[med-svn] [Git][med-team/drop-seq][master] Reduce the dependencies of drop-seq-tools (Closes: #982352)
Emmanuel Bourg
gitlab at salsa.debian.org
Tue Feb 9 20:22:47 GMT 2021
Emmanuel Bourg pushed to branch master at Debian Med / drop-seq
Commits:
32a75df6 by Emmanuel Bourg at 2021-02-09T13:05:18+01:00
Reduce the dependencies of drop-seq-tools (Closes: #982352)
- - - - -
6 changed files:
- README.md
- + debian/ant.properties
- debian/changelog
- debian/patches/debian_packaged_libs.patch
- debian/rules
- src/ant/defs.xml
Changes:
=====================================
README.md
=====================================
@@ -6,6 +6,6 @@ You may also use this address to be added to the Drop-seq Google group.
See https://github.com/broadinstitute/Drop-seq/releases to download binaries.
-See [Drop-seq alignment cookbook](doc/Drop-seq_Alignment_Cookbook.pdf) for detailed usage of these tools.
+See [Drop-seq alignment cookbook](https://github.com/broadinstitute/Drop-seq/blob/master/doc/Drop-seq_Alignment_Cookbook.pdf) for detailed usage of these tools.
-See [Census-seq computational protocols](doc/Census-seq_Computational_Protcools.pdf) for detailed usage of Census-Seq tools.
\ No newline at end of file
+See [Census-seq computational protocols](doc/Census-seq_Computational_Protcools.pdf) for detailed usage of Census-Seq tools.
=====================================
debian/ant.properties
=====================================
@@ -0,0 +1 @@
+picard.executable.dir=/usr/bin/picard-tools
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+drop-seq (2.4.0+dfsg-5) unstable; urgency=medium
+
+ * Team upload.
+ * Reduce the dependencies of drop-seq-tools (Closes: #982352)
+
+ -- Emmanuel Bourg <ebourg at apache.org> Tue, 09 Feb 2021 13:03:43 +0100
+
drop-seq (2.4.0+dfsg-4) unstable; urgency=medium
* Reduce heap size for 32bit architectures
=====================================
debian/patches/debian_packaged_libs.patch
=====================================
@@ -2,42 +2,6 @@ Author: Andreas Tille <tille at debian.org>
Last-Update: Tue, 19 May 2020 14:42:01 +0200
Description: Use Debian packaged Java libs
---- a/build.xml
-+++ b/build.xml
-@@ -35,19 +35,19 @@
- <property name="classes.test" location="testclasses"/>
- <property name="test.output" location="dist/test"/>
- <property name="javadoc" location="javadoc"/>
-- <property name="picard.executable.dir" location="../../3rdParty/picard"/>
-+ <property name="picard.executable.dir" location="/usr/bin/picard-tools"/>
- <property name="public.dir" location="."/>
-
- <!-- INIT -->
- <path id="classpath">
-- <fileset dir="${lib}">
-+ <fileset dir="/usr/share/java">
- <include name="*.jar"/>
- </fileset>
- </path>
- <path id="test.classpath">
- <pathelement location="${classes}"/>
- <path refid="classpath"/>
-- <fileset dir="${lib}/test">
-+ <fileset dir="/usr/share/java">
- <include name="*.jar"/>
- </fileset>
- </path>
-@@ -106,10 +106,7 @@
- <target name="jar-executable" depends="compile-src">
- <mkdir dir="${dist}"/>
- <pathconvert property="classpath.manifest" refid="classpath" pathsep=" ">
-- <chainedmapper>
- <flattenmapper/>
-- <globmapper from="*.jar" to="lib/*.jar"/>
-- </chainedmapper>
- </pathconvert>
- <delete file="${dist}/dropseq.jar"/>
- <jar destfile="${dist}/dropseq.jar" compress="no">
--- a/src/ant/defs.xml
+++ b/src/ant/defs.xml
@@ -122,12 +122,14 @@
=====================================
debian/rules
=====================================
@@ -13,6 +13,24 @@ JAVA_HOME := /usr/lib/jvm/default-java
%:
dh $@ --with javahelper
+override_dh_auto_configure:
+ dh_auto_configure
+ mkdir -p lib/test
+ ln -s /usr/share/java/commons-collections4.jar lib/commons-collections4.jar
+ ln -s /usr/share/java/commons-io.jar lib/commons-io.jar
+ ln -s /usr/share/java/commons-lang.jar lib/commons-lang.jar
+ ln -s /usr/share/java/commons-math3.jar lib/commons-math3.jar
+ ln -s /usr/share/java/htsjdk.jar lib/htsjdk.jar
+ ln -s /usr/share/java/la4j.jar lib/la4j.jar
+ ln -s /usr/share/java/picard.jar lib/picard.jar
+ ln -s /usr/share/java/snakeyaml.jar lib/snakeyaml.jar
+
+ ln -s /usr/share/java/testng.jar lib/test/testng.jar
+ ln -s /usr/share/java/junit4.jar lib/test/junit.jar
+
+override_dh_auto_clean:
+ rm -Rf lib
+
override_dh_fixperms:
dh_fixperms
find debian/drop-seq-testdata/usr/share -type f -exec chmod -x \{\} \;
=====================================
src/ant/defs.xml
=====================================
@@ -24,11 +24,6 @@
<!-- To be included in build.xml -->
<!-- Get GIT hash, if available, otherwise leave it blank. -->
-<exec executable="git" outputproperty="repository.revision" failifexecutionfails="true" errorproperty="">
- <arg value="log"/>
- <arg value="-1"/>
- <arg value="--pretty=format:%h_%at"/>
-</exec>
<property name="repository.revision" value=""/>
@@ -127,12 +122,14 @@
xmlns:jacoco="antlib:org.jacoco.ant"
to the <project> element in the file where this file is included.
-->
+<!-- jacoco is not packaged for Debianso we can not run this test
<property name="jacoco.dir" location="jacoco_reports"/>
<property name="jacoco.binary" location="${jacoco.dir}/jacoco.exec"/>
<taskdef uri="antlib:org.jacoco.ant" resource="org/jacoco/ant/antlib.xml">
<classpath path="${public.dir}/lib/test/jacocoant.jar"/>
</taskdef>
+-->
<!-- Unfortunately can't invoke a macro from inside <jacoco:coverage>, so testng invocation is duplicated -->
<target name="coverage" depends="compile-tests">
@@ -174,5 +171,7 @@
</jacoco:report>
</target>
+<!-- jacoco is not packaged for Debianso we can not run this test
<target name="coverage-and-report" depends="coverage, coverage-report"
description="Run unit test suite with coverage and generate report"/>
+-->
View it on GitLab: https://salsa.debian.org/med-team/drop-seq/-/commit/32a75df6acc1ff6eabb6a032bab0708e93081c3f
--
View it on GitLab: https://salsa.debian.org/med-team/drop-seq/-/commit/32a75df6acc1ff6eabb6a032bab0708e93081c3f
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