From: Afif Elghraoui Date: Sun, 22 Jan 2017 07:48:21 +0000 (+0000) Subject: pbbam (0.7.4+ds-1) unstable; urgency=medium X-Git-Tag: archive/raspbian/0.19.0+dfsg-4+rpi1~1^2~2 X-Git-Url: https://dgit.raspbian.org/?a=commitdiff_plain;h=66a610dd07200abb8481e873b44fbf045582e26d;p=pbbam.git pbbam (0.7.4+ds-1) unstable; urgency=medium * New upstream release snapshot - Exclude dependency convenience copy - Update patches - Update running of tests at build-time - Update .install files - Update autopkgtest commands * Use debhelper compat 10 * libpbbam-dev: depend on libssl-dev [dgit import unpatched pbbam 0.7.4+ds-1] --- 66a610dd07200abb8481e873b44fbf045582e26d diff --cc debian/README.source index 0000000,0000000..c29c516 new file mode 100644 --- /dev/null +++ b/debian/README.source @@@ -1,0 -1,0 +1,10 @@@ ++pbbam for Debian ++---------------- ++ ++* The swig bindings require a version of swig higher than 3.0.2 (currently in unstable). ++ Without this, python and R bindings cannot be built. ++ ++ ++ ++ -- Afif Elghraoui , Sun, 6 Sep 2015 13:57:45 -0700 ++ diff --cc debian/TODO index 0000000,0000000..c86d636 new file mode 100644 --- /dev/null +++ b/debian/TODO @@@ -1,0 -1,0 +1,5 @@@ ++* Manpages for pbbamtools programs ++ ++* package python and R bindings ++ ++* package API documentation diff --cc debian/changelog index 0000000,0000000..7fa6fb0 new file mode 100644 --- /dev/null +++ b/debian/changelog @@@ -1,0 -1,0 +1,57 @@@ ++pbbam (0.7.4+ds-1) unstable; urgency=medium ++ ++ * New upstream release snapshot ++ - Exclude dependency convenience copy ++ - Update patches ++ - Update running of tests at build-time ++ - Update .install files ++ - Update autopkgtest commands ++ * Use debhelper compat 10 ++ * libpbbam-dev: depend on libssl-dev ++ ++ -- Afif Elghraoui Sat, 21 Jan 2017 23:48:21 -0800 ++ ++pbbam (0.7.0-1) unstable; urgency=medium ++ ++ * Imported Upstream version 0.7.0 ++ * Update patches ++ ++ -- Afif Elghraoui Sun, 30 Oct 2016 14:31:49 -0700 ++ ++pbbam (0.5.0-3) unstable; urgency=low ++ ++ * Fix cmake arguments to properly position LDFLAGS for -Wl,--as-needed. ++ Thanks to Steve Langasek (Closes: #841671) ++ ++ -- Afif Elghraoui Sun, 23 Oct 2016 14:07:27 -0700 ++ ++pbbam (0.5.0-2) unstable; urgency=low ++ ++ * libpbbam-dev: add dependency on libhts-dev ++ ++ -- Afif Elghraoui Sun, 17 Jul 2016 23:29:34 -0700 ++ ++pbbam (0.5.0-1) unstable; urgency=medium ++ ++ * New upstream revision (git 79ab246 from 2016-02-23) ++ * Declare additional copyrights to avoid repacking tarball ++ * Update patches ++ * Update Standards-Version to 3.9.8 ++ * Use encrypted protocols for VCS URLs ++ * Clean up d/control and d/rules ++ * Use dh-exec for library installation rather than sed-within-d/rules ++ * Set up build-time tests for command-line tools ++ * Add binary package for command-line tools ++ * Install library to main library path ++ * Configure autopkgtests ++ * Use documentation page as Homepage ++ * Remove build-dependency on doxygen ++ * Add TODO list ++ ++ -- Afif Elghraoui Tue, 05 Jul 2016 03:25:49 -0700 ++ ++pbbam (0.1.0~20150813+git4e9e417+dfsg-1) unstable; urgency=low ++ ++ * Initial release (Closes: #798220) ++ ++ -- Afif Elghraoui Fri, 18 Sep 2015 02:40:24 -0700 diff --cc debian/compat index 0000000,0000000..f599e28 new file mode 100644 --- /dev/null +++ b/debian/compat @@@ -1,0 -1,0 +1,1 @@@ ++10 diff --cc debian/control index 0000000,0000000..94d6fbd new file mode 100644 --- /dev/null +++ b/debian/control @@@ -1,0 -1,0 +1,84 @@@ ++Source: pbbam ++Section: libs ++Priority: optional ++Maintainer: Debian Med Packaging Team ++Uploaders: Afif Elghraoui ++Build-Depends: ++ debhelper (>= 10), ++ dh-exec, ++ cmake, ++ python, ++# swig3.0, ++ libboost-dev (>= 1.54), ++ zlib1g-dev, ++ libssl-dev, ++ libhts-dev, ++# Test-Depends: ++# libgtest-dev, ++ python-cram, ++ samtools, ++Standards-Version: 3.9.8 ++Homepage: http://pbbam.readthedocs.org/en/latest/index.html ++Vcs-Git: https://anonscm.debian.org/git/debian-med/pbbam.git ++Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/pbbam.git ++ ++Package: pbbamtools ++Section: science ++Architecture: any ++Depends: ++ ${shlibs:Depends}, ++ ${misc:Depends}, ++ libpbbam (= ${binary:Version}), ++Recommends: samtools ++Description: processing Pacific Biosciences binary alignment/map files ++ The BAM format is a binary, compressed, record-oriented container format ++ for raw or aligned sequence reads. The associated SAM format is a text ++ representation of the same data. The specifications for BAM/SAM are maintained ++ by the SAM/BAM Format Specification Working Group. ++ . ++ PacBio-produced BAM files are fully compatible with the BAM specification, ++ but makes use of the extensibility mechanisms of the BAM specification to ++ encode PacBio-specific information. ++ . ++ This package provides command-line utilities for working with PacBio BAM ++ files. ++ ++Package: libpbbam ++Architecture: any ++Multi-Arch: same ++Pre-Depends: ++ ${misc:Pre-Depends} ++Depends: ++ ${shlibs:Depends}, ++ ${misc:Depends}, ++Description: Pacific Biosciences binary alignment/map (BAM) library ++ The BAM format is a binary, compressed, record-oriented container format ++ for raw or aligned sequence reads. The associated SAM format is a text ++ representation of the same data. The specifications for BAM/SAM are maintained ++ by the SAM/BAM Format Specification Working Group. ++ . ++ PacBio-produced BAM files are fully compatible with the BAM specification, ++ but makes use of the extensibility mechanisms of the BAM specification to ++ encode PacBio-specific information. The pbbam library provides tools to ++ work with these files ++ ++Package: libpbbam-dev ++Section: libdevel ++Architecture: any ++Depends: ++ libpbbam (= ${binary:Version}), ++ libhts-dev, ++ libssl-dev, ++ ${misc:Depends}, ++Description: Pacific Biosciences binary alignment/map (BAM) library (headers) ++ The BAM format is a binary, compressed, record-oriented container format ++ for raw or aligned sequence reads. The associated SAM format is a text ++ representation of the same data. The specifications for BAM/SAM are maintained ++ by the SAM/BAM Format Specification Working Group. ++ . ++ PacBio-produced BAM files are fully compatible with the BAM specification, ++ but makes use of the extensibility mechanisms of the BAM specification to ++ encode PacBio-specific information. The pbbam library provides tools to ++ work with these files ++ . ++ This package contains the library header files. diff --cc debian/copyright index 0000000,0000000..431dafc new file mode 100644 --- /dev/null +++ b/debian/copyright @@@ -1,0 -1,0 +1,156 @@@ ++Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ ++Upstream-Name: pbbam ++Upstream-Contact: Pacific Biosciences ++Source: https://github.com/PacificBiosciences/pbbam ++Files-Excluded: third-party ++ ++Files: * ++Copyright: 2014-2016 Pacific Biosciences of California, Inc. ++License: PacBio-BSD-3-Clause ++ ++Files: cmake/FindCSharp.cmake ++ cmake/FindMono.cmake ++ cmake/UseCSharp.cmake ++ cmake/UseDotNetFrameworkSdk.cmake ++ cmake/UseMono.cmake ++Copyright: 2006-2010 Mathieu Malaterre ++Comment: These files are from GDCM (as indicated in the file headers). ++ The license terms have been retrieved from there. ++License: MM-BSD-3-Clause ++ ++Files: src/pugixml/* ++Copyright: 2006-2014 Arseny Kapoulkine ++ 2003 Kristen Wegner ++License: MIT ++ ++Files: tools/common/OptionParser.* ++Copyright: 2010 Johannes Weißl ++License: BSD-3-Clause or BSD-2-Clause ++ ++Files: debian/* ++Copyright: 2015-2016 Afif Elghraoui ++License: PacBio-BSD-3-Clause ++ ++License: PacBio-BSD-3-Clause ++ Redistribution and use in source and binary forms, with or without ++ modification, are permitted (subject to the limitations in the ++ disclaimer below) 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. Neither the name of Pacific Biosciences nor the names of its ++ contributors may be used to endorse or promote products derived ++ from this software without specific prior written permission. ++ . ++ NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE ++ GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC ++ BIOSCIENCES AND ITS 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 PACIFIC BIOSCIENCES OR ITS ++ 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: MM-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. Neither name of Mathieu Malaterre, or CREATIS, nor the names of any ++ contributors (CNRS, INSERM, UCB, Universite Lyon I), 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 AUTHORS 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. Neither the name of the University nor the names of its 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 HOLDERS 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-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 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: 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. diff --cc debian/libpbbam-dev.install index 0000000,0000000..0f2a4df new file mode 100644 --- /dev/null +++ b/debian/libpbbam-dev.install @@@ -1,0 -1,0 +1,1 @@@ ++include/* usr/include diff --cc debian/libpbbam.install index 0000000,0000000..bc95dd6 new file mode 100755 --- /dev/null +++ b/debian/libpbbam.install @@@ -1,0 -1,0 +1,2 @@@ ++#!/usr/bin/dh-exec ++*/lib/* usr/lib/${DEB_HOST_MULTIARCH} diff --cc debian/libpbbam.lintian-overrides index 0000000,0000000..5e4d24f new file mode 100644 --- /dev/null +++ b/debian/libpbbam.lintian-overrides @@@ -1,0 -1,0 +1,6 @@@ ++# Upstream has not yet stabilized the API. ++# This library is so far only used by a closely-related set of programs. ++shlib-without-versioned-soname usr/lib/x86_64-linux-gnu/libpbbam.so libpbbam.so ++# Because of the lack of versioned soname, the library itself contains ++# the libpbbam.so file, so there's no need for a symlink. ++dev-pkg-without-shlib-symlink usr/lib/x86_64-linux-gnu/libpbbam.so usr/lib/x86_64-linux-gnu/libpbbam.so diff --cc debian/libpbbam.triggers index 0000000,0000000..c302335 new file mode 100644 --- /dev/null +++ b/debian/libpbbam.triggers @@@ -1,0 -1,0 +1,1 @@@ ++activate-noawait ldconfig diff --cc debian/patches/remove-bam2sam.patch index 0000000,0000000..a4dec35 new file mode 100644 --- /dev/null +++ b/debian/patches/remove-bam2sam.patch @@@ -1,0 -1,0 +1,18 @@@ ++Description: Exclude the bam2sam utility ++ It is a convenience tool provided by upstream to avoid depending on ++ samtools. We actually have trouble building it in Debian and have ++ easy access to samtools. ++Author: Afif Elghraoui ++Forwarded: not-needed ++Last-Update: 2016-07-04 ++ ++--- pbbam.orig/tools/CMakeLists.txt +++++ pbbam/tools/CMakeLists.txt ++@@ -39,7 +39,6 @@ ++ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${PacBioBAM_CXX_FLAGS}") ++ ++ # tools ++- add_subdirectory(bam2sam) ++ add_subdirectory(pbindex) ++ add_subdirectory(pbindexdump) ++ add_subdirectory(pbmerge) diff --cc debian/patches/series index 0000000,0000000..78015f5 new file mode 100644 --- /dev/null +++ b/debian/patches/series @@@ -1,0 -1,0 +1,2 @@@ ++ssl-md5.patch ++remove-bam2sam.patch diff --cc debian/patches/ssl-md5.patch index 0000000,0000000..9c4ce98 new file mode 100644 --- /dev/null +++ b/debian/patches/ssl-md5.patch @@@ -1,0 -1,0 +1,24 @@@ ++Description: Use libssl for md5.h rather than cram ++ cram/md5.h was part of HTSlib [1] (seems to have been removed in the current ++ development tree), but those headers are not installed by that ++ package's build system. md5.h in particular has a very generic function, ++ served apparently by libssl. Furthermore, the cram/* headers are not intended ++ to be used directly [2]. This patch uses libssl to provide md5.h for this ++ package. ++ . ++ 1. https://anonscm.debian.org/cgit/debian-med/htslib.git/tree/cram/md5.h?id=12251926b9d0265738d701bb0add6fe9d070ccb3 ++ 2. http://sourceforge.net/p/samtools/mailman/message/33488076/ ++Author: Afif Elghraoui ++Forwarded: no ++Last-Update: 2015-10-30 ++--- pbbam.orig/src/MD5.cpp +++++ pbbam/src/MD5.cpp ++@@ -40,7 +40,7 @@ ++ // Author: Brett Bowman ++ ++ #include "pbbam/MD5.h" ++-#include +++#include ++ ++ namespace PacBio { ++ namespace BAM { diff --cc debian/pbbamtools.install index 0000000,0000000..7380180 new file mode 100644 --- /dev/null +++ b/debian/pbbamtools.install @@@ -1,0 -1,0 +1,1 @@@ ++*/bin /usr diff --cc debian/rules index 0000000,0000000..f1eb875 new file mode 100755 --- /dev/null +++ b/debian/rules @@@ -1,0 -1,0 +1,52 @@@ ++#!/usr/bin/make -f ++ ++#DH_VERBOSE = 1 ++export LC_ALL=C.UTF-8 ++include /usr/share/dpkg/default.mk ++ ++DEB_VERSION_UPSTREAM := $(subst +ds,,$(DEB_VERSION_UPSTREAM)) ++generated_data_dir = $(CURDIR)/gendata ++ ++%: ++ dh $@ ++ ++override_dh_auto_configure: ++ dh_auto_configure -- \ ++ -DPacBioBAM_build_shared=ON \ ++ -DPacBioBAM_build_tests=OFF \ ++ -DCMAKE_LIBRARY_PATH=$(DEB_HOST_MULTIARCH) \ ++ -DCMAKE_SKIP_RPATH=ON \ ++ -DHTSLIB_INCLUDE_DIRS=/usr/include \ ++ -DHTSLIB_LIBRARIES="-lssl -lcrypto -lhts" \ ++ -DCMAKE_SHARED_LINKER_FLAGS="$(LDFLAGS)" ++# -DPacBioBAM_wrap_python=ON \ ++# -DPacBioBAM_wrap_r=ON ++ ++override_dh_auto_test: $(subst .t.in,.deb.t,$(wildcard tests/src/cram/pb*.t.in)) ++ mkdir -p $(generated_data_dir) ++ python tests/scripts/generate_data.py $(CURDIR)/tests/data $(generated_data_dir) ++ BINDIR=`find $$PWD -name bin -type d`; \ ++ LIBDIR=`find $$PWD -name lib -type d`; \ ++ PATH="$$BINDIR:$(PATH)" LD_LIBRARY_PATH="$$LIBDIR:$(LD_LIBRARY_PATH)" \ ++ cram -v $^ ++ ++override_dh_installchangelogs: ++ dh_installchangelogs CHANGELOG.md ++ ++override_dh_auto_clean: ++ dh_auto_clean ++ find -name "*.deb.t" -delete ++ $(RM) -r $(generated_data_dir) ++ ++%.deb.t: %.t.in ++ sed \ ++ -e 's/$$BAM2SAM/samtools view/g' \ ++ -e 's/\-\-header\-only/-H/g' \ ++ -e 's/\-\-no\-header//g' \ ++ -e 's|@PacBioBAM_BinDir@/||g' \ ++ -e 's|$$TOOLS_BIN/||g' \ ++ -e 's|@PacBioBAM_TestsDir@|$(CURDIR)/tests|g' \ ++ -e 's|@PacBioBAM_VERSION@|$(DEB_VERSION_UPSTREAM)|g' \ ++ -e 's|@GeneratedTestDataDir@|$(generated_data_dir)|g' \ ++ $< > $@ ++ diff --cc debian/source/format index 0000000,0000000..163aaf8 new file mode 100644 --- /dev/null +++ b/debian/source/format @@@ -1,0 -1,0 +1,1 @@@ ++3.0 (quilt) diff --cc debian/tests/control index 0000000,0000000..98aedfd new file mode 100644 --- /dev/null +++ b/debian/tests/control @@@ -1,0 -1,0 +1,9 @@@ ++Test-Command: debian/rules override_dh_auto_test ++Depends: ++ make, ++ python, ++ pbbamtools, ++ python-cram, ++Restrictions: ++ needs-recommends, ++ rw-build-tree, diff --cc debian/watch index 0000000,0000000..d4dc1e9 new file mode 100644 --- /dev/null +++ b/debian/watch @@@ -1,0 -1,0 +1,2 @@@ ++# Upstream is currently not tagging releases. The library itself does ++# not yet provide a stable interface