[med-svn] [Git][med-team/libgoby-java][master] 5 commits: Revising the short description of goby-java
Pierre Gruet (@pgt)
gitlab at salsa.debian.org
Sun Aug 8 21:00:22 BST 2021
Pierre Gruet pushed to branch master at Debian Med / libgoby-java
Commits:
c3df41f8 by Pierre Gruet at 2021-08-08T21:57:08+02:00
Revising the short description of goby-java
- - - - -
4278611f by Pierre Gruet at 2021-08-08T21:58:33+02:00
Creating goby.jar as a symlink to goby-distribution.jar
- - - - -
320e1ed8 by Pierre Gruet at 2021-08-08T21:58:55+02:00
Adding a manpage for the goby shell script
- - - - -
97fb03fc by Pierre Gruet at 2021-08-08T21:59:41+02:00
Patching the goby shell script for Debian paths
- - - - -
6c8ca392 by Pierre Gruet at 2021-08-08T22:00:12+02:00
Indicating the installed path of the goby jar inside Usage messages of goby
- - - - -
7 changed files:
- debian/control
- + debian/goby-java.links
- + debian/goby-java.manpages
- + debian/manpages/goby.1
- + debian/patches/goby_script.patch
- + debian/patches/path_of_goby_jar_for_Debian.patch
- debian/patches/series
Changes:
=====================================
debian/control
=====================================
@@ -82,7 +82,7 @@ Depends: ${shlibs:Depends},
r-cran-rjava
Recommends: ${java:Recommends},
${maven:OptionalDepends}
-Description: store next-generation sequencing data and intermediary analysis results
+Description: next-generation sequencing data and results analysis tool
Goby is a next-gen data management framework designed to facilitate the
implementation of efficient data analysis pipelines.
.
=====================================
debian/goby-java.links
=====================================
@@ -0,0 +1 @@
+usr/share/java/goby-distribution.jar usr/share/java/goby.jar
=====================================
debian/goby-java.manpages
=====================================
@@ -0,0 +1 @@
+debian/manpages/goby.1
=====================================
debian/manpages/goby.1
=====================================
@@ -0,0 +1,193 @@
+.TH GOBY 1 "08-08-2021"
+.SH NAME
+goby \- Sequencing data and results analysis tool
+.SH SYNOPSIS
+.B \fBgoby\fP <mem> <mode> [\fIOPTIONS\fP]
+
+.SH DESCRIPTION
+
+.B Goby
+provides facilities to manage sequencing data and ease the implementation of
+data analysis pipelines.
+
+.SH MANDATORY INFORMATION
+.TP
+.BR <mem>
+Human-readable amount of memory to allocate to
+.B Goby
+e.g. could be 1m, 145m, 3g, ...
+.TP
+.BR <mode>
+Indicates to use the mode <mode> of
+.B Goby
+when running. <mode> must be one of the following ones (either the long name
+or the short name which is inside parentheses):
+.IP "\(bu" 4
+aggregate-by-peak-distance (abpd)
+.IP "\(bu" 4
+aggregate-by-peak-rpkm-difference (abprd)
+.IP "\(bu" 4
+alignment-to-annotation-counts (atac)
+.IP "\(bu" 4
+alignment-to-counts (altc)
+.IP "\(bu" 4
+alignment-to-pileup (atp)
+.IP "\(bu" 4
+alignment-to-read-set (atrs)
+.IP "\(bu" 4
+alignment-to-text (att)
+.IP "\(bu" 4
+alignment-to-transcript-counts (attc)
+.IP "\(bu" 4
+annotation-penalty (ap)
+.IP "\(bu" 4
+annotations-to-counts (antc)
+.IP "\(bu" 4
+barcode-decoder (bd)
+.IP "\(bu" 4
+base-stats (bs)
+.IP "\(bu" 4
+bisulfite-conversion (bc)
+.IP "\(bu" 4
+build-sequence-cache (bsc)
+.IP "\(bu" 4
+compact-file-stats (cfs)
+.IP "\(bu" 4
+compact-to-fasta (ctf)
+.IP "\(bu" 4
+compact-to-sam (cts)
+.IP "\(bu" 4
+compare-alignment-to-genome (catg)
+.IP "\(bu" 4
+concatenate-alignments (ca)
+.IP "\(bu" 4
+concatenate-compact-reads (ccr)
+.IP "\(bu" 4
+count-archive-to-peak-annotations (catpa)
+.IP "\(bu" 4
+count-archive-to-peak-union-annotations (catpua)
+.IP "\(bu" 4
+counts-to-bedgraph (ctb)
+.IP "\(bu" 4
+counts-to-wiggle (ctw)
+.IP "\(bu" 4
+coverage (c)
+.IP "\(bu" 4
+diff-alignments (da)
+.IP "\(bu" 4
+discover-sequence-variants
+.IP "\(bu" 4
+display-sequence-variations
+.IP "\(bu" 4
+empirical-p (ep)
+.IP "\(bu" 4
+extract-splicing-events (ese)
+.IP "\(bu" 4
+fasta-to-compact (ftc)
+.IP "\(bu" 4
+fdr (f)
+.IP "\(bu" 4
+files-to-attributes (fta)
+.IP "\(bu" 4
+heptamer-weights (hw)
+.IP "\(bu" 4
+infer-sex (hasResult)
+.IP "\(bu" 4
+last-to-compact (ltc)
+.IP "\(bu" 4
+merge-compact-alignments (mca)
+.IP "\(bu" 4
+methyl-stats (ms)
+.IP "\(bu" 4
+read-quality-stats (rqs)
+.IP "\(bu" 4
+reads-to-weights (rtw)
+.IP "\(bu" 4
+reformat-compact-reads (rcr)
+.IP "\(bu" 4
+run-parallel (rp)
+.IP "\(bu" 4
+sam-comparison (sc)
+.IP "\(bu" 4
+sam-extract-reads (ser)
+.IP "\(bu" 4
+sam-to-compact (stc)
+.IP "\(bu" 4
+sam-to-compact-old (stco)
+.IP "\(bu" 4
+sam-to-compact-samhelper (stcs)
+.IP "\(bu" 4
+sample-quality-scores (sqs)
+.IP "\(bu" 4
+sequence-variation-stats (svs)
+.IP "\(bu" 4
+sequence-variation-stats2 (svs2)
+.IP "\(bu" 4
+set-to-text (stt)
+.IP "\(bu" 4
+simulate-reads (sr)
+.IP "\(bu" 4
+sort (s)
+.IP "\(bu" 4
+sort-1 (s1)
+.IP "\(bu" 4
+split-compact-reads (scr)
+.IP "\(bu" 4
+split-fasta (sf)
+.IP "\(bu" 4
+split-transcripts (st)
+.IP "\(bu" 4
+stats
+.IP "\(bu" 4
+suggest-position-slices (sps)
+.IP "\(bu" 4
+tab-to-column-info (ttci)
+.IP "\(bu" 4
+tally-bases (tb)
+.IP "\(bu" 4
+tally-reads (tr)
+.IP "\(bu" 4
+test-r-connection (trc)
+.IP "\(bu" 4
+trim (t)
+.IP "\(bu" 4
+upgrade (u)
+.IP "\(bu" 4
+vcf-compare (vc)
+.IP "\(bu" 4
+vcf-subset (vs)
+.IP "\(bu" 4
+vcf-to-genotype-map (vtgm)
+.IP "\(bu" 4
+vcf-to-indel-set (vtis)
+.IP "\(bu" 4
+vcf-to-tab (vtt)
+.IP "\(bu" 4
+version (v)
+.IP "\(bu" 4
+within-group-variability (wgv)
+
+.SH OPTIONS
+.TP
+
+\fBmode\-specific\-options\fP
+Each of the above modes has specific options. The complete list of options for
+a given mode <mode> can be get by running
+
+.Vb 1
+.B \& \fBgoby\fP 100m <mode>
+.Ve
+
+which returns a complete list of options for running the mode <mode> as well as
+a description of what this mode provides.
+.TP
+\fB\-h\fP, \fB\-\^\-help\fP
+Displays usage help information
+.TP
+\fB\-H\fP, \fB\-\^\-x\-help\fP
+Displays help for dynamic options
+.TP
+
+.SH AUTHOR
+This manual page was written by Pierre Gruet <pgt at debian.org> from the Debian
+project, but may be used by others.
=====================================
debian/patches/goby_script.patch
=====================================
@@ -0,0 +1,85 @@
+Description: modifying the launcher script to account for Debian paths
+Author: Pierre Gruet <pgt at debian.org>
+Forwarded: no
+Last-Update: 2021-08-08
+
+--- a/goby
++++ b/goby
+@@ -1,7 +1,6 @@
+-#!/bin/bash
++#!/bin/sh -e
+
+ # This script runs Goby with the specified amount of memory.
+-# The script will find the Goby jar if it is located in the same directory as this script
+
+ # Usage: goby mem-requirement mode-name [param]+
+ # Where mem-requirement indicates how much memory Goby should be given (e.g., 1g, 500m).
+@@ -18,42 +17,43 @@
+ shift
+ other_parameters=$*
+ set +x
+-WORKING_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+-if [[ $OSTYPE == "cygwin" ]]; then
+- WORKING_DIR=`cygpath -m "${WORKING_DIR}"`
+-fi
+
+-export GOBY_HOME=${WORKING_DIR}
+-GOBY_JAR=${GOBY_HOME}/goby.jar
++if [ ! -e ~/.goby ]; then
++ mkdir ~/.goby
++ mkdir ~/.goby/config
++fi
++export GOBY_HOME="~/.goby"
++GOBY_JAR=/usr/share/java/goby.jar
+ SLF4J_CONFIG=${GOBY_HOME}/config/goby-logback.xml
+-if [ ! -z ${GOBY_USE_RJAVA} ]; then
+- if [ "${RJAVA_HOME:-notset}" == "notset" ]; then
+- #echo "Trying to set RJAVA_HOME environment variable"
+- cat >/tmp/r-cmd.txt <<EOT
+- system.file("jri",package="rJava")
++
++cat >/tmp/r-cmd.txt <<EOT
++system.file("jri",package="rJava")
+ EOT
+- tmpWithQuotes=`R --no-save </tmp/r-cmd.txt|grep [1]|tail -1 |awk '{print $2}'`
+- temp="${tmpWithQuotes%\"}"
+- temp="${temp#\"}"
+- # echo "$temp"
+- export RJAVA_HOME=${temp}
+- rm -f /tmp/r-cmd.txt
+- fi
+-fi
++tmpWithQuotes=`R --no-save </tmp/r-cmd.txt|grep "\[1\]"|tail -1 |awk '{print $2}'`
++temp="${tmpWithQuotes%\"}"
++temp="${temp#\"}"
++export RJAVA_HOME=${temp}
++rm -f /tmp/r-cmd.txt
++
+ DL_SOMATIC_CLASSPATH=${GOBY_HOME}/somatic.jar
+ if [ ! -e "${DL_SOMATIC_CLASSPATH}" ]; then
+- echo "Model somatic.jar not found. It must be installed at ${GOBY_HOME}/somatic.jar"
++ echo "Model somatic.jar not found."
+ fi
+ DL_GENOTYPE_CLASSPATH=${GOBY_HOME}/genotype.jar
+ if [ ! -e "${DL_SOMATIC_CLASSPATH}" ]; then
+- echo "Model genotype.jar not found. It must be installed at ${GOBY_HOME}/genotype.jar"
++ echo "Model genotype.jar not found."
+ fi
+ DL_FRAMEWORK_CLASSPATH=${GOBY_HOME}/framework.jar
+ if [ ! -e "${DL_FRAMEWORK_CLASSPATH}" ]; then
+- echo "Model framework.jar not found. It must be installed at ${GOBY_HOME}/framework.jar"
++ echo "Model framework.jar not found."
+ fi
++
++# Needed for running Rengine.
++export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$RJAVA_HOME"
++export R_HOME="/usr/lib/R"
++
+ #echo java -ea -Xmx${memory_requirement} -Dlog4j.configuration=${LOG4J_PROPS} -Djava.library.path=${RJAVA_HOME} -jar ${GOBY_JAR} --mode ${other_parameters}
+-java -ea -Djava.ext.dirs=${GOBY_HOME}/ -Xmx${memory_requirement} -Dlogback.configurationFile=${SLF4J_CONFIG} -Djava.library.path=${RJAVA_HOME} -jar ${GOBY_JAR} --mode ${other_parameters}
++java -ea -cp "${GOBY_HOME}" -Xmx${memory_requirement} -Dlogback.configurationFile=${SLF4J_CONFIG} -Djava.library.path=${RJAVA_HOME} -jar ${GOBY_JAR} --mode ${other_parameters}
+ if [ $# -lt 2 ]; then
+ echo "The second argument must be the goby mode you want to run (i.e., goby 1g version). See list of modes in help above."
+-fi
+\ No newline at end of file
++fi
=====================================
debian/patches/path_of_goby_jar_for_Debian.patch
=====================================
@@ -0,0 +1,28 @@
+Description: ensuring the correct Debian path of the goby jar will show up
+ This is important for usage messages that are printed when the user invokes
+ goby with --help.
+Author: Pierre Gruet <pgt at debian.org>
+Forwarded: not-needed
+Last-Update: 2021-08-08
+
+--- a/goby-distribution/src/main/java/org/campagnelab/goby/modes/AbstractGobyMode.java
++++ b/goby-distribution/src/main/java/org/campagnelab/goby/modes/AbstractGobyMode.java
+@@ -33,6 +33,6 @@
+ }
+
+ protected AbstractGobyMode() {
+- super("goby.jar");
++ super("/usr/share/java/goby.jar");
+ }
+ }
+--- a/goby-distribution/src/main/java/org/campagnelab/goby/modes/GobyDriver.java
++++ b/goby-distribution/src/main/java/org/campagnelab/goby/modes/GobyDriver.java
+@@ -38,7 +38,7 @@
+ */
+ private static final Logger LOG = LoggerFactory.getLogger(GobyDriver.class);
+
+- private static final String DRIVER_JAR_NAME = "goby.jar";
++ private static final String DRIVER_JAR_NAME = "/usr/share/java/goby.jar";
+
+ public GobyDriver() {
+ super(DRIVER_JAR_NAME);
=====================================
debian/patches/series
=====================================
@@ -9,3 +9,5 @@ inclusions_in_SplitTranscriptsMode.patch
catch_IOException_LineIterator.patch
computing_fisher_pvalue_hypergeom.patch
exclude_not_runnable_tests.patch
+goby_script.patch
+path_of_goby_jar_for_Debian.patch
View it on GitLab: https://salsa.debian.org/med-team/libgoby-java/-/compare/aedb2043c3b9d1fd0eb36ed6e695bca71440db76...6c8ca392327222d46119ac507f8094e35449cc58
--
View it on GitLab: https://salsa.debian.org/med-team/libgoby-java/-/compare/aedb2043c3b9d1fd0eb36ed6e695bca71440db76...6c8ca392327222d46119ac507f8094e35449cc58
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