[med-svn] [trinityrnaseq] 01/01: build-dep update libjung-free-java, automake, jaligner, libjs-jquery
Michael Crusoe
misterc-guest at moszumanska.debian.org
Tue Aug 25 18:29:06 UTC 2015
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch master
in repository trinityrnaseq.
commit f905b63865b80912da52b6132cac7472ea336a56
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date: Fri Aug 21 18:47:54 2015 -0700
build-dep update libjung-free-java, automake, jaligner, libjs-jquery
updated path to fastool in d/copyright
silenced lintian warnings about test-data tarballs from upstream
refreshed noExitTester patch
---
debian/changelog | 2 +-
debian/control | 9 ++++++---
debian/copyright | 2 +-
debian/lintian-overrides | 2 ++
debian/patches/fix-jsquery | 43 +++++++++++++++++++++++++++++++++++++++++++
debian/patches/noExitTester | 2 +-
debian/patches/series | 1 +
7 files changed, 55 insertions(+), 6 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index 18a8510..5c2b3e4 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -2,4 +2,4 @@ trinityrnaseq (2.0.6+dfsg-1) UNRELEASED; urgency=low
* Initial release (Closes: #777697)
- -- Michael R. Crusoe <michael.crusoe at gmail.com> Thu, 24 May 2012 14:30:13 +0200
+ -- Michael R. Crusoe <crusoe at ucdavis.edu> Thu, 24 May 2012 14:30:13 +0200
diff --git a/debian/control b/debian/control
index 4cc8808..f215cc6 100644
--- a/debian/control
+++ b/debian/control
@@ -1,16 +1,19 @@
Source: trinityrnaseq
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Michael R. Crusoe
+Uploaders: Michael R. Crusoe <crusoe at ucdavis.edu>
Section: science
Priority: optional
Build-Depends: debhelper (>= 9),
autotools-dev,
+ automake1.11,
jellyfish (>= 2.1.4),
- libjung-java,
+ libjung-free-java,
javahelper,
libgetopt-java,
default-jdk,
- parafly
+ parafly,
+ libjs-jquery,
+ jaligner
Standards-Version: 3.9.6
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/trinityrnaseq.git
Vcs-Git: git://anonscm.debian.org/debian-med/trinityrnaseq.git
diff --git a/debian/copyright b/debian/copyright
index 7bf4fd3..0615a0f 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -21,7 +21,7 @@ Copyright: © 2011 The Broad Institute, Inc
Comment: trinity-plugins/slclust is from http://sourceforge.net/projects/slclust/
License: BSD-3-clause
-Files: trinity-plugin/*Fastool*
+Files: trinity-plugins/*Fastool*
Copyright: (c) 2012 Francesco Strozzi
Comment: https://github.com/fstrozzi/Fastool
License: Expat
diff --git a/debian/lintian-overrides b/debian/lintian-overrides
index 3cb29c6..6fb9c91 100644
--- a/debian/lintian-overrides
+++ b/debian/lintian-overrides
@@ -1,2 +1,4 @@
trinityrnaseq: executable-not-elf-or-script usr/lib/trinityrnaseq/*
trinityrnaseq: image-file-in-usr-lib usr/lib/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/*
+trinityrnaseq: package-contains-timestamped-gzip usr/lib/trinityrnaseq/Analysis/DifferentialExpression/cluster_sample_data/MLF_ESC_NPC.cuff.genes.fpkm.matrix.gz
+trinityrnaseq: package-contains-timestamped-gzip usr/lib/trinityrnaseq/sample_data/*
diff --git a/debian/patches/fix-jsquery b/debian/patches/fix-jsquery
new file mode 100644
index 0000000..5e43a60
--- /dev/null
+++ b/debian/patches/fix-jsquery
@@ -0,0 +1,43 @@
+Description: Use libjs-jquery
+Author: Michael R. Crusoe <crusoe at ucdavis.edu>
+
+--- trinityrnaseq.orig/Analysis/GenomeViewPlugin/test.html
++++ trinityrnaseq/Analysis/GenomeViewPlugin/test.html
+@@ -9,7 +9,7 @@
+ <link rel="stylesheet" type="text/css" href="CSS/common.css" />
+ <script src="http://www.java.com/js/deployJava.js" type="text/javascript"></script>
+ <script src="http://genomeview.org/start/genomeview.js" type="text/javascript"></script>
+-<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.7.1/jquery.min.js" type="text/javascript"></script>
++<script src="/usr/share/javascript/jquery/jquery.min.js" type="text/javascript"></script>
+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
+ </head>
+ <body>
+@@ -60,4 +60,4 @@
+ </ul>
+
+ </body>
+-</html>
+\ No newline at end of file
++</html>
+--- trinityrnaseq.orig/Analysis/GenomeViewPlugin/trinity_to_genomeview_html.pl
++++ trinityrnaseq/Analysis/GenomeViewPlugin/trinity_to_genomeview_html.pl
+@@ -33,7 +33,7 @@
+ -src => 'http://genomeview.org/start/genomeview.js',
+ },
+ { -type => 'text/javascript',
+- -src => 'http://ajax.googleapis.com/ajax/libs/jquery/1.7.1/jquery.min.js',
++ -src => '/usr/share/javascript/jquery/jquery.min.js',
+ }
+ ]
+
+--- trinityrnaseq.orig/Analysis/GenomeViewPlugin/test_session.html
++++ trinityrnaseq/Analysis/GenomeViewPlugin/test_session.html
+@@ -9,7 +9,7 @@
+ <link rel="stylesheet" type="text/css" href="CSS/common.css" />
+ <script src="http://www.java.com/js/deployJava.js" type="text/javascript"></script>
+ <script src="http://genomeview.org/start/genomeview.js" type="text/javascript"></script>
+-<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.7.1/jquery.min.js" type="text/javascript"></script>
++<script src="/usr/share/javascript/jquery/jquery.min.js" type="text/javascript"></script>
+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
+ </head>
+ <body>
diff --git a/debian/patches/noExitTester b/debian/patches/noExitTester
index 0eaa9c8..628311a 100644
--- a/debian/patches/noExitTester
+++ b/debian/patches/noExitTester
@@ -1,7 +1,7 @@
Description:NoExitTester
--- trinityrnaseq.orig/Trinity
+++ trinityrnaseq/Trinity
-@@ -2191,32 +2191,6 @@
+@@ -2193,32 +2193,6 @@
die "Error, cannot find 'java'. Please be sure it is available within your \${PATH} setting and then try again.";
}
diff --git a/debian/patches/series b/debian/patches/series
index 8ce756e..0f88e83 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -5,3 +5,4 @@ update-paths
collections15-to-4
0001-fix_gcc5.patch.patch
0002-fix_istream_failure_call.patch
+fix-jsquery
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/trinityrnaseq.git
More information about the debian-med-commit
mailing list