[med-svn] [Git][med-team/quast][master] 4 commits: DEP3

Fri Jun 26 10:32:04 BST 2020


Andreas Tille pushed to branch master at Debian Med / quast


Commits:
4f0b66d9 by Andreas Tille at 2020-06-26T11:24:15+02:00
DEP3

- - - - -
8909d1a6 by Andreas Tille at 2020-06-26T11:25:08+02:00
Override executable with language extension

- - - - -
2a674262 by Andreas Tille at 2020-06-26T11:26:24+02:00
License name

- - - - -
5ce9317b by Andreas Tille at 2020-06-26T11:30:22+02:00
Fix extra license

- - - - -


6 changed files:

- debian/copyright
- + debian/lintian-overrides
- debian/patches/adjustPythonImportPaths.patch
- debian/patches/noBwa.patch
- debian/patches/pathonPaths.patch
- debian/rules


Changes:

=====================================
debian/copyright
=====================================
@@ -25,12 +25,36 @@ Copyright: © 2020 Alexey Gurevich
                   and others
 License: GPL-2
 
+Files: quast_libs/html_saver/static/flot/*
+Copyright: 2007-2009 IOLA and Ole Laursen
+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:
+ .
+ The above copyright notice and this permission notice shall be
+ included in all copies or substantial portions of the Software.
+ .
+ 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.
+
 Files: debian/*
 Copyright: © 2020 Steffen Moeller <moeller at debian.org>
                   Andreas Tille <tille at debian.org>
 License: GPL-2
 
-License: GPL-2.0
+License: GPL-2
  This package 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 at version 2 of the License.
@@ -43,5 +67,5 @@ License: GPL-2.0
  You should have received a copy of the GNU General Public License
  along with this program. If not, see <https://www.gnu.org/licenses/>
  .
- On Debian systems, the complete text of the GNU General
- Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
+ On Debian systems, the complete text of the GNU General Public
+ License version 2 can be found in "/usr/share/common-licenses/GPL-2".


=====================================
debian/lintian-overrides
=====================================
@@ -0,0 +1,2 @@
+# see https://lists.debian.org/debian-med/2018/06/msg00043.html
+quast: script-with-language-extension usr/bin/*.*


=====================================
debian/patches/adjustPythonImportPaths.patch
=====================================
@@ -1,5 +1,7 @@
-Index: quast/quast_libs/run_busco.py
-===================================================================
+Author: Steffen Moeller
+Last-Update: 2020-06-24 18:05:32 +0200
+Description: Use Debian packaged busco
+
 --- quast.orig/quast_libs/run_busco.py
 +++ quast/quast_libs/run_busco.py
 @@ -13,7 +13,7 @@ import shutil
@@ -11,10 +13,3 @@ Index: quast/quast_libs/run_busco.py
  from quast_libs.log import get_logger
  from quast_libs.qutils import download_blast_binaries, run_parallel, compile_tool, get_dir_for_download, \
      check_prev_compilation_failed, get_blast_fpath
-@@ -241,4 +241,4 @@ def do(contigs_fpaths, output_dir, logge
-                 'Failed running BUSCO for ' + contigs_fpath + '. See the log for detailed information.')
-     if not qconfig.debug:
-         cleanup(output_dir)
--    logger.info('Done.')
-\ No newline at end of file
-+    logger.info('Done.')


=====================================
debian/patches/noBwa.patch
=====================================
@@ -1,5 +1,7 @@
-Index: quast/setup.py
-===================================================================
+Author: Steffen Moeller
+Last-Update: 2020-06-24 18:05:32 +0200
+Description: Use Debian packaged bwa
+
 --- quast.orig/setup.py
 +++ quast/setup.py
 @@ -34,11 +34,10 @@ except:


=====================================
debian/patches/pathonPaths.patch
=====================================
@@ -1,5 +1,7 @@
-Index: quast/dnanexus/src/quast.py
-===================================================================
+Author: Steffen Moeller
+Last-Update: 2020-06-24 18:05:32 +0200
+Description: Fix Python3 path
+
 --- quast.orig/dnanexus/src/quast.py
 +++ quast/dnanexus/src/quast.py
 @@ -1,4 +1,4 @@


=====================================
debian/rules
=====================================
@@ -13,3 +13,7 @@ override_dh_auto_clean:
 	rm -f quast_libs/version.py
 	# files generated while testing
 	rm -f quast_test_output/quast.log quast_test_output/quast_corrected_input/contigs_1.fasta quast_test_output/quast_corrected_input/contigs_2.fasta quast_test_output/quast_corrected_input/reference.fasta
+
+override_dh_install:
+	dh_install
+	find debian -name LICENSE.txt -delete



View it on GitLab: https://salsa.debian.org/med-team/quast/-/compare/84bbda79c0b456fd8c661d89e47acc91b6072a62...5ce9317b366ff6d08fed3e7f31219bcd7e1615f9

-- 
View it on GitLab: https://salsa.debian.org/med-team/quast/-/compare/84bbda79c0b456fd8c661d89e47acc91b6072a62...5ce9317b366ff6d08fed3e7f31219bcd7e1615f9
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20200626/280b295e/attachment-0001.html>
