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debian/changelog
View file @ c4041866
......@@ -2,11 +2,14 @@ salmon (0.12.0+ds1-1) UNRELEASED; urgency=medium
* Team upload.
* New upstream version
Closes: #909767
* debhelper 11
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.2.1
* Remove debian/gbp.conf
* Build-Depends: libbz2-dev, liblzma-dev
* Use python3-sphinx exclusively
* Do not parse d/changelog
-- Andreas Tille <tille@debian.org> Tue, 11 Dec 2018 19:29:39 +0100
......
debian/control
View file @ c4041866
......@@ -27,8 +27,8 @@ Build-Depends: debhelper (>= 11~),
libtclap-dev,
help2man,
sphinx-doc,
python-sphinx | python3-sphinx,
python-sphinx-rtd-theme | python3-sphinx-rtd-theme,
python3-sphinx,
python3-sphinx-rtd-theme,
zlib1g-dev,
libeigen3-dev,
libbz2-dev,
......
debian/copyright
View file @ c4041866
......@@ -36,15 +36,8 @@ Copyright: (c) 2014 Thomas Heller
(c) 2003-2012 Christopher M. Kohlhoff <chris@kohlhoff.com>
License: BSL-1.0
Files: include/btree*.h
include/safe_btree*.h
Copyright: 2013 Google Inc.
License: Apache-2.0
Files: include/ezETAProgressBar.hpp
include/fastapprox.h
src/bwtindex.c
src/is.c
Copyright: 2011, 2012 Remik Ziemlinski
2011, 2012 Paul Mineiro <paul@mineiro.com>
(c) 2008 Genome Research Ltd (GRL)
......@@ -52,53 +45,15 @@ Copyright: 2011, 2012 Remik Ziemlinski
License: Expat
Files: include/format.h
src/format.cc
Copyright: (c) 2012 - 2015, Victor Zverovich
License: BSD-2-clause
Files: src/QSufSort.c
Copyright: 1999, N. Jesper Larsson <jesper@cs.lth.se>
License: other
This software may be used freely for any purpose. However, when distributed,
the original source must be clearly stated, and, when the source code is
distributed, the copyright notice must be retained and any alterations in
the code must be clearly marked. No warranty is given regarding the quality
of this software
Files: include/atomicops.h
include/concurrentqueue.h
include/readerwriterqueue.h
Copyright: ©2013 Cameron Desrochers
License: BSD-cameron-descrochers
Files: debian/rapmap/*
Copyright: (c) 2014-2016 COMputational BIology and Network Evolution lab
License: GPL-3+
Comment:
Taken from RapMap (https://github.com/COMBINE-lab/RapMap) with the following
license statement:
Since RapMap uses Jellyfish, it must be released under the GPL.
However, this is currently the only GPL dependency. If it can be
replaced, I'd like to re-license RapMap under the BSD license. I'd be
happy to accept pull-requests that replace the Jellyfish components
with a library released under a more liberal license (BSD-compatible).
Files: debian/rapmap/BooPHF.hpp
Copyright: ©2015 Guillaume Rizk
License: Expat
Comment:
This project is now BBHash, see
https://github.com/rizkg/BBHash/blob/master/LICENSE.
Files: debian/rapmap/kseq.h
Copyright: (c) 2008, 2009, 2011 Attractive Chaos <attractor@live.co.uk>
License: Expat
Files: debian/rapmap/macros.h
debian/rapmap/rank9b.*
Copyright: ©2007-2013 Sebastiano Vigna
License: LGPL-3+
License: BSD-cameron-descrochers
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
......@@ -159,23 +114,6 @@ License: GPL-3+
License version 3 can be found in the file
`/usr/share/common-licenses/GPL-3'.
License: LGPL-3+
This library is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published by the
Free Software Foundation; either version 3 of the License, or (at your option)
any later version.
.
This library 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 Lesser General Public License
for more details.
.
You should have received a copy of the GNU Lesser General Public License
along with this program; if not, see <http://www.gnu.org/licenses/>.
.
On Debian systems, the full text of the GNU Lesser General Public License
version 3 can be found in the file `/usr/share/common-licenses/LGPL-3'.
License: BSL-1.0
Permission is hereby granted, free of charge, to any person or organization
obtaining a copy of the software and accompanying documentation covered by this
......@@ -199,22 +137,6 @@ License: BSL-1.0
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.
License: Apache-2.0
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.
.
On Debian systems, the full text of the Apache License, Version 2.0 can be
found in the file `/usr/share/common-licenses/Apache-2.0'
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:
......
debian/patches/use_debian_packaged_libs.patch
View file @ c4041866
Author: Andreas Tille <tille@debian.org>
Last-Update: Tue, 11 Dec 2018 19:29:39 +0100
Description: Use Debian packaged libraries and make sure these are linked dynamically
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -477,6 +477,7 @@ message("BOOST LIBRARIES = ${Boost_LIBRA
......@@ -76,3 +80,85 @@
set(FAST_MALLOC_LIB "")
set(HAVE_FAST_MALLOC FALSE)
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -1,6 +1,6 @@
include_directories(
${GAT_SOURCE_DIR}/include
-${GAT_SOURCE_DIR}/include/eigen3
+/usr/include/eigen3
${GAT_SOURCE_DIR}/external
${GAT_SOURCE_DIR}/external/cereal/include
${GAT_SOURCE_DIR}/external/install/include
@@ -8,8 +8,8 @@ ${GAT_SOURCE_DIR}/external/install/inclu
${ZLIB_INCLUDE_DIR}
${TBB_INCLUDE_DIRS}
${Boost_INCLUDE_DIRS}
-${GAT_SOURCE_DIR}/external/install/include/rapmap
-${GAT_SOURCE_DIR}/external/install/include/rapmap/digestpp
+/usr/include/rapmap
+/usr/include/rapmap/digestpp
${ICU_INC_DIRS}
)
@@ -199,8 +199,8 @@ add_executable(unitTests ${UNIT_TESTS_SR
#set_target_properties(salmon_core salmon PROPERTIES LINK_SEARCH_END_STATIC TRUE)
# our suffix array construction libraries
-set (SUFFARRAY_LIB ${GAT_SOURCE_DIR}/external/install/lib/libdivsufsort.a)
-set (SUFFARRAY64_LIB ${GAT_SOURCE_DIR}/external/install/lib/libdivsufsort64.a)
+set (SUFFARRAY_LIB divsufsort)
+set (SUFFARRAY64_LIB divsufsort64)
# Link the executable
@@ -209,20 +209,20 @@ target_link_libraries(salmon
salmon_core
alevin_core
gff
- ${Boost_LIBRARIES}
+ boost_iostreams boost_filesystem boost_system boost_timer boost_chrono boost_program_options boost_regex
${ICU_LIBS}
- ${GAT_SOURCE_DIR}/external/install/lib/libstaden-read.a
- ${ZLIB_LIBRARY}
+ staden-read
+ z
${SUFFARRAY_LIB}
${SUFFARRAY64_LIB}
#${GAT_SOURCE_DIR}/external/install/lib/libbwa.a
m
- ${LIBLZMA_LIBRARIES}
+ lzma
${BZIP2_LIBRARIES}
- ${TBB_LIBRARIES}
+ tbb tbbmalloc
${LIBSALMON_LINKER_FLAGS}
${NON_APPLECLANG_LIBS}
- ${FAST_MALLOC_LIB}
+ jemalloc
${LIBRT}
ksw2pp
${CMAKE_DL_LIBS}
@@ -234,17 +234,17 @@ target_link_libraries(unitTests
salmon_core
alevin_core
gff
- ${Boost_LIBRARIES}
+ boost_iostreams boost_filesystem boost_system boost_timer boost_chrono boost_program_options boost_regex
${ICU_LIBS}
- ${GAT_SOURCE_DIR}/external/install/lib/libstaden-read.a
- ${ZLIB_LIBRARY}
+ staden-read
+ z
${SUFFARRAY_LIB}
${SUFFARRAY64_LIB}
#${GAT_SOURCE_DIR}/external/install/lib/libbwa.a
m
- ${LIBLZMA_LIBRARIES}
+ lzma
${BZIP2_LIBRARIES}
- ${TBB_LIBRARIES}
+ tbb tbbmalloc
${LIBSALMON_LINKER_FLAGS}
${NON_APPLECLANG_LIBS}
${LIBRT}
debian/rules
View file @ c4041866
......@@ -2,8 +2,7 @@
# DH_VERBOSE := 1
DEBVERS := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}')
VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//')
include /usr/share/dpkg/default.mk
# Fails to build when trying to enhance hardening
export DEB_BUILD_MAINT_OPTIONS = hardening=+bindnow
......@@ -14,11 +13,13 @@ CMAKE_EXTRA_FLAGS += -DDEBIAN_BUILD=1 \
-DBZIP2_LIBRARIES=-lbz2 \
-DBZIP2_INCLUDE_DIR=/usr/include \
-DLIBLZMA_INCLUDE_DIR=/usr/include/ \
-DLIBLZMA_LIBRARY=-llzma \
-DLIBLZMA_LIBRARY=lzma \
-DLIBLZMA_HAS_AUTO_DECODER=1 \
-DLIBLZMA_HAS_EASY_ENCODER=1 \
-DLIBLZMA_HAS_LZMA_PRESET=1 \
-DCMAKE_MODULE_PATH=/usr/share/cmake/Modules
-DCMAKE_MODULE_PATH=/usr/share/cmake/Modules \
-DTBB_WILL_RECONFIGURE=FALSE \
-DBOOST_WILL_RECONFIGURE=FALSE
%:
dh $@ --with sphinxdoc
......@@ -28,31 +29,6 @@ override_dh_auto_configure:
cp -av /usr/share/rapmap/src/* $(CURDIR)/external/install/src/rapmap
dh_auto_configure -- $(CMAKE_EXTRA_FLAGS)
__override_dh_auto_configure:
cp -rv debian/rapmap/RapMap*.h* \
debian/rapmap/*Boo???.hpp \
debian/rapmap/IndexHeader.hpp \
debian/rapmap/HitManager.hpp \
debian/rapmap/JFRaw.hpp \
debian/rapmap/SA*.hpp \
debian/rapmap/kseq.h \
debian/rapmap/SpinLock.hpp \
debian/rapmap/ScopedTimer.hpp \
debian/rapmap/bit_*.h \
debian/rapmap/rank9b.h \
debian/rapmap/macros.h \
debian/rapmap/PairAlignmentFormatter.hpp \
debian/rapmap/SingleAlignmentFormatter.hpp \
debian/rapmap/SparseHashSerializer.hpp \
debian/rapmap/sparsepp \
include/
cp -v debian/rapmap/bit_array.c \
debian/rapmap/rank9b.cpp \
debian/rapmap/RapMap*.cpp \
debian/rapmap/HitManager.cpp \
src/
dh_auto_configure
override_dh_auto_build:
dh_auto_build
mv doc/source/license.rst doc/ # unused
......@@ -62,7 +38,7 @@ override_dh_auto_build:
help2man --no-discard-stderr --no-info --name="highly-accurate, transcript-level quantification estimates from RNA-seq data"\
./salmon > ../../debian/salmon.1 && \
for option in index quant swim; do help2man --no-discard-stderr \
--version-string="${VERSION}" --no-info "./salmon --no-version-check $${option}" \
--version-string="$(DEB_VERSION_UPSTREAM)" --no-info "./salmon --no-version-check $${option}" \
--include=../../debian/salmon-$${option}-man-include \
> ../../debian/salmon-$${option}.1; done
......