Commit ef11ee6f authored by Michael R. Crusoe's avatar Michael R. Crusoe

remove simplecov & Turn

parent 4d0a3a7e
......@@ -6,7 +6,8 @@ Uploaders: Michael R. Crusoe <crusoe@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
......@@ -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@cam.ac.uk>
License: MIT
Files: debian/*
Copyright: 2015 Michael R. Crusoe <crusoe@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.
debian/fix-trinity-output.1
Author: Michael R. Crusoe <crusoe@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
remove-simplecov
......@@ -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
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