[Debian-med-packaging] [SCM] picard-tools branch, master, updated. upstream/1.24-11-gdabef42
Shaun Jackman
sjackman at debian.org
Mon Jul 5 19:24:10 UTC 2010
The following commit has been merged in the master branch:
commit dabef427f6aea79b4c4106410824f3cb92b87125
Author: Shaun Jackman <sjackman at debian.org>
Date: Mon Jul 5 12:19:13 2010 -0700
* build.xml (picard.jar): Add the R scripts.
* debian/install: Rename to picard-tools.install.
* debian/control (picard-tools): New section.
* debian/rules (override_dh_link): Add picard-tools.jar symlink.
* debian/bin/picard-tools: New file.
* debian/libsam-java.install: Ditto.
* debian/picard-tools.1: Ditto.
* debian/picard-tools.manpages: Ditto.
* debian/patches/debian-changes-1.24-1: Refresh.
* debian/patches/series: Ditto.
diff --git a/debian/bin/picard-tools b/debian/bin/picard-tools
new file mode 100755
index 0000000..930a00e
--- /dev/null
+++ b/debian/bin/picard-tools
@@ -0,0 +1,60 @@
+#!/bin/sh
+set -eu
+if [ `basename -- $0` = picard-tools ]; then
+ if [ $# = 0 ]; then
+ cat 1>&2 <<EOF
+picard-tools: missing command argument
+Try \`picard-tools --help' for more information.
+EOF
+ exit 1
+ fi
+ command=`basename -- $1`
+ shift
+else
+ command=`basename $0`
+fi
+
+case $command in
+ BamToBfq) main=net.sf.picard.fastq.BamToBfq;;
+ BuildBamIndex) main=net.sf.picard.util.BuildBamIndex;;
+ CalculateHsMetrics) main=net.sf.picard.analysis.directed.CalculateHsMetrics;;
+ CleanSam) main=net.sf.picard.sam.CleanSam;;
+ CollectAlignmentSummaryMetrics) main=net.sf.picard.analysis.CollectAlignmentSummaryMetrics;;
+ CollectGcBiasMetrics) main=net.sf.picard.analysis.CollectGcBiasMetrics;;
+ CollectInsertSizeMetrics) main=net.sf.picard.analysis.CollectInsertSizeMetrics;;
+ CompareSAMs) main=net.sf.picard.sam.CompareSAMs;;
+ CreateSequenceDictionary) main=net.sf.picard.sam.CreateSequenceDictionary;;
+ EstimateLibraryComplexity) main=net.sf.picard.sam.EstimateLibraryComplexity;;
+ FastqToSam) main=net.sf.picard.sam.FastqToSam;;
+ FixMateInformation) main=net.sf.picard.sam.FixMateInformation;;
+ MarkDuplicates) main=net.sf.picard.sam.MarkDuplicates;;
+ MeanQualityByCycle) main=net.sf.picard.analysis.MeanQualityByCycle;;
+ MergeBamAlignment) main=net.sf.picard.sam.MergeBamAlignment;;
+ MergeSamFiles) main=net.sf.picard.sam.MergeSamFiles;;
+ NormalizeFasta) main=net.sf.picard.reference.NormalizeFasta;;
+ QualityScoreDistribution) main=net.sf.picard.analysis.QualityScoreDistribution;;
+ ReplaceSamHeader) main=net.sf.picard.sam.ReplaceSamHeader;;
+ RevertSam) main=net.sf.picard.sam.RevertSam;;
+ SamFormatConverter) main=net.sf.picard.sam.SamFormatConverter;;
+ SamToFastq) main=net.sf.picard.sam.SamToFastq;;
+ SortSam) main=net.sf.picard.sam.SortSam;;
+ ValidateSamFile) main=net.sf.picard.sam.ValidateSamFile;;
+ ViewSam) main=net.sf.picard.sam.ViewSam;;
+
+ --help)
+ cat <<EOF
+Usage: picard-tools COMMAND [OPTION]...
+See \`man picard-tools' for a list of COMMANDs.
+EOF
+ exit 0;;
+ --version)
+ cat <<EOF
+picard-tools
+Copyright 2010 The Broad Institute
+EOF
+ exit 0;;
+ *) echo 1>&2 picard-tools: unrecognized command "'$command'"; exit 1
+esac
+
+p=/usr/share/java
+exec java -cp $p/picard.jar:$p/sam.jar $main "$@"
diff --git a/debian/control b/debian/control
index 264df95..6a59757 100644
--- a/debian/control
+++ b/debian/control
@@ -1,5 +1,5 @@
Source: picard-tools
-Section: java
+Section: science
Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
DM-Upload-Allowed: yes
@@ -12,8 +12,34 @@ Vcs-Git: git://git.debian.org/git/debian-med/picard-tools.git
Vcs-Browser: http://git.debian.org/?p=debian-med/picard-tools.git
Package: libsam-java
+Section: java
Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
+Depends: ${misc:Depends}
+Suggests: picard-tools
Description: Java library to manipulate SAM and BAM files
SAM (Sequence Alignment/Map) format is a generic format for storing
large nucleotide sequence alignments.
+
+Package: picard-tools
+Section: science
+Architecture: any
+Depends: openjdk-6-jre|java-runtime, ${misc:Depends},
+ libsam-java
+Suggests: r-base-core
+Description: Command line tools to manipulate SAM and BAM files
+ SAM (Sequence Alignment/Map) format is a generic format for storing
+ large nucleotide sequence alignments. Picard Tools includes these
+ utilities to manipulate SAM and BAM files:
+ BamToBfq MeanQualityByCycle
+ BuildBamIndex MergeBamAlignment
+ CalculateHsMetrics MergeSamFiles
+ CleanSam NormalizeFasta
+ CollectAlignmentSummaryMetrics QualityScoreDistribution
+ CollectGcBiasMetrics ReplaceSamHeader
+ CollectInsertSizeMetrics RevertSam
+ CompareSAMs SamFormatConverter
+ CreateSequenceDictionary SamToFastq
+ EstimateLibraryComplexity SortSam
+ FastqToSam ValidateSamFile
+ FixMateInformation ViewSam
+ MarkDuplicates
diff --git a/debian/install b/debian/install
deleted file mode 100644
index b90eb97..0000000
--- a/debian/install
+++ /dev/null
@@ -1 +0,0 @@
-dist/*.jar usr/share/java
diff --git a/debian/libsam-java.install b/debian/libsam-java.install
new file mode 100644
index 0000000..6379168
--- /dev/null
+++ b/debian/libsam-java.install
@@ -0,0 +1 @@
+dist/sam-*.jar usr/share/java
diff --git a/debian/patches/debian-changes-1.22-1 b/debian/patches/debian-changes-1.22-1
deleted file mode 100644
index 883fe98..0000000
--- a/debian/patches/debian-changes-1.22-1
+++ /dev/null
@@ -1,64 +0,0 @@
-Description: Upstream changes introduced in version 1.22-1
- This patch has been created by dpkg-source during the package build.
- Here's the last changelog entry, hopefully it gives details on why
- those changes were made:
- .
- picard-tools (1.22-1) UNRELEASED; urgency=low
- .
- * Initial release. Closes: #586015.
- .
- The person named in the Author field signed this changelog entry.
-Author: Shaun Jackman <sjackman at debian.org>
-Bug-Debian: http://bugs.debian.org/586015
-
----
-The information above should follow the Patch Tagging Guidelines, please
-checkout http://dep.debian.net/deps/dep3/ to learn about the format. Here
-are templates for supplementary fields that you might want to add:
-
-Origin: <vendor|upstream|other>, <url of original patch>
-Bug: <url in upstream bugtracker>
-Bug-Debian: http://bugs.debian.org/<bugnumber>
-Forwarded: <no|not-needed|url proving that it has been forwarded>
-Reviewed-By: <name and email of someone who approved the patch>
-Last-Update: <YYYY-MM-DD>
-
-Index: picard-tools/build.xml
-===================================================================
---- picard-tools.orig/build.xml
-+++ picard-tools/build.xml
-@@ -23,7 +23,7 @@
- ~ THE SOFTWARE.
- -->
-
--<project name="picard-public" basedir="." default="all">
-+<project name="picard-public" basedir="." default="sam-jar">
-
- <property name="src" value="src/java"/>
- <property name="src.scripts" value="src/scripts"/>
-@@ -63,6 +63,7 @@
- <fileset dir="${lib}">
- <include name="**/*.jar"/>
- </fileset>
-+ <pathelement path="/usr/share/java/testng.jar"/>
- </path>
- </target>
-
-@@ -93,7 +94,7 @@
- sourcepath="" srcdir="${src}"
- includes ="net/sf/samtools/**/*.*"
- excludes = "net/sf/picard/**/*.*"
-- executable="${JAVA_HOME_1_5}/bin/javac"
-+ executable="javac"
- compiler="javac1.5" fork="true">
- <!--<compilerarg value="-Xlint:all"/>-->
- <!--<compilerarg value="-Xlint:unchecked"/>-->
-@@ -122,7 +123,7 @@
- optimize="${javac.opt}"
- debug="${javac.debug}"
- includes ="net/sf/samtools/**/*.*"
-- executable="${JAVA_HOME_1_5}/bin/javac"
-+ executable="javac"
- compiler="javac1.5" fork="true"> <!-- Force SAM-JDK to be built with 1.5 -->
- <!--<compilerarg value="-Xlint:unchecked"/>-->
- <src path="${src.test}"/>
diff --git a/debian/patches/debian-changes-1.24-1 b/debian/patches/debian-changes-1.24-1
new file mode 100644
index 0000000..4a4c077
--- /dev/null
+++ b/debian/patches/debian-changes-1.24-1
@@ -0,0 +1,50 @@
+--- picard-tools-1.24.orig/build.xml
++++ picard-tools-1.24/build.xml
+@@ -23,7 +23,7 @@
+ ~ THE SOFTWARE.
+ -->
+
+-<project name="picard-public" basedir="." default="all">
++<project name="picard-public" basedir="." default="jar">
+
+ <property name="src" value="src/java"/>
+ <property name="src.scripts" value="src/scripts"/>
+@@ -63,6 +63,7 @@
+ <fileset dir="${lib}">
+ <include name="**/*.jar"/>
+ </fileset>
++ <pathelement path="/usr/share/java/testng.jar"/>
+ </path>
+ </target>
+
+@@ -93,7 +94,7 @@
+ sourcepath="" srcdir="${src}"
+ includes ="net/sf/samtools/**/*.*"
+ excludes = "net/sf/picard/**/*.*"
+- executable="${JAVA_HOME_1_5}/bin/javac"
++ executable="javac"
+ compiler="javac1.5" fork="true">
+ <!--<compilerarg value="-Xlint:all"/>-->
+ <!--<compilerarg value="-Xlint:unchecked"/>-->
+@@ -122,7 +123,7 @@
+ optimize="${javac.opt}"
+ debug="${javac.debug}"
+ includes ="net/sf/samtools/**/*.*"
+- executable="${JAVA_HOME_1_5}/bin/javac"
++ executable="javac"
+ compiler="javac1.5" fork="true"> <!-- Force SAM-JDK to be built with 1.5 -->
+ <!--<compilerarg value="-Xlint:unchecked"/>-->
+ <src path="${src.test}"/>
+@@ -199,9 +200,12 @@
+ <mkdir dir="${dist}"/>
+ <jar destfile="${dist}/picard-${picard-version}.jar" compress="no">
+ <fileset dir="${classes}" includes ="net/sf/picard/**/*.*"/>
++ <fileset dir="${src.scripts}" includes="**/*.R"/>
+ </jar>
+ </target>
+
++ <target name="jar" depends="sam-jar, picard-jar" />
++
+ <target name="javadoc" depends="init" description="Generates the project javadoc.">
+ <javadoc
+ sourcepath="${src}"
diff --git a/debian/patches/series b/debian/patches/series
index 0a0097e..4d3a446 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1 @@
-debian-changes-1.22-1
+debian-changes-1.24-1
diff --git a/debian/picard-tools.1 b/debian/picard-tools.1
new file mode 100644
index 0000000..f1878a9
--- /dev/null
+++ b/debian/picard-tools.1
@@ -0,0 +1,41 @@
+.TH picard-tools "1" "July 2010" "picard-tools 1.24" "User Commands"
+.SH NAME
+picard-tools \- manipulate SAM and BAM files
+.SH SYNOPSIS
+\fBpicard-tools\fR \fICOMMAND\fR [\fIOPTION\fR]...
+.SH DESCRIPTION
+SAM (Sequence Alignment/Map) format is a generic format for storing
+large nucleotide sequence alignments.
+
+Picard Tools includes these utilities to manipulate SAM and BAM files:
+ BamToBfq
+ BuildBamIndex
+ CalculateHsMetrics
+ CleanSam
+ CollectAlignmentSummaryMetrics
+ CollectGcBiasMetrics
+ CollectInsertSizeMetrics
+ CompareSAMs
+ CreateSequenceDictionary
+ EstimateLibraryComplexity
+ FastqToSam
+ FixMateInformation
+ MarkDuplicates
+ MeanQualityByCycle
+ MergeBamAlignment
+ MergeSamFiles
+ NormalizeFasta
+ QualityScoreDistribution
+ ReplaceSamHeader
+ RevertSam
+ SamFormatConverter
+ SamToFastq
+ SortSam
+ ValidateSamFile
+ ViewSam
+.SH "REPORTING BUGS"
+samtools-devel at lists.sourceforge.net
+.SH COPYRIGHT
+Copyright 2010 The Broad Institute
+.SH "SEE ALSO"
+http://picard.sourceforge.net/
diff --git a/debian/picard-tools.install b/debian/picard-tools.install
new file mode 100644
index 0000000..5b681a1
--- /dev/null
+++ b/debian/picard-tools.install
@@ -0,0 +1,2 @@
+debian/bin/picard-tools usr/bin
+dist/picard-*.jar usr/share/java
diff --git a/debian/picard-tools.manpages b/debian/picard-tools.manpages
new file mode 100644
index 0000000..7ea7892
--- /dev/null
+++ b/debian/picard-tools.manpages
@@ -0,0 +1 @@
+debian/picard-tools.1
diff --git a/debian/rules b/debian/rules
index 647f22f..60a4aef 100755
--- a/debian/rules
+++ b/debian/rules
@@ -27,4 +27,5 @@ get-orig-source:
@echo " "$(TARBALL)" created; move it to the right destination to build the package"
override_dh_link:
- dh_link usr/share/java/sam-$(SRC_VERSION).jar usr/share/java/sam.jar
+ dh_link -p libsam-java usr/share/java/sam-$(SRC_VERSION).jar usr/share/java/sam.jar
+ dh_link -p picard-tools usr/share/java/picard-$(SRC_VERSION).jar usr/share/java/picard.jar
--
manipulate SAM and BAM files
More information about the Debian-med-packaging
mailing list