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debian/changelog
View file @ 256b14c3
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@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@debian.org> Mon, 10 Sep 2018 19:37:49 +0000
spades (3.11.1+dfsg-2) unstable; urgency=medium
......
debian/control
View file @ 256b14c3
......@@ -3,7 +3,8 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
Uploaders: Andreas Tille <tille@debian.org>,
Afif Elghraoui <afif@debian.org>,
Sascha Steinbiss <satta@debian.org>,
Michael R. Crusoe <michael.crusoe@gmail.com>
Michael R. Crusoe <michael.crusoe@gmail.com>,
Alexandre Mestiashvili <mestia@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
View file @ 256b14c3
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@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@live.co.uk>
License: MIT
License: Expat
Files: ext/include/libcxx/sort.hpp
Copyright: LLVM Developers <llvm-dev@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/patches/0113_adjust_paths.patch deleted 100644 → 0
View file @ d4bd1d89
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@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
View file @ 256b14c3
Subject: Adjust spades_home var to install files under /usr/share/spades
From: Alex Mestiashvili <amestia@rsh2.donotuse.de>
Forwarded: not-needed
--- spades.orig/spades_init.py
+++ spades/spades_init.py
@@ -32,7 +32,7 @@
......
debian/patches/series
View file @ 256b14c3
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
View file @ 256b14c3
From: Michael R. Crusoe <michael.crusoe@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
View file @ 256b14c3
......@@ -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
View file @ 256b14c3
# Upstream does not provide signed tarballs
spades source: debian-watch-may-check-gpg-signature
spades source: debian-watch-does-not-check-gpg-signature