[med-svn] [Git][med-team/ugene][master] 4 commits: Install plugins_checker
Michael R. Crusoe (@crusoe)
gitlab at salsa.debian.org
Sat Aug 23 16:19:48 BST 2025
Michael R. Crusoe pushed to branch master at Debian Med / ugene
Commits:
81b534da by Michael R. Crusoe at 2025-08-23T14:12:56+01:00
Install plugins_checker
- - - - -
6cf0e76f by Michael R. Crusoe at 2025-08-23T14:12:59+01:00
Revert "Skip dh_dwz"
This reverts commit 09eda3078d548fa757152e5fdac3725105f3c4e6.
- - - - -
7f6b4fab by Michael R. Crusoe at 2025-08-23T14:14:23+01:00
d/rules: link the data folder into /usr/share/lib/ugene
- - - - -
60b164eb by Michael R. Crusoe at 2025-08-23T16:19:21+01:00
Added patch to fix detection of many external programs.
- - - - -
6 changed files:
- debian/changelog
- debian/control
- + debian/patches/plugin-paths
- debian/patches/series
- debian/rules
- debian/ugene.install
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+ugene (52.1+dfsg-2) unstable; urgency=medium
+
+ * Team upload.
+ * Install plugins_checker
+ * d/rules: link the data folder into /usr/share/lib/ugene
+ * Added patch to fix detection of bcftools and tabix.
+
+ -- Michael R. Crusoe <crusoe at debian.org> Sat, 23 Aug 2025 14:12:29 +0100
+
ugene (52.1+dfsg-1) unstable; urgency=medium
* New upstream version 52.1+dfsg
@@ -7,6 +16,7 @@ ugene (52.1+dfsg-1) unstable; urgency=medium
[ Michael R. Crusoe ]
* d/control: restrict building to 64-bit architectures.
+ * New upstream version
-- Pierre Gruet <pgt at debian.org> Sat, 23 Aug 2025 07:52:18 +0200
=====================================
debian/control
=====================================
@@ -44,22 +44,27 @@ Recommends: bedtools,
clustalw,
cutadapt,
default-jre-headless,
+ fasttree,
fastqc,
hisat2,
hmmer,
hmmer2,
+ iqtree,
kalign,
- kraken,
+ kraken2,
macs,
mafft,
metaphlan2,
mrbayes,
muscle,
ncbi-blast+,
+ ncbi-tools-bin,
phyml,
primer3,
r-base,
samtools,
+ snpeff,
+ stringtie,
spades,
t-coffee,
trimmomatic,
=====================================
debian/patches/plugin-paths
=====================================
@@ -0,0 +1,81 @@
+From: Michael R. Crusoe <crusoe at debian.org>
+Subject: Update plugin detection for modern versions
+--- ugene.orig/src/plugins/external_tool_support/src/samtools/BcfToolsSupport.cpp
++++ ugene/src/plugins/external_tool_support/src/samtools/BcfToolsSupport.cpp
+@@ -42,7 +42,7 @@
+ executableFileName = "bcftools";
+ #endif
+
+- validationMessageRegExp = "bcftools \\(Tools for data in the VCF/BCF formats\\)";
++ validationMessageRegExp = "bcftools \\(Tools for variant calling and manipulating VCFs and BCFs\\)";
+ description = "<i>BCFtools</i> is a set of utilities for data in the VCF/BCF formats";
+ versionRegExp = QRegExp("Version: (\\d+.\\d+.\\d+)");
+
+--- ugene.orig/src/plugins/external_tool_support/src/samtools/TabixSupport.cpp
++++ ugene/src/plugins/external_tool_support/src/samtools/TabixSupport.cpp
+@@ -47,7 +47,7 @@
+ #endif
+
+ muted = true;
+- validationArguments << "-help";
++ validationArguments << "--help";
+ validationMessageRegExp = "tabix";
+ description = tr("<i>Tabix</i> is a generic indexer for TAB-delimited genome position files");
+ versionRegExp = QRegExp("Version: (\\d+.\\d+.\\d+)");
+--- ugene.orig/src/plugins/external_tool_support/src/cufflinks/CufflinksSupport.cpp
++++ ugene/src/plugins/external_tool_support/src/cufflinks/CufflinksSupport.cpp
+@@ -120,7 +120,7 @@
+ #elif defined(Q_OS_UNIX)
+ executableFileName = "gffread";
+ #endif
+- validationMessageRegExp = "gffread <input_gff>";
++ validationMessageRegExp = "gffread [-g <genomic_seqs_fasta>";
+ validationArguments << "--help";
+ description = CufflinksSupport::tr("<i>Gffread</i> is used to verify or perform various operations on GFF files.");
+ }
+--- ugene.orig/src/plugins/external_tool_support/src/mafft/MAFFTSupport.cpp
++++ ugene/src/plugins/external_tool_support/src/mafft/MAFFTSupport.cpp
+@@ -56,8 +56,8 @@
+ warnIcon = QIcon(":external_tool_support/images/cmdline_warn.png");
+ }
+
+- executableFileName = "mafft.bat";
+- validationArguments << "-help";
++ executableFileName = "mafft";
++ validationArguments << "--help";
+ validationMessageRegExp = "MAFFT";
+ description = tr("<i>MAFFT</i> is a multiple sequence alignment program for unix-like operating systems. ");
+ versionRegExp = QRegExp("MAFFT v(\\d+\\.\\d+\\w)");
+--- ugene.orig/src/plugins/external_tool_support/src/blast/BlastSupport.cpp
++++ ugene/src/plugins/external_tool_support/src/blast/BlastSupport.cpp
+@@ -106,7 +106,7 @@
+ description = tr("The <i>tblastx</i> translates the query nucleotide sequence in all six possible frames and compares it against the six-frame translations of a nucleotide sequence database.");
+ versionRegExp = QRegExp("Translated Query-Translated Subject BLAST (\\d+\\.\\d+\\.\\d+)");
+ } else if (id == ET_RPSBLAST_ID) {
+- executableFileName = isOsWindows() ? "rpsblast.exe" : "rpsblast";
++ executableFileName = isOsWindows() ? "rpsblast.exe" : "rpsblast+";
+ validationMessageRegExp = "Reverse Position Specific BLAST";
+ description = "";
+ versionRegExp = QRegExp("Reverse Position Specific BLAST (\\d+\\.\\d+\\.\\d+)");
+--- ugene.orig/src/plugins/external_tool_support/src/snpeff/SnpEffSupport.cpp
++++ ugene/src/plugins/external_tool_support/src/snpeff/SnpEffSupport.cpp
+@@ -49,7 +49,7 @@
+ warnIcon = QIcon(":external_tool_support/images/cmdline_warn.png");
+ }
+
+- executableFileName = "snpEff.jar";
++ executableFileName = "snpEff";
+
+ validationMessageRegExp = "Usage: snpEff \\[command\\] \\[options\\] \\[files\\]";
+ description = tr("<i>SnpEff</i>: Genetic variant annotation and effect prediction toolbox.");
+--- ugene.orig/src/plugins/external_tool_support/src/trimmomatic/TrimmomaticSupport.cpp
++++ ugene/src/plugins/external_tool_support/src/trimmomatic/TrimmomaticSupport.cpp
+@@ -52,7 +52,7 @@
+ toolKitName = "Trimmomatic";
+ description = tr("<i>Trimmomatic</i> is a flexible read trimming tool for Illumina NGS data.");
+
+- executableFileName = "trimmomatic.jar";
++ executableFileName = "/usr/share/java/trimmomatic.jar";
+ validationArguments << "-h";
+ validationMessageRegExp = "PE \\[-version\\] \\[-threads <threads>\\] \\[-phred33|-phred64\\] \\[-trimlog <trimLogFile>\\]";
+
=====================================
debian/patches/series
=====================================
@@ -8,3 +8,4 @@ plugins_directory.patch
undefined_references.patch
signed_char_neighbour_table.patch
gcc-15.patch
+plugin-paths
=====================================
debian/rules
=====================================
@@ -28,30 +28,24 @@ override_dh_auto_configure:
#override_dh_auto_build:
# $(MAKE)
-override_dh_auto_clean:
- dh_auto_clean
+execute_after_dh_auto_clean:
rm -rf src/_debug src/_release ugene
rm -f .qmake.stash
rm -f src/libs_3rdparty/sqlite3/Makefile src/libs_3rdparty/sqlite3/Makefile.Debug src/libs_3rdparty/sqlite3/Makefile.Release
-override_dh_auto_install:
- dh_auto_install
+execute_after_dh_auto_install:
# This should be default:
# $(MAKE) INSTALL_ROOT=$$(pwd)/debian/$(DEB_SOURCE) install
# Remove data dir which goes to ugene-data package
rm -rf debian/$(DEB_SOURCE)/usr/share/$(DEB_SOURCE)
-override_dh_fixperms-indep:
- dh_fixperms
+execute_after_dh_install:
+ cd debian/ugene/usr/lib/ugene && ln -s ../../share/data ./
+
+execute_after_dh_fixperms-indep:
rmdir debian/ugene-data/usr/share/ugene/data/manuals/ || true # remove dir if empty
chmod -x debian/ugene-data/usr/share/ugene/data/genome_lengths/*.genome
rm -f debian/ugene-data/usr/share/ugene/data/license
override_dh_shlibdeps:
dh_shlibdeps -l$(CURDIR)/debian/tmp/usr/lib/ugene/plugins/:$(CURDIR)/debian/tmp/usr/lib/ugene:$(CURDIR)/debian/$(DEB_SOURCE)/usr/lib/$(DEB_SOURCE)/
-
-override_dh_dwz:
- echo "Do not run dh_dwz since it just results in:"
- echo " dwz: debian/ugene/usr/lib/ugene/libU2View.so.1.0.0: Couldn't find DIE referenced by DW_OP_GNU_parameter_ref"
- echo " dwz: debian/ugene/usr/lib/ugene/plugins/libexternal_tool_support.so.1.0.0: Couldn't find DIE referenced by DW_OP_GNU_parameter_ref"
- echo " dh_dwz: dwz -q -mdebian/ugene/usr/lib/debug/.dwz/x86_64-linux-gnu/ugene.debug -M/usr/lib/debug/.dwz/x86_64-linux-gnu/ugene.debug ..."
=====================================
debian/ugene.install
=====================================
@@ -1,4 +1,5 @@
src/_release/ugene* usr/bin
+src/_release/plugins_checker usr/bin
src/_release/*.so usr/lib/ugene
debian/tmp/usr/plugins usr/lib/ugene
debian/tmp/usr/ugene.png usr/share/pixmaps
View it on GitLab: https://salsa.debian.org/med-team/ugene/-/compare/d4d681c3a5f1468d8343bb05e75b043f8492e4b4...60b164eb265ed5548dcd0eb0ba432b4933c90c7c
--
View it on GitLab: https://salsa.debian.org/med-team/ugene/-/compare/d4d681c3a5f1468d8343bb05e75b043f8492e4b4...60b164eb265ed5548dcd0eb0ba432b4933c90c7c
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