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 <ebo...@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 <ti...@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 You're receiving this email because of your account on salsa.debian.org.
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