[med-svn] [Git][med-team/trinityrnaseq][master] 4 commits: debian/javabuild: updated to correct path to the Butterfly source

Mon Nov 8 12:31:10 GMT 2021


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 <crusoe at debian.org>  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 <ahmed at users.sf.net>
 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 <tille at debian.org>
+From: Andreas Tille <tille at debian.org>
 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 <crusoe at debian.org>
 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 <michael.crusoe at gmail.com>
-Subject: Add LDFALGS CPPFLAGS and unshadw CFALGS for seqtk-trinity-0.0.2
-
+From: Michael R. Crusoe <crusoe at debian.org>
+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 <crusoe at debian.org>
 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 <michael.crusoe at gmail.com>
+Author: Michael R. Crusoe <crusoe at debian.org>
 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 <michael.crusoe at gmail.com>
+Author: Michael R. Crusoe <crusoe at debian.org>
 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 <crusoe at debian.org>
 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 <michael.crusoe at gmail.com>
+From: Michael R. Crusoe <crusoe at debian.org>
 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 <mcrusoe at msu.edu>
-Forwarded: no
+Author: Michael R. Crusoe <crusoe at debian.org>
+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
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