FastQC: add dockerfile and environment.yml

This commit is contained in:
Phil Ewels 2020-03-06 11:56:08 +00:00
parent b3cc751e78
commit 198e9a85eb
3 changed files with 27 additions and 5 deletions

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@ -19,20 +19,26 @@ jobs:
# Find the tool wrappers that changed # Find the tool wrappers that changed
# Annoyingly, matrix can't take dynamic variables # Annoyingly, matrix can't take dynamic variables
- name: Find changed tools - name: Find changed tools
run: TOOLS=$( git diff --name-only $GITHUB_SHA | egrep -o 'tools\/[^\/]+\/' | sort | uniq | awk NF ) run: |
TOOLS=$( git diff --name-only HEAD~ | egrep -o 'tools\/[^\/]+\/' | sort | uniq | awk NF )
echo "Tools that appear to have been updated:"
echo $TOOLS
# Save so that GitHub Actions can see this variable in the next step
echo "::set-env name=TOOLS::$TOOLS"
- name: Build images - name: Build images
run: | run: |
echo "Running the docker build"
echo $TOOLS
for d in tools/*; do for d in tools/*; do
echo "In directory $d"
for TOOL in $TOOLS; do for TOOL in $TOOLS; do
$TOOL echo "Tool is $TOOL"
if echo $d/ | grep -q "$TOOL"; then if echo $d/ | grep -q "$TOOL"; then
cd "$GITHUB_WORKSPACE/$d" cd "$GITHUB_WORKSPACE/$d"
TOOLNAME=$(basename `pwd`) TOOLNAME=$(basename `pwd`)
IMGNAME=docker.pkg.github.com/${GITHUB_REPOSITORY,,}/${TOOLNAME,,}:$GITHUB_SHA IMGNAME=docker.pkg.github.com/${GITHUB_REPOSITORY,,}/${TOOLNAME,,}:$GITHUB_SHA
echo $IMGNAME echo "Image name is: $IMGNAME"
docker login -u ${{ github.actor }} -p ${{ secrets.GITHUB_TOKEN }} docker.pkg.github.com docker login -u ${{ github.actor }} -p ${{ secrets.GITHUB_TOKEN }} docker.pkg.github.com
docker build -t $IMGNAME . docker build -t $IMGNAME .
docker push $IMGNAME docker push $IMGNAME

7
tools/fastqc/Dockerfile Normal file
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@ -0,0 +1,7 @@
FROM nfcore/base:1.7
LABEL authors="phil.ewels@scilifelab.se" \
description="Docker image for nf-core modules fastqc"
COPY environment.yml /
RUN conda env create -f /environment.yml && conda clean -a
ENV PATH /opt/conda/envs/nf-core-modules-fastqc/bin:$PATH

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@ -0,0 +1,9 @@
# You can use this file to create a conda environment for this pipeline:
# conda env create -f environment.yml
name: nf-core-modules-fastqc
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- fastqc=0.11.8