Verified Commit e351c0bb authored by Aurélien Ginolhac's avatar Aurélien Ginolhac 🚴
Browse files

picard script to deal with Java options

parent 67a6be3a
......@@ -2,7 +2,7 @@ FROM rocker/r-ubuntu:20.04
LABEL org.opencontainers.image.authors="Aurelien Ginolhac <aurelien.ginolhac@uni.lu>"
# build with: docker build -t ginolhac/snake-chip-seq:0.1 - < Dockerfile
# build with: docker build -t ginolhac/snake-chip-seq:0.1 .
# docker push ginolhac/snake-chip-seq:0.1
LABEL version="0.1"
......@@ -58,8 +58,9 @@ RUN cd /opt && \
# Picard tools
ARG PIC_VERSION="2.25.6"
RUN cd /opt && \
wget --no-check-certificate https://github.com/broadinstitute/picard/releases/download/${PIC_VERSION}/picard.jar && \
echo -e '#!/bin/bash\njava -jar /opt/picard.jar $@' > /usr/local/bin/picard && chmod +x /usr/local/bin/picard
wget --no-check-certificate https://github.com/broadinstitute/picard/releases/download/${PIC_VERSION}/picard.jar
COPY workflow/scripts/picard /usr/local/bin/picard
# AdapterRemoval
ARG AR_VERSION="2.3.2"
......@@ -133,7 +134,7 @@ RUN python3 -m pip install snakemake multiqc pandas pyBigWig pysam macs2 deeptoo
# BiocManager 1.30.16, for BioC 3.12, #FIXME SPP is 1.16.0 if fine, avoid installing 1.15.2 line 148
RUN install2.r --error littler BiocManager && \
/usr/local/lib/R/site-library/littler/examples/installBioc.r DESeq2 Rsubread apeglm pheatmap vsn Rsamtools && \
install2.r --error hexbin ggrepel cowplot spp tidyverse UpSetR
install2.r --error hexbin ggrepel cowplot tidyverse UpSetR # spp
# DESeq2 is 1.30.1
# Rsubread is 2.4.3
# apeglm 1.12.0
......@@ -145,6 +146,7 @@ RUN cd /opt && \
tar -xf ${PHANTOMPEAKQUALTOOLS_VERSION}.tar.gz && rm ${PHANTOMPEAKQUALTOOLS_VERSION}.tar.gz && \
cd phantompeakqualtools-${PHANTOMPEAKQUALTOOLS_VERSION} && \
wget https://github.com/hms-dbmi/spp/archive/1.15.2.tar.gz && \
install2.r --error caTools optparse reshape2 && \
Rscript -e 'install.packages("1.15.2.tar.gz")' && ln -s /opt/phantompeakqualtools-1.2.2/run_spp.R /usr/local/bin/
# clean up
......
#!/bin/bash
script_args=()
while [ $OPTIND -le "$#" ]
do
# fetch the -Xmx option for java machine
if getopts X: option
then
case $option
in
X) JAVAOPTS="-X$OPTARG";;
esac
else
# paste all the rest of the command line
script_args+=("${!OPTIND}")
((OPTIND++))
fi
done
java $JAVAOPTS -jar /opt/picard.jar ${script_args[@]}
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