[DRE-commits] [ruby-fix-trinity-output] 03/04: remove simplecov & Turn

Wed Sep 30 05:59:25 UTC 2015

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misterc-guest pushed a commit to branch master
in repository ruby-fix-trinity-output.

commit ef11ee6fdd544184ff20cef7c46795e396b5d9fb
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date:   Sat Sep 19 23:45:16 2015 -0700

    remove simplecov & Turn
---
 debian/control                  | 12 ++++++++---
 debian/copyright                | 45 ++++++++++++++++++++---------------------
 debian/manpages                 |  1 +
 debian/patches/remove-simplecov | 14 +++++++++++++
 debian/patches/series           |  1 +
 debian/rules                    |  6 ++++++
 6 files changed, 53 insertions(+), 26 deletions(-)

diff --git a/debian/control b/debian/control
index 6e9df54..cfd05d9 100644
--- a/debian/control
+++ b/debian/control
@@ -6,7 +6,8 @@ Uploaders: Michael R. Crusoe <crusoe at ucdavis.edu>
 Build-Depends: debhelper (>= 9~),
                gem2deb,
                rake,
-               ruby-trollop (>= 2.0)
+               ruby-trollop (>= 2.0),
+               help2man
 Standards-Version: 3.9.6
 Vcs-Git: git://anonscm.debian.org/pkg-ruby-extras/ruby-fix-trinity-output.git
 Vcs-Browser: https://anonscm.debian.org/cgit/pkg-ruby-extras/ruby-fix-trinity-output.git
@@ -21,5 +22,10 @@ Depends: ruby | ruby-interpreter,
          ruby-trollop (>= 2.0),
          ${misc:Depends},
          ${shlibs:Depends}
-Description: Fix output fastq files from Trinity
- See readme
+Description: Fix output fastq files from trinityrnaseq
+ trinityrnaseq outputs fastq files that have been 'corrected'
+ .
+ Unfortunately these files are no longer properly paired and therefore can't be
+ used in most aligners such as bowtie2 and snap-aligner. This script attempts
+ to fix that and produce 2 properly paired fastq files and a fastq file
+ containing single reads
diff --git a/debian/copyright b/debian/copyright
index fc84a44..8224968 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -3,33 +3,32 @@ Upstream-Name: fix-trinity-output
 Source: http://rubygems.org/gems/fix-trinity-output
 
 Files: *
-Copyright: <years> <put author's name and email here>
-           <years> <likewise for another author>
-License: GPL-2+ (FIXME)
+Copyright: 2014 Chris Boursnell <cmb211 at cam.ac.uk>
+License: MIT
 
 Files: debian/*
 Copyright: 2015 Michael R. Crusoe <crusoe at ucdavis.edu>
-License: GPL-2+ (FIXME)
+License: MIT
 Comment: the Debian packaging is licensed under the same terms as the original package.
 
-License: GPL-2+ (FIXME)
- This program is free software; you can redistribute it
- and/or modify it under the terms of the GNU General Public
- License as published by the Free Software Foundation; either
- version 2 of the License, or (at your option) any later
- version.
+License: MIT
+ Permission is hereby granted, free of charge, to any person
+ obtaining a copy of this software and associated documentation
+ files (the "Software"), to deal in the Software without
+ restriction, including without limitation the rights to use,
+ copy, modify, merge, publish, distribute, sublicense, and/or sell
+ copies of the Software, and to permit persons to whom the
+ Software is furnished to do so, subject to the following
+ conditions:
  .
- This program is distributed in the hope that it will be
- useful, but WITHOUT ANY WARRANTY; without even the implied
- warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- PURPOSE.  See the GNU General Public License for more
- details.
+ The above copyright notice and this permission notice shall be
+ included in all copies or substantial portions of the Software.
  .
- You should have received a copy of the GNU General Public
- License along with this package; if not, write to the Free
- Software Foundation, Inc., 51 Franklin St, Fifth Floor,
- Boston, MA  02110-1301 USA
- .
- On Debian systems, the full text of the GNU General Public
- License version 2 can be found in the file
- `/usr/share/common-licenses/GPL-2'.
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ OTHER DEALINGS IN THE SOFTWARE.
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..ab7e277
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/fix-trinity-output.1
diff --git a/debian/patches/remove-simplecov b/debian/patches/remove-simplecov
new file mode 100644
index 0000000..39bda50
--- /dev/null
+++ b/debian/patches/remove-simplecov
@@ -0,0 +1,14 @@
+Author: Michael R. Crusoe <crusoe at ucdavis.edu>
+Description: drop simplecov & Turn
+
+--- ruby-fix-trinity-output.orig/test/helper.rb
++++ ruby-fix-trinity-output/test/helper.rb
+@@ -1,8 +1,4 @@
+-require 'simplecov'
+ require 'test/unit'
+ begin; require 'turn/autorun'; rescue LoadError; end
+ require 'shoulda-context'
+ require 'fix-trinity-output'
+-
+-Turn.config.format = :pretty
+-Turn.config.trace = 5
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..60986ec
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+remove-simplecov
diff --git a/debian/rules b/debian/rules
index acfc5fe..78ceeed 100755
--- a/debian/rules
+++ b/debian/rules
@@ -16,3 +16,9 @@
 
 %:
 	dh $@ --buildsystem=ruby --with ruby
+
+override_dh_auto_build:
+	dh_auto_build
+	help2man --name "Fix output fastq files from Trinity" \
+		--version-string="1.0.0" bin/fix-trinity-output > \
+		debian/fix-trinity-output.1

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/pkg-ruby-extras/ruby-fix-trinity-output.git

