Andreas Tille pushed to branch master at Debian Med / sibelia
Commits:
92d4b42f by Andreas Tille at 2020-03-26T06:16:04+01:00
Fix copyright
- - - - -
7e4092a6 by Andreas Tille at 2020-03-26T07:34:51+01:00
Fix LAGAN_DIR
- - - - -
a2784e34 by Andreas Tille at 2020-03-26T07:38:27+01:00
Add missing line
- - - - -
2 changed files:
- debian/copyright
- debian/patches/use_debian_packaged_lagan.patch
Changes:
=====================================
debian/copyright
=====================================
@@ -15,6 +15,35 @@ Copyright: 2011-2018 Saint-Petersburg Academic University
Ilya Minkin, Nikolay Vyahhi, Mikhail Kolmogorov, Son Pham
License: GPL-2
+Files: src/resource.cpp
+Copyright: 2001 Robert Penner
+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:
+ .
+ - Redistributions of source code must retain the above copyright notice, this
+ list of conditions and the following disclaimer.
+ .
+ - 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.
+ .
+ - Neither the name of the author nor the names of contributors may 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: debian/*
Copyright: 2019 Andreas Tille <[email protected]>
License: GPL-2
=====================================
debian/patches/use_debian_packaged_lagan.patch
=====================================
@@ -13,3 +13,14 @@ Description: Use Debian packaged lagan
install(PROGRAMS csibelia/C-Sibelia.py DESTINATION bin)
install(PROGRAMS annotation/snpEffAnnotate.py DESTINATION bin)
install(DIRECTORY annotation/snpEff DESTINATION ${LIB_DIR})
+--- a/src/csibelia/C-Sibelia.py
++++ b/src/csibelia/C-Sibelia.py
+@@ -20,7 +20,7 @@ LINE_LENGTH = 60
+ MINIMUM_CONTEXT_SIZE = 30
+ BLOCKS_FILE = 'blocks_sequences.fasta'
+ INSTALL_DIR = os.path.dirname(os.path.abspath(__file__))
+-LAGAN_DIR = os.path.join(INSTALL_DIR, '..', 'lib', 'Sibelia', 'lagan')
++LAGAN_DIR = '/usr/bin'
+ os.environ['LAGAN_DIR'] = LAGAN_DIR
+
+ FastaRecord = collections.namedtuple('FastaRecord', ['seq', 'description',
'id'])
View it on GitLab:
https://salsa.debian.org/med-team/sibelia/-/compare/95f9bf96514cbb8bfdc6584223c58f0ef3aba719...a2784e346df07096e0352f27f24f2a5d2e752868
--
View it on GitLab:
https://salsa.debian.org/med-team/sibelia/-/compare/95f9bf96514cbb8bfdc6584223c58f0ef3aba719...a2784e346df07096e0352f27f24f2a5d2e752868
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