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commit e470052b6bbac2938dc04aac917ee4eee2d39f74 Author: Afif Elghraoui <[email protected]> Date: Sun Dec 13 00:33:58 2015 -0800 Initial packaging --- debian/changelog | 5 ++ debian/compat | 1 + debian/control | 97 ++++++++++++++++++++++ debian/copyright | 41 +++++++++ debian/patches/fix-syntax-error.patch | 17 ++++ debian/patches/intervaltree-import-statement.patch | 21 +++++ debian/patches/series | 2 + debian/pbbanana.docs | 1 + debian/pbbanana.install | 1 + debian/pbhoney.docs | 1 + debian/pbhoney.examples | 1 + debian/pbhoney.install | 1 + debian/pbhoney.links | 1 + debian/pbjelly.docs | 1 + debian/pbjelly.examples | 2 + debian/pbjelly.install | 1 + debian/pbjelly.links | 1 + debian/pbsuite-common.install | 2 + debian/rules | 16 ++++ debian/source/format | 1 + debian/watch | 3 + 21 files changed, 217 insertions(+) diff --git a/debian/changelog b/debian/changelog new file mode 100644 index 0000000..af3d8c0 --- /dev/null +++ b/debian/changelog @@ -0,0 +1,5 @@ +pbsuite (15.8.24+dfsg-1) UNRELEASED; urgency=low + + * Initial release (Closes: #807802) + + -- Afif Elghraoui <[email protected]> Fri, 20 Nov 2015 00:26:51 -0800 diff --git a/debian/compat b/debian/compat new file mode 100644 index 0000000..ec63514 --- /dev/null +++ b/debian/compat @@ -0,0 +1 @@ +9 diff --git a/debian/control b/debian/control new file mode 100644 index 0000000..a482232 --- /dev/null +++ b/debian/control @@ -0,0 +1,97 @@ +Source: pbsuite +Section: science +Priority: optional +Maintainer: Debian Med Packaging Team <[email protected]> +Uploaders: + Afif Elghraoui <[email protected]> +Build-Depends: + debhelper (>= 9), + dh-python, + python-all, +Standards-Version: 3.9.6 +Homepage: http://sourceforge.net/projects/pb-jelly +Vcs-Git: git://anonscm.debian.org/debian-med/pbsuite.git +Vcs-Browser: http://anonscm.debian.org/cgit/debian-med/pbsuite.git + +Package: pbsuite +Section: metapackages +Architecture: all +Depends: + ${misc:Depends}, + pbjelly, + pbhoney, + pbbanana, +Description: software for Pacific Biosciences sequencing data + The PBSuite contains two projects created for analysis of + Pacific Biosciences long-read sequencing data. + * PBJelly - genome upgrading tool + * PBHoney - structural variation discovery + +# TODO - this should be named python-pbsuite-utils +Package: pbsuite-common +Architecture: all +Depends: + ${misc:Depends}, + ${python:Depends}, + python-pysam (>= 0.8.0), +Description: software for Pacific Biosciences sequencing data -- common files + The PBSuite currently contains two projects created and maintained + by Adam English for analysis of Pacific Biosciences long-read + sequencing data. + * PBJelly - genome upgrading tool + * PBHoney - structural variation discovery + . + This package contains common files for the suite. + +Package: pbjelly +Architecture: all +Depends: + ${misc:Depends}, + ${python:Depends}, + pbsuite-common (= ${source:Version}), + python-networkx, + blasr, +Description: genome assembly upgrading tool + PBJelly is a highly automated pipeline that aligns long sequencing + reads (such as PacBio RS reads or long 454 reads in fasta format) + to high-confidence draft assembles. PBJelly fills or reduces as + many captured gaps as possible to produce upgraded draft genomes. + +Package: pbhoney +Architecture: all +Depends: + ${misc:Depends}, + ${python:Depends}, + pbsuite-common (= ${source:Version}), + pbbanana (= ${source:Version}), + python-intervaltree-bio, + python-pysam (>= 0.8.0), + python-networkx, + python-h5py (>= 2.0.1), + python-numpy, + blasr, + samtools, +Recommends: + pbdagcon, +Description: genomic structural variation discovery + PBHoney is an implementation of two variant-identification + approaches designed to exploit the high mappability of long reads + (i.e., greater than 10,000 bp). PBHoney considers both intra-read + discordance and soft-clipped tails of long reads to identify + structural variants. + +Package: pbbanana +Depends: + ${misc:Depends}, + ${python:Depends}, + pbsuite-common (= ${source:Version}), + python-networkx, + pbjelly (= ${source:Version}), + blasr, +Architecture: all +Description: additional utilities for the pbsuite + PBBanana contains some assembly and consensus utilities + for the PBSuite. + * OLCAssembly - A shortcut to calling pacbio's Allora Assembler + * Polish - A quick consensus caller + * PBJNovo - DeNovo Assembler of PacBio only reads diff --git a/debian/copyright b/debian/copyright new file mode 100644 index 0000000..7c909de --- /dev/null +++ b/debian/copyright @@ -0,0 +1,41 @@ +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: pbsuite +Source: http://sourceforge.net/p/pb-jelly/code-0/HEAD/tree/ +Files-Excluded: + bin/pbdagcon + bin/sawriter + pbsuite/*.pyc + pbsuite/utils/*.pyc + pbsuite/honey/*.pyc + pbsuite/jelly/*.pyc + pbsuite/banana/*.pyc + +Files: * +Copyright: 2013 Baylor College of Medicine +License: BSD-2-Clause + +Files: debian/* +Copyright: 2015 Afif Elghraoui <[email protected]> +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 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. diff --git a/debian/patches/fix-syntax-error.patch b/debian/patches/fix-syntax-error.patch new file mode 100644 index 0000000..57900c7 --- /dev/null +++ b/debian/patches/fix-syntax-error.patch @@ -0,0 +1,17 @@ +Description: Fix syntax error in pbbanana that prevents byte-compilation +Author: Afif Elghraoui <[email protected]> +Forwarded: no +Last-Update: 2015-12-12 +--- pbsuite.orig/pbsuite/banana/SeqAsm.py ++++ pbsuite/pbsuite/banana/SeqAsm.py +@@ -5,8 +5,8 @@ + + USAGE= "%prog A small assembler that quickly guesses at consensus of small, completely overlapping sequences""" + +-ss = ["CGCGTACGCG", +- [" ++#ss = ["CGCGTACGCG", ++# [" + a = "dsa jld lal" + b = "dsajld kll" + c = "dsc jle kal" diff --git a/debian/patches/intervaltree-import-statement.patch b/debian/patches/intervaltree-import-statement.patch new file mode 100644 index 0000000..010fa6c --- /dev/null +++ b/debian/patches/intervaltree-import-statement.patch @@ -0,0 +1,21 @@ +Description: Fix intervaltree_bio import statement for successor project + As mentioned on upstream's help forums [1], the original import statement + here refers to the PyInterval package. That has been succeeded by + intervaltree-bio. This patch adjusts the import statement to + work with the successor package. + . + 1. http://sourceforge.net/p/pb-jelly/discussion/pbhtiks/thread/05f86d70/#fa4b +Author: Afif Elghraoui <[email protected]> +Forwarded: no +Last-Update: 2015-12-12 +--- pbsuite.orig/pbsuite/honey/ComplexResolver.py ++++ pbsuite/pbsuite/honey/ComplexResolver.py +@@ -1,7 +1,7 @@ + #!/usr/bin/env python + import itertools, copy, argparse + from collections import defaultdict, Counter +-from intervaltree import bio ++import intervaltree_bio as bio + from pbsuite.utils.setupLogging import * + import networkx as nx + diff --git a/debian/patches/series b/debian/patches/series new file mode 100644 index 0000000..93f72fe --- /dev/null +++ b/debian/patches/series @@ -0,0 +1,2 @@ +fix-syntax-error.patch +intervaltree-import-statement.patch diff --git a/debian/pbbanana.docs b/debian/pbbanana.docs new file mode 100644 index 0000000..6ab11e5 --- /dev/null +++ b/debian/pbbanana.docs @@ -0,0 +1 @@ +docs/BananaReadme.txt diff --git a/debian/pbbanana.install b/debian/pbbanana.install new file mode 100644 index 0000000..7345f34 --- /dev/null +++ b/debian/pbbanana.install @@ -0,0 +1 @@ +pbsuite/banana usr/lib/python2.7/dist-packages/pbsuite diff --git a/debian/pbhoney.docs b/debian/pbhoney.docs new file mode 100644 index 0000000..d518584 --- /dev/null +++ b/debian/pbhoney.docs @@ -0,0 +1 @@ +docs/HoneyReadme.txt diff --git a/debian/pbhoney.examples b/debian/pbhoney.examples new file mode 100644 index 0000000..5490b2d --- /dev/null +++ b/debian/pbhoney.examples @@ -0,0 +1 @@ +docs/honeyExample diff --git a/debian/pbhoney.install b/debian/pbhoney.install new file mode 100644 index 0000000..5cd82d8 --- /dev/null +++ b/debian/pbhoney.install @@ -0,0 +1 @@ +pbsuite/honey usr/lib/python2.7/dist-packages/pbsuite diff --git a/debian/pbhoney.links b/debian/pbhoney.links new file mode 100644 index 0000000..d6ab3ae --- /dev/null +++ b/debian/pbhoney.links @@ -0,0 +1 @@ +/usr/lib/python2.7/dist-packages/pbsuite/honey/Honey.py /usr/bin/pbhoney diff --git a/debian/pbjelly.docs b/debian/pbjelly.docs new file mode 100644 index 0000000..dd0de3a --- /dev/null +++ b/debian/pbjelly.docs @@ -0,0 +1 @@ +docs/JellyReadme.txt diff --git a/debian/pbjelly.examples b/debian/pbjelly.examples new file mode 100644 index 0000000..872ea3e --- /dev/null +++ b/debian/pbjelly.examples @@ -0,0 +1,2 @@ +docs/TemplateProtocol.xml +docs/jellyExample diff --git a/debian/pbjelly.install b/debian/pbjelly.install new file mode 100644 index 0000000..5dee1b5 --- /dev/null +++ b/debian/pbjelly.install @@ -0,0 +1 @@ +pbsuite/jelly usr/lib/python2.7/dist-packages/pbsuite diff --git a/debian/pbjelly.links b/debian/pbjelly.links new file mode 100644 index 0000000..4c93a4a --- /dev/null +++ b/debian/pbjelly.links @@ -0,0 +1 @@ +/usr/lib/python2.7/dist-packages/pbsuite/jelly/Jelly.py /usr/bin/pbjelly diff --git a/debian/pbsuite-common.install b/debian/pbsuite-common.install new file mode 100644 index 0000000..39543f9 --- /dev/null +++ b/debian/pbsuite-common.install @@ -0,0 +1,2 @@ +pbsuite/utils usr/lib/python2.7/dist-packages/pbsuite +pbsuite/__init__.py usr/lib/python2.7/dist-packages/pbsuite diff --git a/debian/rules b/debian/rules new file mode 100755 index 0000000..feb6431 --- /dev/null +++ b/debian/rules @@ -0,0 +1,16 @@ +#!/usr/bin/make -f + +#DH_VERBOSE = 1 + +#include /usr/share/dpkg/default.mk + +%: + dh $@ --with python2 --build-system=pybuild + +override_dh_auto_build: + dh_auto_build + python -m compileall pbsuite + +override_dh_auto_clean: + dh_auto_clean + find -name "*.pyc" -delete diff --git a/debian/source/format b/debian/source/format new file mode 100644 index 0000000..163aaf8 --- /dev/null +++ b/debian/source/format @@ -0,0 +1 @@ +3.0 (quilt) diff --git a/debian/watch b/debian/watch new file mode 100644 index 0000000..c677a8f --- /dev/null +++ b/debian/watch @@ -0,0 +1,3 @@ +version=3 + +http://sf.net/pbsuite/pbsuite-(.*)\.tar\.gz -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/pbsuite.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
