Commit e0b0d8ab authored by Jasper Koehorst's avatar Jasper Koehorst
Browse files

Merge branch 'master' of https://git.wur.nl/unlock/docker

# Conflicts:
#	Dockerfile
parents 3beb0268 59558626
......@@ -72,10 +72,11 @@ RUN pip3 install pysam numpy matplotlib checkm-genome && \
RUN python3 -m pip install gtdbtk
ENV GTDBTK_DATA_PATH=/unlock/references/databases/GTDBTK/release202/
## picrust2 (conda)
COPY conda/picrust2_env.yml /picrust2_env.yml
RUN source /root/miniconda/bin/activate && \
conda create -n picrust2 -c bioconda -c conda-forge picrust2=2.4.1 && \
conda env update --name picrust2 --file /picrust2_env.yml && \
conda deactivate
## Needed for faTools
......@@ -86,7 +87,9 @@ ENV SDKMAN=/root/.sdkman/candidates/maven/current/bin:/root/.sdkman/candidates/j
ENV CHECKM=/unlock/infrastructure/binaries/hmmer/hmmer-3.3.2/bin:/unlock/infrastructure/binaries/pplacer/pplacer-Linux-v1.1.alpha17/bin:/unlock/infrastructure/binaries/prodigal/v2.6.3
# note: CheckM and GTDB-Tk overlap with hmmer,prodigal and are not added to GTDBTK
ENV GTDBTK=/unlock/infrastructure/binaries/Mash/mash-Linux64-v2.3:/unlock/infrastructure/binaries/FastTree/FastTree_v2.1.11:/unlock/infrastructure/binaries/Mash/mash-Linux64-v2.3:/unlock/infrastructure/binaries/fastANI/fastANI_v1.33
ENV PATH=$PATH:$SDKMAN:$CHECKM:$GTDBTK
######################################
######################################
......
name: picrust2
dependencies:
- pip:
- requests
- rdflib
- biopython
\ No newline at end of file
......@@ -59,6 +59,12 @@ grep "[0-9]\+_irods:" $yaml | awk '{print $2}' | sort | uniq | xargs dirname | x
# Download run files from iRODS
grep "[0-9]\+_irods:" $yaml | awk '{print $2}' | sort | uniq | awk '{print "java -jar /unlock/infrastructure/binaries/irods/IRODSTransfer.jar --pull --local "$1" --files "$1" --force"}' | sh
# Start a conda environment when needed
conda_env=`grep conda $yaml | awk -F": " '{print $2}'`
if ! [[ -z "$conda" ]]; then
source /root/miniconda/bin/activate && conda activate $conda_env
fi
# Run workflow with or without provenance
if $prov; then
cwltool --tmpdir-prefix /unlock/rancher/unlockcwl --no-container --preserve-entire-environment --outdir $destination_path --provenance $destination_path/PROVENANCE $cwl $yaml
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment