[med-svn] [pbsuite] 02/02: Initial packaging
Afif Elghraoui
afif-guest at moszumanska.debian.org
Sun Dec 13 08:35:04 UTC 2015
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a commit to branch master
in repository pbsuite.
commit e470052b6bbac2938dc04aac917ee4eee2d39f74
Author: Afif Elghraoui <afif at ghraoui.name>
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 <afif at ghraoui.name> 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 <debian-med-packaging at lists.alioth.debian.org>
+Uploaders:
+ Afif Elghraoui <afif at ghraoui.name>
+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 <afif at ghraoui.name>
+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 <afif at ghraoui.name>
+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 <afif at ghraoui.name>
+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
--
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