picard script to deal with Java options

Dockerfile

@@ -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

workflow/scripts/picard

+#!/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[@]}
+