Commit 4a829491 authored by Blaise Li's avatar Blaise Li
Browse files

Generate a rulegraph for each run.

parent b8ffb7b9
......@@ -98,7 +98,7 @@ megabytes_resource=$(echo "${kilobytes_tot} / 1100" | bc)
#cmd="(cd ${output_dir}; snakemake -s ${snakefile} --configfile ${config_base} --resources mem_mb=${megabytes_resource} $@)"
# TODO: check that this works
cmd="(cd ${output_dir}; snakemake -s ${snakefile_base} --configfile ${config_base} --resources mem_mb=${megabytes_resource} $@)"
cmd="(cd ${output_dir}; snakemake -s ${snakefile_base} --configfile ${config_base} --rulegraph | dot -Tpdf > rulegraph.pdf; snakemake -s ${snakefile_base} --configfile ${config_base} --resources mem_mb=${megabytes_resource} $@)"
echo ${cmd} | tee -a ${log_base}.log
# https://unix.stackexchange.com/a/245610/55127
......
......@@ -36,6 +36,8 @@ From:python:3.7-buster
apt-get -y update
# Useful for interactive work using the container
apt-get -y install vim
# To be able to generate rule graphs of the workflows
apt-get -y install graphviz
# run_pipeline.sh (and maybe other tools) needs bc
apt-get -y install bc rsync
apt-get -y install bedops bedtools bowtie2 cutadapt subread hisat2 parallel samtools
......
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