Michael R. Crusoe pushed to branch master at Debian Med / trinityrnaseq
Commits: 80c72a35 by Michael R. Crusoe at 2021-11-08T10:44:26+01:00 debian/javabuild: updated to correct path to the Butterfly source - - - - - e31909c5 by Michael R. Crusoe at 2021-11-08T11:42:36+01:00 forward more patches - - - - - f5e6572b by Michael R. Crusoe at 2021-11-08T11:42:37+01:00 combine some related patches - - - - - 45515ca9 by Michael R. Crusoe at 2021-11-08T12:44:38+01:00 release 2.13.2+dfsg-2 - - - - - 17 changed files: - debian/changelog - debian/clean - debian/copyright - debian/javabuild - debian/patches/fix-gcc-10.patch - debian/patches/fix_system_paths - debian/patches/hardening - − debian/patches/jellyfish-path - debian/patches/seqtk-trinity-hardening - debian/patches/series - debian/patches/skip_blat - debian/patches/skip_gatk_test - debian/patches/skip_tximportData_tests - debian/patches/strip_m64 - debian/patches/submake - debian/patches/update-paths - debian/rules Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,12 @@ +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 <[email protected]> Mon, 08 Nov 2021 12:44:15 +0100 + trinityrnaseq (2.13.2+dfsg-1) unstable; urgency=medium * New upstream version ===================================== debian/clean ===================================== @@ -1,3 +1,2 @@ trinity-plugins/ParaFly/config.log trinity-plugins/ParaFly/config.status -Butterfly/src/sample_data/c1.graph.allProbPaths.fasta ===================================== debian/copyright ===================================== @@ -34,8 +34,7 @@ Files: debian/* Copyright: (c) 2015 Michigan State University License: BSD-3-clause -#Files: Butterfly/src/src/NWalign.java -Files: debian/patches/butterfly +Files: Butterfly/Butterfly/src/src/NWalign.java Copyright: Ahmed Moustafa <[email protected]> License: GPL-2+ ===================================== debian/javabuild ===================================== @@ -1 +1 @@ -Butterfly.jar Butterfly/src/src +Butterfly.jar Butterfly/Butterfly/src/src ===================================== debian/patches/fix-gcc-10.patch ===================================== @@ -1,7 +1,8 @@ -Description: Fix gcc-10 build issue +Subject: Fix gcc-10 build issue Bug-Debian: https://bugs.debian.org/966876 -Author: Andreas Tille <[email protected]> +From: Andreas Tille <[email protected]> Last-Update: Wed, 05 Aug 2020 12:44:59 +0200 +Forwarded: https://github.com/trinityrnaseq/bamsifter/commit/2fed73b5dd400ed8ba38f3f63b385e0faff26045 --- trinityrnaseq.orig/trinity-plugins/bamsifter/sift_bam_max_cov.cpp +++ trinityrnaseq/trinity-plugins/bamsifter/sift_bam_max_cov.cpp ===================================== debian/patches/fix_system_paths ===================================== @@ -2463,6 +2463,15 @@ Forwarded: not-needed my $usage = "\n\nusage: $0 reads.fa hash_size\n\n"; +@@ -11,7 +10,7 @@ + my $hash_size = $ARGV[1] or die $usage; + + +-my $JELLYFISH_DIR = $FindBin::RealBin . "/../../trinity-plugins/jellyfish-1.1.3"; ++my $JELLYFISH_DIR = "/usr"; + my $CPU = 4; + my $min_kmer_cov = 1; + --- trinityrnaseq.orig/util/misc/run_read_simulator_per_gene.pl +++ trinityrnaseq/util/misc/run_read_simulator_per_gene.pl @@ -5,8 +5,6 @@ ===================================== debian/patches/hardening ===================================== @@ -1,5 +1,7 @@ From: Michael R. Crusoe <[email protected]> Subject: add standard CXXFLAGS CPPFLAGS to Chrysalis & scaffold_iworm_contigs +Forwarded: https://github.com/trinityrnaseq/Chrysalis/pull/1 +and https://github.com/trinityrnaseq/trinityrnaseq/pull/1090 --- trinityrnaseq.orig/Chrysalis/Makefile +++ trinityrnaseq/Chrysalis/Makefile @@ -1,10 +1,10 @@ ===================================== debian/patches/jellyfish-path deleted ===================================== @@ -1,12 +0,0 @@ -Description:Jellyfish path ---- trinityrnaseq.orig/util/misc/run_jellyfish.pl -+++ trinityrnaseq/util/misc/run_jellyfish.pl -@@ -11,7 +11,7 @@ - my $hash_size = $ARGV[1] or die $usage; - - --my $JELLYFISH_DIR = $FindBin::RealBin . "/../../trinity-plugins/jellyfish-1.1.3"; -+my $JELLYFISH_DIR = "/usr"; - my $CPU = 4; - my $min_kmer_cov = 1; - ===================================== debian/patches/seqtk-trinity-hardening ===================================== @@ -1,6 +1,6 @@ -From: Michael R. Crusoe <[email protected]> -Subject: Add LDFALGS CPPFLAGS and unshadw CFALGS for seqtk-trinity-0.0.2 - +From: Michael R. Crusoe <[email protected]> +Subject: Add LDFALGS CPPFLAGS and unshadow CFALGS +Forwarded: https://github.com/trinityrnaseq/seqtk-trinity/pull/1/files --- a/trinity-plugins/seqtk-trinity/Makefile +++ b/trinity-plugins/seqtk-trinity/Makefile @@ -1,10 +1,10 @@ ===================================== debian/patches/series ===================================== @@ -1,5 +1,4 @@ which_command_v -jellyfish-path update-paths collections15-to-4 0002-fix_istream_failure_call.patch ===================================== debian/patches/skip_blat ===================================== @@ -1,5 +1,6 @@ -Author: Michael R. Crusoe <michael.crusoe> +Author: Michael R. Crusoe <[email protected]> Description: skip tests with a dependency on blat +Forwarded: not-needed --- trinityrnaseq.orig/trinity_ext_sample_data/Makefile +++ trinityrnaseq/trinity_ext_sample_data/Makefile @@ -11,7 +11,6 @@ ===================================== debian/patches/skip_gatk_test ===================================== @@ -1,5 +1,6 @@ -Author: Michael R. Crusoe <[email protected]> +Author: Michael R. Crusoe <[email protected]> Description: Skip tests that require GATK4 until it gets packaged +Forwarded: not-needed --- trinityrnaseq.orig/trinity_ext_sample_data/Makefile +++ trinityrnaseq/trinity_ext_sample_data/Makefile @@ -8,7 +8,6 @@ ===================================== debian/patches/skip_tximportData_tests ===================================== @@ -1,5 +1,6 @@ -Author: Michael R. Crusoe <[email protected]> +Author: Michael R. Crusoe <[email protected]> Description: r-bioc-tximportdata is 400MiB+ package +Forwarded: not-needed --- trinityrnaseq.orig/trinity_ext_sample_data/Makefile +++ trinityrnaseq/trinity_ext_sample_data/Makefile @@ -8,7 +8,6 @@ ===================================== debian/patches/strip_m64 ===================================== @@ -1,5 +1,6 @@ From: Michael R. Crusoe <[email protected]> Subject: remove -m64 flag, hopefully helps arm64 compile +Forwarded: not-needed --- trinityrnaseq.orig/Chrysalis/CMakeLists.txt +++ trinityrnaseq/Chrysalis/CMakeLists.txt @@ -13,7 +13,7 @@ ===================================== debian/patches/submake ===================================== @@ -1,5 +1,8 @@ -From: Michael R. Crusoe <[email protected]> +From: Michael R. Crusoe <[email protected]> Subject: Enable better use of sub-make +Forwarded: https://github.com/trinityrnaseq/Inchworm/pull/1 +and https://github.com/trinityrnaseq/trinity_ext_sample_data/pull/2 +and https://github.com/trinityrnaseq/trinityrnaseq/pull/1091 --- trinityrnaseq.orig/Inchworm/Makefile +++ trinityrnaseq/Inchworm/Makefile @@ -1,8 +1,8 @@ ===================================== debian/patches/update-paths ===================================== @@ -1,6 +1,6 @@ Description: Updates the main Trinity program to use FHS paths -Author: Michael R. Crusoe <[email protected]> -Forwarded: no +Author: Michael R. Crusoe <[email protected]> +Forwarded: not-needed Last-Updated: 2015-02-22 --- trinityrnaseq.orig/Trinity ===================================== debian/rules ===================================== @@ -46,7 +46,7 @@ override_dh_auto_clean: override_dh_auto_test: ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS))) java -cp Butterfly.jar TransAssembly_allProbPaths -N 10000 -L 300 \ - -F 300 -C Butterfly/src/sample_data/c1.graph --stderr -V 20 + -F 300 -C Butterfly/Butterfly/src/sample_data/c1.graph --stderr -V 20 endif override_dh_auto_install: View it on GitLab: https://salsa.debian.org/med-team/trinityrnaseq/-/compare/5179a51e66583ac0501467f2cc53a489c7d98e57...45515ca9019bb7722044c6f808c73deb642686e2 -- View it on GitLab: https://salsa.debian.org/med-team/trinityrnaseq/-/compare/5179a51e66583ac0501467f2cc53a489c7d98e57...45515ca9019bb7722044c6f808c73deb642686e2 You're receiving this email because of your account on salsa.debian.org.
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