Unverified Commit f5642ccc authored by Laurent Modolo's avatar Laurent Modolo
Browse files

Merge branch 'master' into dev

parents 3a681558 ea7618fc
[submodule "src/sge_modules"]
path = src/.psmn_modules
url = gitlab_lbmc:PSMN/modules.git
......@@ -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,...)
......
......@@ -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
......
......@@ -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
......
......@@ -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
......
......@@ -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
#!/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
#!/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
#!/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
#!/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
#!/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
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*
......
#!/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
#!/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
#!/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
#!/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
#!/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
#!/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
#!/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
#!/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)}'
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