trinityrnaseq (2.15.2+dfsg-1) unstable; urgency=medium * New upstream version * Delete patch R_4.2_fix, it was applied upstream. -- Michael R. Crusoe Wed, 21 Aug 2024 23:59:34 +0200 trinityrnaseq (2.15.1+dfsg-5) unstable; urgency=medium * Team upload. * Add support for loong64 Closes: #1059072 -- Andreas Tille Sat, 23 Dec 2023 23:34:33 +0100 trinityrnaseq (2.15.1+dfsg-4) unstable; urgency=medium * d/control: also restrict architectures for the -examples binary package. -- Michael R. Crusoe Thu, 05 Oct 2023 16:10:30 +0200 trinityrnaseq (2.15.1+dfsg-3) unstable; urgency=medium * d/control: tighten architecture list to those with necessary dependencies. -- Michael R. Crusoe Mon, 02 Oct 2023 12:25:24 +0200 trinityrnaseq (2.15.1+dfsg-2) unstable; urgency=medium * d/control: move many deps of the binary package to recommends/suggests. As not all deps are needed for all usages, this enables usage on architectures where some deps are not available. -- Michael R. Crusoe Wed, 13 Sep 2023 22:02:31 +0200 trinityrnaseq (2.15.1+dfsg-1) unstable; urgency=medium [ Michael R. Crusoe ] * d/watch: update for GitHub API breakage [ Andreas Tille ] * Standards-Version: 4.6.2 (routine-update) [ Michael R. Crusoe ] * d/control: update homepage * d/control: remove unused test-deps * d/source/lintian-overrides: note that we clean up the config.{log,status} automatically. * d/patches/R_4.2_fix: fix for R 4.2.x+. Closes: #1006336, #1004773 -- Michael R. Crusoe Tue, 12 Sep 2023 17:12:30 +0200 trinityrnaseq (2.14.0+dfsg-1) unstable; urgency=medium * New upstream version * Refresh patches -- Michael R. Crusoe Sun, 10 Apr 2022 18:07:36 +0200 trinityrnaseq (2.13.2+dfsg-3) unstable; urgency=medium * Team upload * Applying a new patch to build against newest libjung-free-java, adding a versioned dependency -- Pierre Gruet Mon, 15 Nov 2021 21:52:59 +0100 trinityrnaseq (2.13.2+dfsg-2) unstable; urgency=medium * debian/javabuild: updated to correct path to the Butterfly source * debian/copyright: Now that the Butterfly source is back in the upstream tarball, adjust the paths accordingly here as well. * debian/patches: forwarded many patches upstream -- Michael R. Crusoe Mon, 08 Nov 2021 12:44:15 +0100 trinityrnaseq (2.13.2+dfsg-1) unstable; urgency=medium * New upstream version * watch file standard 4 (routine-update) * Freshen patches * debian/tests/control: dep on libpicard-java * debian/rules: adjust cmake invocation * new patch: debian/patches/which_command_v to use 'command -v' instead of which * New upstream version * Standards-Version: 4.6.0 (routine-update) * Refresh patches -- Michael R. Crusoe Sun, 07 Nov 2021 17:28:45 +0100 trinityrnaseq (2.11.0+dfsg-6) unstable; urgency=medium * fix typo in debian/test/control. -- Michael R. Crusoe Tue, 19 Jan 2021 14:16:26 +0100 trinityrnaseq (2.11.0+dfsg-5) unstable; urgency=medium * Add r-bioc-dexseq to the deps for the trinityrnaseq binary package. * Standards-Version: 4.5.1 (routine-update) -- Michael R. Crusoe Tue, 19 Jan 2021 10:47:31 +0100 trinityrnaseq (2.11.0+dfsg-4) unstable; urgency=medium * Add patch to remove m64 flag. Hopefully helps arm64 to compile. -- Michael R. Crusoe Tue, 19 Jan 2021 07:33:58 +0100 trinityrnaseq (2.11.0+dfsg-3) unstable; urgency=medium * debian/tests/control: adjust so that the tests don't have to pass on archs where we don't build -- Michael R. Crusoe Sat, 24 Oct 2020 17:14:03 +0200 trinityrnaseq (2.11.0+dfsg-2) unstable; urgency=medium * debian/patches/STAR_genomeSAindexNbases: Attempt to fix the DTU STAR test error * debian/patches/skip_DTU_STAR_test: skip the test until a better fix is found -- Michael R. Crusoe Mon, 12 Oct 2020 15:16:52 +0200 trinityrnaseq (2.11.0+dfsg-1) unstable; urgency=medium [ Andreas Tille ] * Fix gcc-10 build issue Closes: #966876 * debhelper-compat 13 (routine-update) * Review Files-Excluded for moved and removed files as well as new binary *.jars * Remove redundant debian/gbp.conf * Remove __pycache__ from installed package [ Michael R. Crusoe ] * Correct location of bamsifter installation * debian/patches/fix_system_paths: fix expected path for ParaFly * debian/patches/update-paths: fix paths to Butterfly.jar * Enable more features and tests with r-cran-{argparse,dexseq} & tabix -- Michael R. Crusoe Fri, 09 Oct 2020 15:13:36 +0200 trinityrnaseq (2.10.0+dfsg-1) unstable; urgency=medium * Eliminate warning about missing hardening flags * New upstream version * debhelper-compat 12 * debian/control: Added python3-htseq, rna-star, picard-tools, gmap, histat2, subread, kallisto, r-bioc-{edger,deseq2,rots,ctc,biobase,qvalue,goseq,tximport,dexseq,glimma}, r-cran-{ape,fastcluster,gplots,argparse,goplot,readr,tidyverse}, liburi-perl deps, and python3-hisat2 * Standards-Version: 4.5.0 (routine-update) * Refresh patches * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * Use secure URI in Homepage field. * debian/rules: seqtk-trinity now has a unversioned path * debian/patches/butterfly: restore missing Butterfly sources * debian/patches/submake: use $(MAKE) consistently * Install the new bamsfilter plugin * Install trinity-plugins/COLLECTL/examine_resource_usage_profiling.pl * Install trinity-plugins/DEXseq_util/dexseq_prepare_annotation.py * Install PyLib/Pipeliner.py * Set PICARD_HOME default of /usr/share/java * Skip tests that require GATK4 until it gets packaged * Skip tests that require r-bioc-tximportdata * Skip the remaining tests waiting for new packages * debian/tests/runtests: s/ADTTMP/AUTOPKGTEST_TMP/g * Remove trailing whitespace in debian/changelog (routine-update) * debian/upstream/metadata: add Repository{,-Browse}, Bug-{Database,Submit} -- Michael R. Crusoe Tue, 28 Apr 2020 09:07:17 +0200 trinityrnaseq (2.6.6+dfsg-6) unstable; urgency=medium * -examples: Don't hardcode number of --CPU (especially above 2). Fixes the autopkgtests when the number of CPUs/cores is less than 4 and blastn's intransigency to accept a larger value to -num_threads. -- Michael R. Crusoe Fri, 04 Jan 2019 03:38:40 -0800 trinityrnaseq (2.6.6+dfsg-5) unstable; urgency=medium * Added missing dependency on ncbi-blast+ to the binary package. -- Michael R. Crusoe Thu, 03 Jan 2019 01:15:29 -0800 trinityrnaseq (2.6.6+dfsg-4) unstable; urgency=medium * Default to Python 3, as needed. * Use better Java version check from upstream -- Michael R. Crusoe Wed, 02 Jan 2019 00:48:52 -0800 trinityrnaseq (2.6.6+dfsg-3) unstable; urgency=medium * debian/control: add numpy dependency, required for Analysis/SuperTranscripts/Trinity_gene_splice_modeler.py -- Michael R. Crusoe Tue, 01 Jan 2019 08:34:35 -0800 trinityrnaseq (2.6.6+dfsg-2) unstable; urgency=medium * debian/trinityrnaseq.install: Add BubbleUpClustering binary -- Michael R. Crusoe Mon, 31 Dec 2018 15:30:16 -0800 trinityrnaseq (2.6.6+dfsg-1) unstable; urgency=medium * Team upload. [ Michael R. Crusoe ] * New upstream release, now with the sample data returned Closes: #897877 * Build and ship seqtk-trinity [ Andreas Tille ] * debhelper 11 * Point Vcs fields to salsa.debian.org * Standards-Version: 4.2.1 * Secure URI in copyright format * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target * Remove trailing whitespace in debian/changelog * Remove trailing whitespace in debian/copyright * Fix permissions and Perl interpreter path -- Andreas Tille Fri, 14 Dec 2018 08:58:49 +0100 trinityrnaseq (2.5.1+dfsg-2) unstable; urgency=medium * Team upload. [ Aurelien Jarno ] * Build with glibc 2.27 (fix for cannot find -lieee) -- Andreas Tille Sat, 17 Feb 2018 09:04:18 +0100 trinityrnaseq (2.5.1+dfsg-1) unstable; urgency=medium * New upstream release. Updated watch file. * NeedlemanWunschGotohBanded.java moved into trinityrnasq_jaligner package * Much of the sample data is missing from upstream's tarball, so some tests have been turned off -- Michael R. Crusoe Sun, 11 Feb 2018 09:13:04 -0800 trinityrnaseq (2.2.0+dfsg-4) unstable; urgency=medium [ Steffen Moeller ] * debian/upstream/metadata - Completed references to registries - yamllint clean * debian/copyright - Corrected upstream-name to 'Trinity' [ Michael R. Crusoe ] * Removed unneeded dependency on r-bioc-edger -- Michael R. Crusoe Sat, 18 Nov 2017 05:00:08 -0800 trinityrnaseq (2.2.0+dfsg-3) unstable; urgency=medium * Team upload [ Gert Wollny ] * Fix build gcc 7 Closes: #853687 [ Andreas Tille ] * debhelper 10 Closes: #865262 * Standards-Version: 4.1.0 (no changes needed) * hardening=+all * remove unused lintian override * Build-Depends: bowtie2, yellyfish Closes: #860645 -- Andreas Tille Fri, 01 Sep 2017 21:57:01 +0200 trinityrnaseq (2.2.0+dfsg-2) unstable; urgency=medium * Team upload. * Fix build on GCC 6 (Closes: #831110) -- Sascha Steinbiss Fri, 05 Aug 2016 19:21:49 +0000 trinityrnaseq (2.2.0+dfsg-1) unstable; urgency=medium [ Andreas Tille ] * Team upload * d/watch: Use xz compression for upstream source [ Michael R. Crusoe ] * new upstream version * prune d/copyright excludes * refresh patches, drop a few included upstream * Standards-Version: '3.9.7' -> '3.9.8' -- Michael R. Crusoe Mon, 23 May 2016 11:46:45 -0700 trinityrnaseq (2.1.1+dfsg2-1) unstable; urgency=low * Properly harden Chrysalis binaries * Drop Galaxy plugin * Increment dfsg version for the above -- Michael R. Crusoe Thu, 25 Feb 2016 00:03:48 -0800 trinityrnaseq (2.1.1+dfsg-2) unstable; urgency=medium * Split install of arch-dependent & arch-independent files, fixes FTBFS (Closes: #813958) -- Michael R. Crusoe Sun, 07 Feb 2016 01:21:41 -0800 trinityrnaseq (2.1.1+dfsg-1) unstable; urgency=low * Initial release (Closes: #777697) -- Michael R. Crusoe Thu, 22 Oct 2015 08:31:56 -0700