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new Dockerfile for new container gatk4 #603

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szilvajuhos merged 2 commits into from
Jun 20, 2018
Merged

new Dockerfile for new container gatk4 #603

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4779a13
new Dockerfile for new container gatk4
maxulysse Jun 20, 2018
b7951de
use bioconda to install gatk4
maxulysse Jun 20, 2018
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5 changes: 3 additions & 2 deletions buildContainers.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -179,6 +179,7 @@ def defineContainersList(){
return [
'freebayes',
'gatk',
'gatk4',
'igvtools',
'mutect1',
'picard',
Expand Down Expand Up @@ -207,8 +208,8 @@ def helpMessage() {
log.info " --containers: Choose which containers to build"
log.info " Default: all"
log.info " Possible values:"
log.info " all, freebayes, gatk, igvtools, mutect1, picard, qctools"
log.info " r-base, runallelecount, sarek, snpeff"
log.info " all, freebayes, gatk, gatk4, igvtools, mutect1, picard"
log.info " qctools, r-base, runallelecount, sarek, snpeff"
log.info " snpeffgrch37, snpeffgrch38, vepgrch37, vepgrch38"
log.info " --docker: Build containers using Docker"
log.info " --help"
Expand Down
15 changes: 15 additions & 0 deletions containers/gatk4/Dockerfile
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@@ -0,0 +1,15 @@
FROM nfcore/base:latest

LABEL \
author="Maxime Garcia" \
description="GATK4 Image for Sarek" \
maintainer="maxime.garcia@scilifelab.se"

COPY environment.yml /

RUN \
conda env create -f /environment.yml && \
conda clean -a

# Export PATH
ENV PATH /opt/conda/envs/sarek-gatk4-2.0/bin:$PATH
19 changes: 0 additions & 19 deletions containers/gatk4/Singularity
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9 changes: 9 additions & 0 deletions containers/gatk4/environment.yml
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@@ -0,0 +1,9 @@
# You can use this file to create a conda environment:
# conda env create -f environment.yml
name: sarek-gatk4-2.0
channels:
- bioconda
- conda-forge
- defaults
dependencies:
- gatk4=4.0.4.0
4 changes: 2 additions & 2 deletions scripts/do_all.sh
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Expand Up @@ -57,8 +57,8 @@ function toLower() {

if [[ $TOOL = docker ]] && [[ GRCh37,GRCh38 =~ $GENOME ]]
then
nextflow run buildContainers.nf -profile ${PROFILE} --verbose --docker ${PUSH} --repository ${REPOSITORY} --tag ${TAG} --containers freebayes,gatk,igvtools,mutect1,picard,qctools,r-base,runallelecount,sarek,snpeff
nextflow run buildContainers.nf -profile ${PROFILE} --verbose --docker ${PUSH} --repository ${REPOSITORY} --tag ${TAG} --containers freebayes,gatk,gatk4,igvtools,mutect1,picard,qctools,r-base,runallelecount,sarek,snpeff
nextflow run buildContainers.nf -profile ${PROFILE} --verbose --docker ${PUSH} --repository ${REPOSITORY} --tag ${TAG} --containers snpeff$(toLower ${GENOME}),vep$(toLower ${GENOME})
else
nextflow run buildContainers.nf -profile ${PROFILE} --verbose --singularity --repository ${REPOSITORY} --tag ${TAG} --containerPath containers/ --containers freebayes,gatk,igvtools,mutect1,picard,qctools,r-base,runallelecount,sarek,snpeff$(toLower ${GENOME}),vep$(toLower ${GENOME})
nextflow run buildContainers.nf -profile ${PROFILE} --verbose --singularity --repository ${REPOSITORY} --tag ${TAG} --containerPath containers/ --containers freebayes,gatk,gatk4,igvtools,mutect1,picard,qctools,r-base,runallelecount,sarek,snpeff$(toLower ${GENOME}),vep$(toLower ${GENOME})
fi
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