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Aurélien Ginolhac
snakemake-chip-seq
Commits
e351c0bb
Verified
Commit
e351c0bb
authored
Jul 08, 2021
by
Aurélien Ginolhac
🚴
Browse files
picard script to deal with Java options
parent
67a6be3a
Changes
2
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Dockerfile
View file @
e351c0bb
...
...
@@ -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
0 → 100755
View file @
e351c0bb
#!/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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