[med-svn] [Git][med-team/trinityrnaseq][master] 6 commits: Salmon >= 0.9 is now available, bump Standards-Version

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / trinityrnaseq


Commits:
7a1fe78f by Andreas Tille at 2018-12-14T07:06:31Z
Salmon >= 0.9 is now available, bump Standards-Version

- - - - -
976a963e by Andreas Tille at 2018-12-14T07:09:18Z
Secure URI in copyright format

- - - - -
ee7c4f49 by Andreas Tille at 2018-12-14T07:25:40Z
Respect DEB_BUILD_OPTIONS in override_dh_auto_test target

- - - - -
2289ae36 by Andreas Tille at 2018-12-14T07:25:40Z
Remove trailing whitespace in debian/changelog

- - - - -
a994cc12 by Andreas Tille at 2018-12-14T07:25:40Z
Remove trailing whitespace in debian/copyright

- - - - -
2416db0e by Andreas Tille at 2018-12-14T07:58:01Z
Fix permissions and Perl interpreter path

- - - - -


4 changed files:

- debian/changelog
- debian/control
- debian/copyright
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,16 +1,21 @@
 trinityrnaseq (2.6.6+dfsg-1) UNRELEASED; urgency=medium
 
+  * Team upload.
+
   [ Michael R. Crusoe ]
   * New upstream release, now with the sample data returned
     Closes: #897877
   * Build and ship seqtk-trinity
-  
-  TODO: update salmon to v0.9; required for this version
 
   [ Andreas Tille ]
   * debhelper 11
   * Point Vcs fields to salsa.debian.org
-  * Standards-Version: 4.1.5
+  * 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
 
  -- Michael R. Crusoe <michael.crusoe at gmail.com>  Sat, 17 Feb 2018 07:38:23 -0800
 
@@ -52,7 +57,7 @@ trinityrnaseq (2.2.0+dfsg-3) unstable; urgency=medium
 
   [ Gert Wollny ]
   * Fix build gcc 7
-    Closes: #853687  
+    Closes: #853687
 
   [ Andreas Tille ]
   * debhelper 10


=====================================
debian/control
=====================================
@@ -17,7 +17,7 @@ Build-Depends: debhelper (>= 11~),
                jellyfish,
                salmon,
                zlib1g-dev
-Standards-Version: 4.1.5
+Standards-Version: 4.2.1
 Vcs-Browser: https://salsa.debian.org/med-team/trinityrnaseq
 Vcs-Git: https://salsa.debian.org/med-team/trinityrnaseq.git
 Homepage: http://trinityrnaseq.github.io/


=====================================
debian/copyright
=====================================
@@ -1,4 +1,4 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: Trinity
 Source: https://github.com/trinityrnaseq/trinityrnaseq/archive/v2.0.3.tar.gz
 Files-Excluded:  util/support_scripts/*.jar
@@ -151,9 +151,9 @@ License: GPL-3
  (GPLv3).
  It is provided "as is" without warranty of any kind.
  You can find the terms and conditions at
- http://www.opensource.org/licenses/gpl-3.0.html. 
+ http://www.opensource.org/licenses/gpl-3.0.html.
  Please note that incorporating the whole software or parts of its code in
- proprietary software 
+ proprietary software
  is prohibited under the current license. .
  .
  On Debian systems, the full text of the GNU General Public


=====================================
debian/rules
=====================================
@@ -38,8 +38,10 @@ override_dh_auto_clean:
 	cd trinity-plugins && $(MAKE) clean || true
 
 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
+endif
 
 override_dh_auto_install:
 	for target in ${SOURCE_DIRECTORIES_ALL}; do dh_auto_install \
@@ -66,3 +68,9 @@ override_dh_install-indep:
 		${EXBASEDIR}/trinity_ext_sample_data/__regression_tests/test_GraphFromFasta/runMe.sh \
 		${EXBASEDIR}/trinity_ext_sample_data/test_Inchworm/runMe_MPI.sh \
 
+override_dh_fixperms:
+	dh_fixperms
+	find debian -name genwig.sh -exec chmod +x \{\} \;
+	for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \
+	    sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' $${pl} ; \
+	done



View it on GitLab: https://salsa.debian.org/med-team/trinityrnaseq/compare/4a3293a9ae4ca639561033097e074f9b4229240b...2416db0e74cbd6e943fe884e543f525e759f1a34

-- 
View it on GitLab: https://salsa.debian.org/med-team/trinityrnaseq/compare/4a3293a9ae4ca639561033097e074f9b4229240b...2416db0e74cbd6e943fe884e543f525e759f1a34
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