[med-svn] [Git][med-team/spades][master] 7 commits: Remove duplicated docs from /usr/share/spades
Alexandre Mestiashvili
gitlab at salsa.debian.org
Mon Sep 10 21:04:07 BST 2018
Alexandre Mestiashvili pushed to branch master at Debian Med / spades
Commits:
dfce4dfe by Alexandre Mestiashvili at 2018-09-10T19:15:48Z
Remove duplicated docs from /usr/share/spades
- - - - -
7ff1a40d by Alexandre Mestiashvili at 2018-09-10T19:23:44Z
Drop unused patch 0113_a.. , refresh patch header for 0018_a..
- - - - -
897663a8 by Alexandre Mestiashvili at 2018-09-10T19:27:22Z
Update d/patches/spelling
- - - - -
84a4b3a7 by Alexandre Mestiashvili at 2018-09-10T19:34:27Z
Bump Policy to 4.2.1, add myself to uploaders
- - - - -
d4305453 by Alexandre Mestiashvili at 2018-09-10T19:37:24Z
Use https for copyright Format field, s/MIT/Expat/
- - - - -
2b929396 by Alexandre Mestiashvili at 2018-09-10T19:47:45Z
Rename overridden tag to debian-watch-does-not-check-gpg-signature
- - - - -
256b14c3 by Alexandre Mestiashvili at 2018-09-10T19:48:35Z
Update changelog
Gbp-Dch: Ignore
- - - - -
10 changed files:
- debian/changelog
- debian/control
- debian/copyright
- debian/docs
- − debian/patches/0113_adjust_paths.patch
- debian/patches/0118_adjust_spades_home_again.patch
- debian/patches/series
- debian/patches/spelling
- debian/rules
- debian/source.lintian-overrides
Changes:
=====================================
debian/changelog
=====================================
@@ -1,12 +1,26 @@
-spades (3.12.0+dfsg-1) UNRELEASED; urgency=medium
+spades (3.12.0+dfsg-1) unstable; urgency=medium
+ [ Andreas Tille ]
* New upstream version
Closes: #897867
* Fix watch file
- * Standards-Version: 4.1.5
* Add dh-python
- -- Andreas Tille <tille at debian.org> Wed, 18 Jul 2018 07:49:49 +0200
+ [ Alexandre Mestiashvili ]
+ * Add tmp link for tests for spades-bwa
+ * Update override_dh_auto_test: implement a workaround so dh_auto_test
+ can access data files
+ * Add bwa to d/tests/control
+ * Remove *.pyc files
+ * Add patch 0118_adjust_spades_home_again.patch
+ replacing 0113_adjust_paths.patch
+ * Update d/patches/spelling
+ * Remove duplicated docs from /usr/share/spades
+ * Bump Policy to 4.2.1, add myself to uploaders
+ * Use https for copyright Format field, s/MIT/Expat/
+ * Rename overridden tag to debian-watch-does-not-check-gpg-signature
+
+ -- Alexandre Mestiashvili <mestia at debian.org> Mon, 10 Sep 2018 19:37:49 +0000
spades (3.11.1+dfsg-2) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -3,7 +3,8 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Andreas Tille <tille at debian.org>,
Afif Elghraoui <afif at debian.org>,
Sascha Steinbiss <satta at debian.org>,
- Michael R. Crusoe <michael.crusoe at gmail.com>
+ Michael R. Crusoe <michael.crusoe at gmail.com>,
+ Alexandre Mestiashvili <mestia at debian.org>
Section: science
Priority: optional
Build-Depends: debhelper (>= 11~),
@@ -27,7 +28,7 @@ Build-Depends: debhelper (>= 11~),
bwa,
libbwa-dev,
lynx
-Standards-Version: 4.1.5
+Standards-Version: 4.2.1
Vcs-Browser: https://salsa.debian.org/med-team/spades
Vcs-Git: https://salsa.debian.org/med-team/spades.git
Homepage: http://cab.spbu.ru/software/spades/
=====================================
debian/copyright
=====================================
@@ -1,4 +1,4 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: SPAdes
Upstream-Contact: spades.support at bioinf.spbau.ru
Source: http://spades.bioinf.spbau.ru/
@@ -49,24 +49,6 @@ License: GPL-2+
Comment:
Assumed to be under GPL-2+ due to upstream's source header.
-License: GPL-2+
- 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.
- .
- 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.
- .
- You should have received a copy of the GNU General Public License along
- with this program; if not, write to the Free Software Foundation, Inc.,
- 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- .
- On Debian systems you can find the full test of the GNU General Public
- License version 2 at /usr/share/common-licenses/GPL-2.
-
Files: src/projects/hammer/parallel_radix_sort.hpp
Copyright: (c) 2010 Takuya Akiba
License: BSD-3-clause-Akiba
@@ -176,47 +158,19 @@ Copyright: (c) 2003-2015 University of Illinois at Urbana-Champaign.
All rights reserved.
License: UoI-NCSA
-License: UoI-NCSA
- Permission is hereby granted, free of charge, to any person obtaining a copy of
- this software and associated documentation files (the "Software"), to deal with
- 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:
- .
- * Redistributions of source code must retain the above copyright notice,
- this list of conditions and the following disclaimers.
- .
- * Redistributions in binary form must reproduce the above copyright notice,
- this list of conditions and the following disclaimers in the
- documentation and/or other materials provided with the distribution.
- .
- * Neither the names of the LLVM Team, University of Illinois at
- Urbana-Champaign, nor the names of its contributors may be used to
- endorse or promote products derived from this Software without specific
- prior written permission.
- .
- 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
- CONTRIBUTORS 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 WITH THE
- SOFTWARE.
-
Files: ext/include/bamtools/*
ext/src/bamtools/*
Copyright: (c) 2009-2010 Derek Barnett, Erik Garrison, Gabor Marth, Michael Stromberg
-License: MIT
+License: Expat
Files: ext/include/kseq/*
ext/src/samtools/bcftools/kmin.*
Copyright: (c) 2008-2011 Attractive Chaos <attractor at live.co.uk>
-License: MIT
+License: Expat
Files: ext/include/libcxx/sort.hpp
Copyright: LLVM Developers <llvm-dev at lists.llvm.org>
-License: MIT
+License: Expat
Comment: This file is taken from LLVM's libc++.
See http://llvm.org/docs/DeveloperPolicy.html#license.
@@ -225,73 +179,27 @@ Copyright: (c) 1992, 1993, 1994 Henry Spencer.
(c) 1992, 1993, 1994 The Regents of the University of California. All rights reserved.
License: BSD-3-clause
-License: BSD-3-clause
- 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 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 materials provided with the distribution.
- 3. The names of its contributors may not be used to endorse or promote
- products derived from this software without specific prior written
- permission.
- .
- 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 OWNER 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.
-
Files: ext/src/samtools/*
Copyright: (c) 2008-2009 Genome Research Ltd.
(c) 2003-2006, 2008-2010 Heng Li
(c) 2008 Broad Institute / Massachusetts Institute of Technology
-License: MIT
+License: Expat
Files: ext/include/city/*
ext/src/cityhash/*
Copyright: (c) 2011 Google, Inc.
-License: MIT
+License: Expat
Files: ext/include/cxxopts/*
Copyright: (c) 2014, 2015, 2016 Jarryd Beck
-License: MIT
+License: Expat
Files: ext/include/boomphf/BooPHF.h
Copyright: (c) 2015 Guillaume Rizk
-License: MIT
+License: Expat
Comment:
MIT licensed as part of BBHash (https://github.com/rizkg/BBHash)
-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: ext/include/btree/*
Copyright: 2013 Google Inc.
License: Apache-2
@@ -304,19 +212,6 @@ Files: ext/include/cuckoo/*
Copyright: 2013, Carnegie Mellon University and Intel Corporation
License: Apache-2
-License: Apache-2
- Licensed under the Apache License, Version 2.0 (the "License");
- you may not use this file except in compliance with the License.
- You may obtain a copy of the License at
- .
- http://www.apache.org/licenses/LICENSE-2.0
- .
- Unless required by applicable law or agreed to in writing, software
- distributed under the License is distributed on an "AS IS" BASIS,
- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- See the License for the specific language governing permissions and
- limitations under the License.
-
Files: ext/include/cppformat/*
ext/src/cppformat/*
Copyright: (c) 2012-2014 Victor Zverovich
@@ -328,48 +223,11 @@ Copyright: (c) 2015 Saint Petersburg State University
(c) 2011 Dmitry Vyukov. All rights reserved.
License: BSD-2-clause
-License: BSD-2-clause
- 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 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 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 OWNER 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.
-
Files: ext/include/getopt_pp/*
ext/src/getopt_pp/*
Copyright: (C) 2007, 2008 Daniel Gutson, FuDePAN
License: GPL-3+
-License: GPL-3+
- 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 3 of the License, or (at your option) any later
- version.
- .
- 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.
- .
- You should have received a copy of the GNU General Public License along with
- this program. If not, see <http://www.gnu.org/licenses/>.
- .
- On Debian systems, the complete text of the GNU General
- Public License can be found in `/usr/share/common-licenses/GPL-3'.
-
Files: src/cmake/Modules/GetGitRevisionDescription.*
Copyright: 2009-2010 Iowa State University
License: Boost-1
@@ -447,3 +305,145 @@ License: BSDlike-libbzip2
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: Apache-2
+ Licensed under the Apache License, Version 2.0 (the "License");
+ you may not use this file except in compliance with the License.
+ You may obtain a copy of the License at
+ .
+ http://www.apache.org/licenses/LICENSE-2.0
+ .
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
+
+License: BSD-2-clause
+ 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 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 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 OWNER 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: BSD-3-clause
+ 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 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 materials provided with the distribution.
+ 3. The names of its contributors may not be used to endorse or promote
+ products derived from this software without specific prior written
+ permission.
+ .
+ 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 OWNER 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: 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 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.
+
+License: GPL-2+
+ 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.
+ .
+ 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.
+ .
+ You should have received a copy of the GNU General Public License along
+ with this program; if not, write to the Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ .
+ On Debian systems you can find the full test of the GNU General Public
+ License version 2 at /usr/share/common-licenses/GPL-2.
+
+License: GPL-3+
+ 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 3 of the License, or (at your option) any later
+ version.
+ .
+ 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.
+ .
+ You should have received a copy of the GNU General Public License along with
+ this program. If not, see <http://www.gnu.org/licenses/>.
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License can be found in `/usr/share/common-licenses/GPL-3'.
+
+License: UoI-NCSA
+ Permission is hereby granted, free of charge, to any person obtaining a copy of
+ this software and associated documentation files (the "Software"), to deal with
+ 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:
+ .
+ * Redistributions of source code must retain the above copyright notice,
+ this list of conditions and the following disclaimers.
+ .
+ * Redistributions in binary form must reproduce the above copyright notice,
+ this list of conditions and the following disclaimers in the
+ documentation and/or other materials provided with the distribution.
+ .
+ * Neither the names of the LLVM Team, University of Illinois at
+ Urbana-Champaign, nor the names of its contributors may be used to
+ endorse or promote products derived from this Software without specific
+ prior written permission.
+ .
+ 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
+ CONTRIBUTORS 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 WITH THE
+ SOFTWARE.
=====================================
debian/docs
=====================================
@@ -1 +1,2 @@
*manual.html
+manual.md
=====================================
debian/patches/0113_adjust_paths.patch deleted
=====================================
@@ -1,53 +0,0 @@
-Description: adjust runtime paths
- Debian stores components od SPAdes in different places than expected by
- upstream. This patch makes it look in the right locations.
-Author: Sascha Steinbiss <satta at debian.org>
---- a/spades_init.py
-+++ b/spades_init.py
-@@ -29,7 +29,12 @@ def init():
- global ext_python_modules_home
-
- # users configuration (spades_init.py and spades binary are in the same directory)
-- if isfile(os.path.join(spades_home, 'spades-core')):
-+ if os.path.isfile('/usr/lib/spades/bin/spades'):
-+ bin_home = '/usr/lib/spades/bin/'
-+ spades_home = '/usr/share/spades'
-+ python_modules_home = spades_home
-+ ext_python_modules_home = spades_home
-+ elif os.path.isfile(os.path.join(spades_home, 'spades')):
- install_prefix = dirname(spades_home)
- bin_home = join(install_prefix, 'bin')
- spades_home = join(install_prefix, 'share', 'spades')
-@@ -44,4 +49,3 @@ def init():
-
- if __name__ == '__main__':
- spades_py_path = join(dirname(realpath(__file__)), 'spades.py')
-- sys.stderr.write('Please use ' + spades_py_path + ' for running SPAdes genome assembler\n')
---- a/truspades.py
-+++ b/truspades.py
-@@ -13,8 +13,14 @@ import sys
- import shutil
- import spades_init
- spades_init.init()
--truspades_home = spades_init.spades_home
--spades_home = os.path.abspath(os.path.dirname(os.path.realpath(__file__)))
-+
-+if os.path.isfile('/usr/lib/spades/bin/spades'):
-+ truspades_home = '/usr/share/spades'
-+ spades_home = '/usr/lib/spades/bin/'
-+else:
-+ truspades_home = spades_init.spades_home
-+ spades_home = os.path.abspath(os.path.dirname(os.path.realpath(__file__)))
-+
- spades_version = spades_init.spades_version
-
- import SeqIO # TODO: add to ext/scr/python_libs
-@@ -90,7 +96,7 @@ class ReferenceConstructionLauncher:
- def __call__(self, barcode_id):
- reference_construction.CounstructSubreference(os.path.join(self.sam_dir, barcode_id + ".sam"), reference_construction.ReadReference(self.reference), os.path.join(self.result_dir, barcode_id))
- return 0
--
-+
- def ConstructSubreferences(dataset, options):
- reference_construction.ConstructSubreferences(dataset, options.reference, options.output_dir, options.index, options.threads, log = None)
-
=====================================
debian/patches/0118_adjust_spades_home_again.patch
=====================================
@@ -1,3 +1,6 @@
+Subject: Adjust spades_home var to install files under /usr/share/spades
+From: Alex Mestiashvili <amestia at rsh2.donotuse.de>
+Forwarded: not-needed
--- spades.orig/spades_init.py
+++ spades/spades_init.py
@@ -32,7 +32,7 @@
=====================================
debian/patches/series
=====================================
@@ -1,4 +1,3 @@
-0118_adjust_spades_home_again.patch
0002_use_debian_packaged_python-joblib.patch
0003_accept-system-bwa.patch
0101_cmake_ignore_removed_python-yaml.patch
@@ -16,6 +15,7 @@
0111_use_full_config_dirs.patch
0116_stable_link_order.patch
0117_build_with_debug.patch
+0118_adjust_spades_home_again.patch
fix-bool-cast
spelling
gcc7.patch
=====================================
debian/patches/spelling
=====================================
@@ -1,8 +1,8 @@
From: Michael R. Crusoe <michael.crusoe at gmail.com>
Subject: Spelling fixes
---- a/manual.html
-+++ b/manual.html
-@@ -750,7 +750,7 @@ For each file you should provide its ful
+--- spades.orig/manual.html
++++ spades/manual.html
+@@ -750,7 +750,7 @@
Make sure that files with right reads are given in the same order as corresponding files with left reads.
<p>
@@ -11,7 +11,7 @@ Subject: Spelling fixes
<pre class="code">
<code>
lib_pe1_left_1.fastq
-@@ -979,7 +979,7 @@ and PacBio CCS and CLR reads:
+@@ -979,7 +979,7 @@
</pre>
<p>
@@ -20,7 +20,7 @@ Subject: Spelling fixes
<pre class="code">
<code>
-@@ -1128,7 +1128,7 @@ Then, <code>contigs.paths</code> will co
+@@ -1128,7 +1128,7 @@
</pre>
<p>
@@ -29,9 +29,9 @@ Subject: Spelling fixes
<pre>
<code>
NODE_3_length_237403_cov_243.207_ID_45
---- a/src/common/assembly_graph/stats/picture_dump.hpp
-+++ b/src/common/assembly_graph/stats/picture_dump.hpp
-@@ -123,7 +123,7 @@ class GenomeMappingStat: public Abstract
+--- spades.orig/src/common/assembly_graph/stats/picture_dump.hpp
++++ spades/src/common/assembly_graph/stats/picture_dump.hpp
+@@ -123,7 +123,7 @@
INFO("Genome mapping results:");
INFO("Covered k+1-mers:" << covered_kp1mers << " of " << (genome_.size() - k_) << " which is "
<< (100.0 * (double) covered_kp1mers / (double) (genome_.size() - k_)) << "%");
@@ -40,9 +40,9 @@ Subject: Spelling fixes
INFO("Continuity failtures " << fail);
}
};
---- a/src/projects/dipspades/kmer_gluing/equal_sequence_gluer.hpp
-+++ b/src/projects/dipspades/kmer_gluing/equal_sequence_gluer.hpp
-@@ -74,9 +74,9 @@ private:
+--- spades.orig/src/projects/dipspades/kmer_gluing/equal_sequence_gluer.hpp
++++ spades/src/projects/dipspades/kmer_gluing/equal_sequence_gluer.hpp
+@@ -74,9 +74,9 @@
pos2 = graph_.length(edge1) - tmp - 1;
}
INFO(pos1 << " " << pos2 << " " << graph_.length(edge1))
@@ -54,9 +54,9 @@ Subject: Spelling fixes
TRACE("New edge1: " << graph_.int_id(split_edges.first) << ", length: " << graph_.length(split_edges.first));
TRACE("New edge2: " << graph_.int_id(split_edges.second) << ", length: " << graph_.length(split_edges.second));
edge1 = split_edges.first;
---- a/src/projects/dipspades/polymorphic_bulge_remover/bulge_gluer.hpp
-+++ b/src/projects/dipspades/polymorphic_bulge_remover/bulge_gluer.hpp
-@@ -74,7 +74,7 @@ public:
+--- spades.orig/src/projects/dipspades/polymorphic_bulge_remover/bulge_gluer.hpp
++++ spades/src/projects/dipspades/polymorphic_bulge_remover/bulge_gluer.hpp
+@@ -74,7 +74,7 @@
auto splitted_bulge = splitter_.SplitBulge(directed_bulge, glue_def_res);
if(IsSplittedBulgeCorrect(splitted_bulge)){
@@ -65,9 +65,9 @@ Subject: Spelling fixes
GlueSplittedBulge(splitted_bulge);
return true;
}
---- a/src/projects/dipspades/polymorphic_bulge_remover/bulge_splitter.hpp
-+++ b/src/projects/dipspades/polymorphic_bulge_remover/bulge_splitter.hpp
-@@ -260,7 +260,7 @@ class SubpathsSplitter {
+--- spades.orig/src/projects/dipspades/polymorphic_bulge_remover/bulge_splitter.hpp
++++ spades/src/projects/dipspades/polymorphic_bulge_remover/bulge_splitter.hpp
+@@ -260,7 +260,7 @@
SplitOppositeEdge(split_res, split_paths.second, split_partlens.second);
// update non splitted path
@@ -76,7 +76,7 @@ Subject: Spelling fixes
if(num_splits.second != 0){
size_t edge_ind = vertices_to_split_[indexes.first].edge_ind_ + 1;
split_paths.first.push_back(default_paths.first[edge_ind]);
-@@ -298,7 +298,7 @@ class SubpathsSplitter {
+@@ -298,7 +298,7 @@
set<size_t> processed_indices;
while(num_done_splits < num_splits_.first + num_splits_.second){
@@ -85,7 +85,7 @@ Subject: Spelling fixes
vertices_to_split_[split_index].owner_path_);
size_t opposite_index = IndexFirstOppositeEdge(split_index, processed_indices);
-@@ -418,8 +418,8 @@ public:
+@@ -418,8 +418,8 @@
if(!PerformSplitting(range1, range2))
return SplitResult(graph_);
@@ -96,7 +96,7 @@ Subject: Spelling fixes
return SplitResult(graph_, split_paths_.first, split_paths_.second);
}
-@@ -445,7 +445,7 @@ public:
+@@ -445,7 +445,7 @@
auto split_res = spaths_splitter.SplitSubpaths(
subpath_range(0, bulge->path1().size() - 1),
subpath_range(0, bulge->path2().size() - 1));
@@ -105,9 +105,9 @@ Subject: Spelling fixes
TRACE("1st new bulge side - " << SimplePathWithVerticesToString(graph_, split_res.path1()));
TRACE("2nd new bulge side - " << SimplePathWithVerticesToString(graph_, split_res.path2()));
return shared_ptr<BaseBulge>(new Bulge(graph_, graph_.k(), split_res.path1(), split_res.path2()));
---- a/src/common/modules/alignment/pacbio/pac_index.hpp
-+++ b/src/common/modules/alignment/pacbio/pac_index.hpp
-@@ -376,7 +376,7 @@ public:
+--- spades.orig/src/common/modules/alignment/pacbio/pac_index.hpp
++++ spades/src/common/modules/alignment/pacbio/pac_index.hpp
+@@ -376,7 +376,7 @@
auto next_iter = iter + 1;
if (next_iter == cur_cluster.end() || !IsConsistent(**iter, **next_iter)) {
if (next_iter != cur_cluster.end()) {
@@ -116,3 +116,14 @@ Subject: Spelling fixes
DEBUG("on "<< (*iter)->str(g_));
DEBUG("and " << (*next_iter)->str(g_));
}
+--- spades.orig/src/projects/hammer/hamcluster.cpp
++++ spades/src/projects/hammer/hamcluster.cpp
+@@ -173,7 +173,7 @@
+
+ size_t big_blocks2 = 0;
+ {
+- INFO("Spliting sub-kmers, pass 2.");
++ INFO("Splitting sub-kmers, pass 2.");
+ SubKMerSplitter Splitter(bfname, kfname);
+ size_t nblocks = 0;
+ std::pair<size_t, size_t> stat =
=====================================
debian/rules
=====================================
@@ -88,6 +88,8 @@ override_dh_install:
override_dh_installdocs:
dh_installdocs
+ rm -f debian/$(DEB_SOURCE)/usr/share/spades/*.html
+ rm -f debian/$(DEB_SOURCE)/usr/share/spades/manual.md
override_dh_installchangelogs:
LANG="C" LANGUAGE="en_US:en" LC_ALL=C.UTF-8 lynx -dump changelog.html > changelog
=====================================
debian/source.lintian-overrides
=====================================
@@ -1,2 +1,2 @@
# Upstream does not provide signed tarballs
-spades source: debian-watch-may-check-gpg-signature
+spades source: debian-watch-does-not-check-gpg-signature
View it on GitLab: https://salsa.debian.org/med-team/spades/compare/d4bd1d8988a60b6e9129b98133b436534be3f0a7...256b14c37019433db4006ee7f3788ce72846bb99
--
View it on GitLab: https://salsa.debian.org/med-team/spades/compare/d4bd1d8988a60b6e9129b98133b436534be3f0a7...256b14c37019433db4006ee7f3788ce72846bb99
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