[DRE-commits] [ruby-crb-blast] 03/03: drop ruby-bindep; ITP#; license update

[Michael Crusoe]

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misterc-guest pushed a commit to branch master
in repository ruby-crb-blast.

commit 01c3af71b81292620c0b2986acba15fbe6018cd0
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date:   Sat Sep 19 21:58:04 2015 -0700

    drop ruby-bindep; ITP#; license update
    
    And better description
---
 debian/changelog |  2 +-
 debian/control   | 21 ++++++++++++++++-----
 debian/copyright | 40 +++++++++++++++++++---------------------
 3 files changed, 36 insertions(+), 27 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index ce725be..e8c9708 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,5 +1,5 @@
 ruby-crb-blast (0.6.4-1) UNRELEASED; urgency=medium
 
-  * Initial release (Closes: #nnnn)
+  * Initial release (Closes: #800737)
 
  -- Michael R. Crusoe <crusoe at ucdavis.edu>  Sat, 19 Sep 2015 21:56:00 -0700
diff --git a/debian/control b/debian/control
index bc29c47..9017a91 100644
--- a/debian/control
+++ b/debian/control
@@ -6,8 +6,6 @@ Uploaders: Michael R. Crusoe <crusoe at ucdavis.edu>
 Build-Depends: debhelper (>= 9~),
                gem2deb,
                rake,
-               ruby-bindeps (>= 1.0),
-               ruby-bindeps (>= 1.0.3),
                ruby-bio (>= 1.4),
                ruby-bio (>= 1.4.3),
                ruby-fixwhich (>= 1.0),
@@ -26,8 +24,6 @@ Package: ruby-crb-blast
 Architecture: all
 XB-Ruby-Versions: ${ruby:Versions}
 Depends: ruby | ruby-interpreter,
-         ruby-bindeps (>= 1.0),
-         ruby-bindeps (>= 1.0.3),
          ruby-bio (>= 1.4),
          ruby-bio (>= 1.4.3),
          ruby-fixwhich (>= 1.0),
@@ -38,4 +34,19 @@ Depends: ruby | ruby-interpreter,
          ${misc:Depends},
          ${shlibs:Depends}
 Description: Run conditional reciprocal best blast
- See summary
+ CRB-BLAST is a novel method for finding orthologs between one set of sequences
+ and another. This is particularly useful in genome and transcriptome
+ annotation.
+ .
+ CRB-BLAST initially performs a standard reciprocal best BLAST. It does this by
+ performing BLAST alignments of query->target and target->query. Reciprocal
+ best BLAST hits are those where the best match for any given query sequence in
+ the query->target alignment is also the best hit of the match in the reverse
+ (target->query) alignment.
+ .
+ Reciprocal best BLAST is a very conservative way to assign orthologs. The main
+ innovation in CRB-BLAST is to learn an appropriate e-value cutoff to apply to
+ each pairwise alignment by taking into account the overall relatedness of the
+ two datasets being compared. This is done by fitting a function to the
+ distribution of alignment e-values over sequence lengths. The function
+ provides the e-value cutoff for a sequence of given length.
diff --git a/debian/copyright b/debian/copyright
index 3fb2577..58e52d0 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -5,31 +5,29 @@ Source: https://github.com/cboursnell/crb-blast
 Files: *
 Copyright: <years> <put author's name and email here>
            <years> <likewise for another author>
-License: GPL-2+ (FIXME)
+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.

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/pkg-ruby-extras/ruby-crb-blast.git