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 <[email protected]> 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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