[med-svn] [Git][med-team/bcalm][master] 6 commits: Build-Depends: cmake
Andreas Tille
gitlab at salsa.debian.org
Fri Sep 27 08:07:10 BST 2019
Andreas Tille pushed to branch master at Debian Med / bcalm
Commits:
a3fe863a by Andreas Tille at 2019-09-27T06:46:57Z
Build-Depends: cmake
- - - - -
e829cacf by Andreas Tille at 2019-09-27T06:48:32Z
Enhance description
- - - - -
575677e2 by Andreas Tille at 2019-09-27T06:49:21Z
Standards-Version: 4.4.0
- - - - -
a890c94f by Andreas Tille at 2019-09-27T06:49:21Z
Remove trailing whitespace in debian/copyright
- - - - -
cb8c4ab6 by Andreas Tille at 2019-09-27T06:55:22Z
Cleanup after `routine-update --force`
- - - - -
351f9bdf by Andreas Tille at 2019-09-27T07:07:01Z
Force export LC_ALL=C.UTF-8 ... which does not help
- - - - -
4 changed files:
- debian/changelog
- debian/control
- debian/copyright
- debian/tests/run-unit-test
Changes:
=====================================
debian/changelog
=====================================
@@ -2,4 +2,4 @@ bcalm (2.2.1-1) UNRELEASED; urgency=medium
* Initial release (Closes: #<bug>)
- -- Shayan Doust <hello at shayandoust.me> Mon, 23 Sep 2019 05:48:54 +0100
+ -- Shayan Doust <hello at shayandoust.me> Fri, 27 Sep 2019 08:49:22 +0200
=====================================
debian/control
=====================================
@@ -4,11 +4,12 @@ Uploaders: Shayan Doust <hello at shayandoust.me>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 12),
- libgatbcore-dev,
- libboost-dev,
- libhdf5-dev,
- zlib1g-dev
-Standards-Version: 4.3.0
+ libgatbcore-dev,
+ libboost-dev,
+ libhdf5-dev,
+ zlib1g-dev,
+ cmake
+Standards-Version: 4.4.0
Vcs-Browser: https://salsa.debian.org/med-team/bcalm
Vcs-Git: https://salsa.debian.org/med-team/bcalm.git
Homepage: https://github.com/GATB/bcalm
@@ -17,7 +18,10 @@ Package: bcalm
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends},
- libgatbcore2
+ libgatbcore2
Description: de Bruijn compaction in low memory
A bioinformatics tool for constructing the compacted de Bruijn graph
from sequencing data.
+ .
+ This is the parallel version of the BCALM software using gatb-core
+ library.
=====================================
debian/copyright
=====================================
@@ -7,10 +7,10 @@ Copyright: 2014 INRIA <https://inria.fr/>
2018 Rayan Chikhi, Antoine Limasset, Paul Medvedev
License: Expat
-Files: thirdparty/concurrentqueue.h
+Files: thirdparty/concurrentqueue.h
thirdparty/lockbasedqueue.h
thirdparty/lockstdqueue.h
- thirdparty/lockstdvector.h
+ thirdparty/lockstdvector.h
Copyright: 2013-2014 Cameron Desrochers
License: BSD-2-Clause
@@ -23,24 +23,24 @@ Copyright: 2019 Shayan Doust <hello at shayandoust.me>
License: Expat
License: BSD-2-Clause
- Redistribution and use in source and binary forms, with or without modification,
+ Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
.
- 1. Redistributions of source code must retain the above copyright notice, this list
+ 1. Redistributions of source code must retain the above copyright notice, this list
of conditions and the following disclaimer.
.
- 2. Redistributions in binary form must reproduce the above copyright notice, this
- list of conditions and the following disclaimer in the documentation and/or other
+ 2. Redistributions in binary form must reproduce the above copyright notice, this
+ list of conditions and the following disclaimer in the documentation and/or other
materials provided with the distribution.
.
- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY
- EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT
- SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
- SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
- OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
- HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
- OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY
+ EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT
+ SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
License: zlib/libpng
@@ -64,19 +64,19 @@ License: zlib/libpng
distribution.
License: Expat
- 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
+ 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
+ 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.
+ 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/tests/run-unit-test
=====================================
@@ -3,6 +3,7 @@ set -e
pkg=bcalm
+export LC_ALL=C.UTF-8
if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
# shellcheck disable=SC2064
View it on GitLab: https://salsa.debian.org/med-team/bcalm/compare/534b1255b0bcc28a89e18dbc0ad50daa657fae00...351f9bdfa72d02f6e4be6c1fb997b7d60097f16b
--
View it on GitLab: https://salsa.debian.org/med-team/bcalm/compare/534b1255b0bcc28a89e18dbc0ad50daa657fae00...351f9bdfa72d02f6e4be6c1fb997b7d60097f16b
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