From: Peter Michael Green Date: Sun, 30 Jul 2017 13:11:07 +0000 (+0100) Subject: Import pbbam_0.7.4+ds-1+rpi1.debian.tar.xz X-Git-Tag: archive/raspbian/0.19.0+dfsg-4+rpi1~4^2 X-Git-Url: https://dgit.raspbian.org/?a=commitdiff_plain;h=55c2f10f6fa8a82fc6205758e06bf6167ae659ef;p=pbbam.git Import pbbam_0.7.4+ds-1+rpi1.debian.tar.xz [dgit import tarball pbbam 0.7.4+ds-1+rpi1 pbbam_0.7.4+ds-1+rpi1.debian.tar.xz] --- 55c2f10f6fa8a82fc6205758e06bf6167ae659ef diff --git a/README.source b/README.source new file mode 100644 index 0000000..c29c516 --- /dev/null +++ b/README.source @@ -0,0 +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 --git a/TODO b/TODO new file mode 100644 index 0000000..c86d636 --- /dev/null +++ b/TODO @@ -0,0 +1,5 @@ +* Manpages for pbbamtools programs + +* package python and R bindings + +* package API documentation diff --git a/changelog b/changelog new file mode 100644 index 0000000..466bbe6 --- /dev/null +++ b/changelog @@ -0,0 +1,63 @@ +pbbam (0.7.4+ds-1+rpi1) stretch-staging; urgency=medium + + * Disable testsuite. + + -- Peter Michael Green Sun, 30 Jul 2017 13:11:07 +0000 + +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 --git a/compat b/compat new file mode 100644 index 0000000..f599e28 --- /dev/null +++ b/compat @@ -0,0 +1 @@ +10 diff --git a/control b/control new file mode 100644 index 0000000..94d6fbd --- /dev/null +++ b/control @@ -0,0 +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 --git a/copyright b/copyright new file mode 100644 index 0000000..431dafc --- /dev/null +++ b/copyright @@ -0,0 +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 --git a/libpbbam-dev.install b/libpbbam-dev.install new file mode 100644 index 0000000..0f2a4df --- /dev/null +++ b/libpbbam-dev.install @@ -0,0 +1 @@ +include/* usr/include diff --git a/libpbbam.install b/libpbbam.install new file mode 100755 index 0000000..bc95dd6 --- /dev/null +++ b/libpbbam.install @@ -0,0 +1,2 @@ +#!/usr/bin/dh-exec +*/lib/* usr/lib/${DEB_HOST_MULTIARCH} diff --git a/libpbbam.lintian-overrides b/libpbbam.lintian-overrides new file mode 100644 index 0000000..5e4d24f --- /dev/null +++ b/libpbbam.lintian-overrides @@ -0,0 +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 --git a/libpbbam.triggers b/libpbbam.triggers new file mode 100644 index 0000000..c302335 --- /dev/null +++ b/libpbbam.triggers @@ -0,0 +1 @@ +activate-noawait ldconfig diff --git a/patches/remove-bam2sam.patch b/patches/remove-bam2sam.patch new file mode 100644 index 0000000..a4dec35 --- /dev/null +++ b/patches/remove-bam2sam.patch @@ -0,0 +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 --git a/patches/series b/patches/series new file mode 100644 index 0000000..78015f5 --- /dev/null +++ b/patches/series @@ -0,0 +1,2 @@ +ssl-md5.patch +remove-bam2sam.patch diff --git a/patches/ssl-md5.patch b/patches/ssl-md5.patch new file mode 100644 index 0000000..9c4ce98 --- /dev/null +++ b/patches/ssl-md5.patch @@ -0,0 +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 --git a/pbbamtools.install b/pbbamtools.install new file mode 100644 index 0000000..7380180 --- /dev/null +++ b/pbbamtools.install @@ -0,0 +1 @@ +*/bin /usr diff --git a/rules b/rules new file mode 100755 index 0000000..293bda5 --- /dev/null +++ b/rules @@ -0,0 +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 --git a/source/format b/source/format new file mode 100644 index 0000000..163aaf8 --- /dev/null +++ b/source/format @@ -0,0 +1 @@ +3.0 (quilt) diff --git a/tests/control b/tests/control new file mode 100644 index 0000000..98aedfd --- /dev/null +++ b/tests/control @@ -0,0 +1,9 @@ +Test-Command: debian/rules override_dh_auto_test +Depends: + make, + python, + pbbamtools, + python-cram, +Restrictions: + needs-recommends, + rw-build-tree, diff --git a/watch b/watch new file mode 100644 index 0000000..d4dc1e9 --- /dev/null +++ b/watch @@ -0,0 +1,2 @@ +# Upstream is currently not tagging releases. The library itself does +# not yet provide a stable interface