Pierre Gruet pushed to branch master at Debian Med / fastqc
Commits: c26a05c1 by Pierre Gruet at 2024-09-08T13:15:39+02:00 Patching files to avoid importing the sis-jhdf5 classes - - - - - 908360d4 by Pierre Gruet at 2024-09-08T13:16:14+02:00 Raising Standards version to 4.7.0 (no change) - - - - - e16cac57 by Pierre Gruet at 2024-09-08T13:18:31+02:00 Adding header to patch - - - - - 4b683b48 by Pierre Gruet at 2024-09-08T15:15:49+02:00 Refreshing patches - - - - - e8d195ba by Pierre Gruet at 2024-09-08T15:18:26+02:00 Upload to unstable - - - - - 5 changed files: - debian/changelog - debian/control - debian/patches/build_xml.patch - + debian/patches/no_hdf5.patch - debian/patches/series Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,12 @@ +fastqc (0.12.1+dfsg-4) unstable; urgency=medium + + * Stopping (build-)depending on libsis-jhdf5-java: + - Patching files to avoid importing the sis-jhdf5 classes + - Refreshing patches + * Raising Standards version to 4.7.0 (no change) + + -- Pierre Gruet <[email protected]> Sun, 08 Sep 2024 15:15:52 +0200 + fastqc (0.12.1+dfsg-3) unstable; urgency=medium * Team upload. ===================================== debian/control ===================================== @@ -11,9 +11,8 @@ Build-Depends: debhelper-compat (= 13), ant, libhtsjdk-java, libjbzip2-java, - libcommons-math3-java, - libsis-jhdf5-java -Standards-Version: 4.6.2 + libcommons-math3-java +Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/fastqc Vcs-Git: https://salsa.debian.org/med-team/fastqc.git Homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ @@ -27,7 +26,6 @@ Depends: ${misc:Depends}, libjbzip2-java, libcommons-math3-java, libfindbin-libs-perl, - libsis-jhdf5-java, default-jre Description: quality control for high throughput sequence data FastQC aims to provide a simple way to do some quality control checks on ===================================== debian/patches/build_xml.patch ===================================== @@ -5,7 +5,7 @@ Description: Use Debian packaged JARs --- a/build.xml +++ b/build.xml -@@ -11,9 +11,10 @@ +@@ -11,9 +11,9 @@ <property name="source" value="11"/> <path id="FastQC.classpath"> <pathelement location="bin"/> @@ -14,7 +14,6 @@ Description: Use Debian packaged JARs - <pathelement location="cisd-jhdf5.jar"/> + <pathelement location="/usr/share/java/jbzip2.jar"/> + <pathelement location="/usr/share/java/htsjdk.jar"/> -+ <pathelement location="/usr/share/java/sis-jhdf5.jar"/> + <pathelement location="/usr/share/java/commons-math3.jar"/> </path> <target name="init"> ===================================== debian/patches/no_hdf5.patch ===================================== @@ -0,0 +1,29 @@ +Description: skipping the imports from classes of sis-jhdf5 +Author: Pierre Gruet <[email protected]> +Forwarded: not-needed +Last-Update: 2024-09-07 + +--- a/build.xml ++++ b/build.xml +@@ -35,6 +35,7 @@ + <javac debug="true" debuglevel="${debuglevel}" destdir="bin" includeantruntime="false" source="${source}" target="${target}"> + <src path="."/> + <exclude name=".pc/**"/> ++ <exclude name="**/Fast5File.java"/> + <classpath refid="FastQC.classpath"/> + </javac> + </target> +--- a/uk/ac/babraham/FastQC/Sequence/SequenceFactory.java ++++ b/uk/ac/babraham/FastQC/Sequence/SequenceFactory.java +@@ -99,9 +99,9 @@ + // We default to using all reads + return new BAMFile(file,false); + } +- else if (file.getName().toLowerCase().endsWith(".fast5")) { ++ /*else if (file.getName().toLowerCase().endsWith(".fast5")) { + return new Fast5File(file); +- } ++ }*/ + else { + return new FastQFile(config,file); + } ===================================== debian/patches/series ===================================== @@ -2,3 +2,4 @@ build_xml.patch fastqc.patch fix-help-call.patch set_configuration_path.patch +no_hdf5.patch View it on GitLab: https://salsa.debian.org/med-team/fastqc/-/compare/fa262229a9dce7765e66e67cdc49a06fa39970f8...e8d195ba4da629c773abb72f33aa08f80fef8d5e -- View it on GitLab: https://salsa.debian.org/med-team/fastqc/-/compare/fa262229a9dce7765e66e67cdc49a06fa39970f8...e8d195ba4da629c773abb72f33aa08f80fef8d5e You're receiving this email because of your account on salsa.debian.org.
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