src/sge_modules"]
-	path = src/psmn_modules
-	url = gitlab_lbmc:PSMN/modules.git

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,...)

README.md

@@ -8,6 +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).
 
 ## Getting Started
 

src/.conda_envs

+/Xnfs/lbmcdb/common/conda/envs/
\ No newline at end of file

src/.conda_packages.sh

+source src/.conda_psmn.sh
+CONDA_ENVS=src/.conda_envs/
+if [ ! -d ${CONDA_ENVS}pigz_2.3.4 ]; then
+  conda create --yes --name pigz_2.3.4 pigz=2.3.4
+fi
+if [ ! -d ${CONDA_ENVS}tophat_2.1.1 ]; then
+  conda create --yes --name tophat_2.1.1 tophat=2.1.1
+fi
+if [ ! -d ${CONDA_ENVS}hisat2_2.0.0 ]; then
+  conda create --yes --name hisat2_2.0.0 hisat2=2.0.0 samtools=1.7
+fi
+if [ ! -d ${CONDA_ENVS}hisat2_2.1.0 ]; then
+  conda create --yes --name hisat2_2.1.0 hisat2=2.1.0 samtools=1.7
+fi
+if [ ! -d ${CONDA_ENVS}rsem_1.3.1 ]; then
+  conda create --yes --name rsem_1.3.1 rsem=1.3.1 samtools=1.3
+fi
+if [ ! -d ${CONDA_ENVS}rsem_1.3.0 ]; then
+  conda create --yes --name rsem_1.3.0 rsem=1.3.0 samtools=1.3
+fi
+if [ ! -d ${CONDA_ENVS}samblaster_0.1.24 ]; then
+  conda create --yes --name samblaster_0.1.24 samblaster=0.1.24
+fi
+if [ ! -d ${CONDA_ENVS}nextflow_0.25.1 ]; then
+  conda create --yes --name nextflow_0.25.1 nextflow=0.25.1
+fi
+if [ ! -d ${CONDA_ENVS}nextflow_19.01.0 ]; then
+  conda create --yes --name nextflow_19.01.0 nextflow=19.01.0
+fi
+if [ ! -d ${CONDA_ENVS}nextflow_0.32.0 ]; then
+  conda create --yes --name nextflow_0.32.0 nextflow=0.32.0
+fi
+if [ ! -d ${CONDA_ENVS}nextflow_0.28.2 ]; then
+  conda create --yes --name nextflow_0.28.2 nextflow=0.28.2
+fi
+if [ ! -d ${CONDA_ENVS}samtools_1.7 ]; then
+  conda create --yes --name samtools_1.7 samtools=1.7
+fi
+if [ ! -d ${CONDA_ENVS}samtools_1.5 ]; then
+  conda create --yes --name samtools_1.5 samtools=1.5
+fi
+if [ ! -d ${CONDA_ENVS}bowtie2_2.3.2 ]; then
+  conda create --yes --name bowtie2_2.3.2 bowtie2=2.3.2 samtools=1.7
+fi
+if [ ! -d ${CONDA_ENVS}bowtie2_2.3.4.1 ]; then
+  conda create --yes --name bowtie2_2.3.4.1 bowtie2=2.3.4.1 samtools=1.7 #&& \
+fi
+if [ ! -d ${CONDA_ENVS}sra-tools_2.8.2 ]; then
+  conda create --yes --name sra-tools_2.8.2 sra-tools=2.8.2
+fi
+if [ ! -d ${CONDA_ENVS}trimmomatic_0.36 ]; then
+  conda create --yes --name trimmomatic_0.36 trimmomatic=0.36
+fi
+if [ ! -d ${CONDA_ENVS}trimmomatic_0.39 ]; then
+  conda create --yes --name trimmomatic_0.39 trimmomatic=0.39
+fi
+if [ ! -d ${CONDA_ENVS}Python_3.6.1 ]; then
+  conda create --yes --name Python_3.6.1 Python=3.6.1
+fi
+if [ ! -d ${CONDA_ENVS}Python_2.7.13 ]; then
+  conda create --yes --name Python_2.7.13 Python=2.7.13
+fi
+if [ ! -d ${CONDA_ENVS}kallisto_0.44.0 ]; then
+  conda create --yes --name kallisto_0.44.0 kallisto=0.44.0
+fi
+if [ ! -d ${CONDA_ENVS}kallisto_0.43.1 ]; then
+  conda create --yes --name kallisto_0.43.1 kallisto=0.43.1
+fi
+if [ ! -d ${CONDA_ENVS}music_1.0.0 ]; then
+  conda create --yes --name music_1.0.0 music=1.0.0
+fi
+if [ ! -d ${CONDA_ENVS}umitools_0.3.4 ]; then
+  conda create --yes --name umitools_0.3.4 umitools=0.3.4
+fi
+if [ ! -d ${CONDA_ENVS}fastp_0.19.7 ]; then
+  conda create --yes --name fastp_0.19.7 fastp=0.19.7
+fi
+if [ ! -d ${CONDA_ENVS}gatk_3.8 ]; then
+  conda create --yes --name gatk_3.8 gatk=3.8
+fi
+if [ ! -d ${CONDA_ENVS}cutadapt_1.14 ]; then
+  conda create --yes --name cutadapt_1.14 cutadapt=1.14
+fi
+if [ ! -d ${CONDA_ENVS}bioawk_1.0 ]; then
+  conda create --yes --name bioawk_1.0 bioawk=1.0
+fi
+if [ ! -d ${CONDA_ENVS}canu_1.7 ]; then
+  conda create --yes --name canu_1.7 canu=1.7
+fi
+if [ ! -d ${CONDA_ENVS}fastqc_0.11.5 ]; then
+  conda create --yes --name fastqc_0.11.5 fastqc=0.11.5
+fi
+if [ ! -d ${CONDA_ENVS}bedtools_2.25.0 ]; then
+  conda create --yes --name bedtools_2.25.0 bedtools=2.25.0
+fi
+if [ ! -d ${CONDA_ENVS}macs2_2.1.2 ]; then
+  conda create --yes --name macs2_2.1.2 macs2=2.1.2
+fi
+if [ ! -d ${CONDA_ENVS}bcftools_1.7 ]; then
+  conda create --yes --name bcftools_1.7 bcftools=1.7
+fi
+if [ ! -d ${CONDA_ENVS}salmon_0.8.2 ]; then
+  conda create --yes --name salmon_0.8.2 salmon=0.8.2
+fi
+if [ ! -d ${CONDA_ENVS}urqt_d62c1f8 ]; then
+  conda create --yes --name urqt_d62c1f8 urqt=d62c1f8
+fi
+if [ ! -d ${CONDA_ENVS}multiqc_0.9 ]; then
+  conda create --yes --name multiqc_0.9 multiqc=0.9
+fi
+if [ ! -d ${CONDA_ENVS}multiqc_1.7 ]; then
+  conda create --yes --name multiqc_1.7 multiqc=1.7
+fi
+if [ ! -d ${CONDA_ENVS}multiqc_1.0 ]; then
+  conda create --yes --name multiqc_1.0 multiqc=1.0
+fi
+if [ ! -d ${CONDA_ENVS}cdhit_4.6.8 ]; then
+  conda create --yes --name cdhit_4.6.8 cdhit=4.6.8
+fi
+if [ ! -d ${CONDA_ENVS}deeptools_3.0.2 ]; then
+  conda create --yes --name deeptools_3.0.2 deeptools=3.0.2
+fi
+if [ ! -d ${CONDA_ENVS}htseq_0.9.1 ]; then
+  conda create --yes --name htseq_0.9.1 htseq=0.9.1
+fi
+if [ ! -d ${CONDA_ENVS}htseq_0.11.2 ]; then
+  conda create --yes --name htseq_0.11.2 htseq=0.11.2
+fi
+if [ ! -d ${CONDA_ENVS}R_3.4.3 ]; then
+  conda create --yes --name R_3.4.3 R=3.4.3
+fi
+if [ ! -d ${CONDA_ENVS}R_3.3.1 ]; then
+  conda create --yes --name R_3.3.1 R=3.3.1
+fi
+if [ ! -d ${CONDA_ENVS}file_handle_0.1.1 ]; then
+  conda create --yes --name file_handle_0.1.1 file_handle=0.1.1
+fi
+if [ ! -d ${CONDA_ENVS}ncdu_1.13 ]; then
+  conda create --yes --name ncdu_1.13 ncdu=1.13
+fi
+if [ ! -d ${CONDA_ENVS}picard_2.18.11 ]; then
+  conda create --yes --name picard_2.18.11 picard=2.18.11
+fi
+if [ ! -d ${CONDA_ENVS}sambamba_0.6.7 ]; then
+  conda create --yes --name sambamba_0.6.7 sambamba=0.6.7
+fi
+if [ ! -d ${CONDA_ENVS}star_2.7.3a ]; then
+  conda create --yes --name star_2.7.3a star=2.7.3a
+fi

src/.conda_psmn.sh

+/Xnfs/lbmcdb/common/conda/init.sh
\ No newline at end of file

src/.docker_modules/bcftools/1.7/docker_init.sh

+#!/bin/sh
+docker build src/docker_modules/bcftools/1.7 -t 'lbmc/bcftools:1.7'

src/.docker_modules/bedtools/2.25.0/docker_init.sh

+#!/bin/sh
+docker build src/docker_modules/bedtools/2.25.0 -t 'lbmc/bedtools:2.25.0'

src/.docker_modules/bioawk/1.0/docker_init.sh

+#!/bin/sh
+docker build src/docker_modules/bioawk/1.0 -t 'lbmc/bioawk:1.0'

src/.docker_modules/bowtie/1.2.2/docker_init.sh

+#!/bin/sh
+docker build src/docker_modules/bowtie/1.2.2 -t 'lbmc/bowtie:1.2.2'

src/.docker_modules/bowtie2/2.3.4.1/docker_init.sh

+#!/bin/sh
+docker build src/docker_modules/bowtie2/2.3.4.1 -t 'lbmc/bowtie2:2.3.4.1'

src/.docker_modules/bwa/0.7.17/docker_init.sh

+#!/bin/sh
+docker build src/docker_modules/bwa/0.7.17 -t 'lbmc/bwa:0.7.17'

src/.docker_modules/canu/1.6/docker_init.sh

+#!/bin/sh
+docker build src/docker_modules/canu/1.6 -t 'lbmc/canu:1.6'