[med-svn] [trinityrnaseq] 01/01: VCS URL secured

Fri Jan 29 20:44:48 UTC 2016

This is an automated email from the git hooks/post-receive script.

misterc-guest pushed a commit to branch master
in repository trinityrnaseq.

commit 689008859657dde6af9a30b2eb7f47982632f8af
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date:   Fri Jan 29 07:29:19 2016 -0800

    VCS URL secured
    
    Drop unpackagable GenomeViewPlugin
    
    Add copyright for code from stackoverflow
---
 debian/control             |  2 +-
 debian/copyright           |  6 ++++++
 debian/patches/fix-jsquery | 43 -------------------------------------------
 debian/patches/series      |  1 -
 4 files changed, 7 insertions(+), 45 deletions(-)

diff --git a/debian/control b/debian/control
index 4d2ab61..f7b3391 100644
--- a/debian/control
+++ b/debian/control
@@ -18,7 +18,7 @@ Build-Depends: debhelper (>= 9),
                libhts-dev
 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
+Vcs-Git: https://anonscm.debian.org/debian-med/trinityrnaseq.git
 Homepage: http://trinityrnaseq.github.io/
 
 Package: trinityrnaseq
diff --git a/debian/copyright b/debian/copyright
index 3dd4c62..40ed223 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -16,6 +16,8 @@ Files-Excluded: trinity-plugins/jellyfish-*.tar.gz
  trinity-plugins/samtools*
  trinity-plugins/slclust/Makefile.bak
  galaxy-plugin/GauravGalaxy/analyze_diff_exp.xml~
+ Analysis/GenomeViewPlugin/*
+ Chrysalis/MakeDepend.dSYM/*
 
 Files: *
 Copyright: © 2011 The Broad Institute, Inc
@@ -23,6 +25,10 @@ Copyright: © 2011 The Broad Institute, Inc
 License: BSD-3-clause
 Comment: trinity-plugins/slclust is from http://sourceforge.net/projects/slclust/
 
+Files: Analysis/DifferentialExpression/R/pairs3.R
+Copyright: 2012 Michael Kuhn <michaelmckuhnde at mckuhn.de>
+License: CC-BY-SA 3.0
+
 Files: Butterfly/src/src/NWalign.java
 Copyright: Ahmed Moustafa <ahmed at users.sf.net>
 License: GPL-2+
diff --git a/debian/patches/fix-jsquery b/debian/patches/fix-jsquery
deleted file mode 100644
index 5e43a60..0000000
--- a/debian/patches/fix-jsquery
+++ /dev/null
@@ -1,43 +0,0 @@
-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/series b/debian/patches/series
index 7ec61e4..dbcacec 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -8,7 +8,6 @@ update-paths
 collections15-to-4
 0001-fix_gcc5.patch.patch
 0002-fix_istream_failure_call.patch
-fix-jsquery
 fix_system_paths
 hardening
 reproducible-build

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/trinityrnaseq.git

