[med-svn] [falconkit] 02/05: Close-to-final packaging
Afif Elghraoui
afif-guest at moszumanska.debian.org
Tue Dec 22 06:53:45 UTC 2015
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a commit to branch master
in repository falconkit.
commit 9f8cabd759b62a4d69f9a30fa18c3899dece1bc6
Author: Afif Elghraoui <afif at ghraoui.name>
Date: Mon Dec 21 19:47:26 2015 -0800
Close-to-final packaging
---
debian/changelog | 5 +++
debian/compat | 1 +
debian/control | 30 +++++++++++++
debian/copyright | 40 ++++++++++++++++++
debian/docs | 2 +
debian/examples | 2 +
debian/falconkit.1 | 38 +++++++++++++++++
debian/manpages | 1 +
debian/patches/add-shebang-lines.patch | 12 ++++++
debian/patches/python-multiarch.patch | 77 ++++++++++++++++++++++++++++++++++
debian/patches/series | 2 +
debian/rules | 28 +++++++++++++
debian/source/format | 1 +
debian/tests/control | 7 ++++
debian/watch | 3 ++
15 files changed, 249 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..fa4199e
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+falconkit (0.1.3+20140820-1) UNRELEASED; urgency=low
+
+ * Initial release from git4a8f86f (Closes: #808708)
+
+ -- Afif Elghraoui <afif at ghraoui.name> Sun, 23 Aug 2015 01:00:12 -0700
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..69660a1
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,30 @@
+Source: falconkit
+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,
+ rename,
+ python-all-dev,
+ python-setuptools,
+ python-networkx,
+ python-pbcore,
+Standards-Version: 3.9.6
+Homepage: https://github.com/PacificBiosciences/FALCON
+Vcs-Git: git://anonscm.debian.org/debian-med/falconkit.git
+Vcs-Browser: http://anonscm.debian.org/cgit/debian-med/falconkit.git
+
+Package: falconkit
+Architecture: any
+Depends:
+ ${shlibs:Depends},
+ ${misc:Depends},
+ ${python:Depends},
+ python-numpy,
+ mummer,
+Description: genome assembly toolkit
+ Falcon is a set of tools for fast aligning long reads for consensus
+ and assembly. It is a simple code collection for efficient assembly of
+ haploid and diploid genomes.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..c470715
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,40 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: falcon
+Upstream-Contact: devnet at pacificbiosciences.com
+Source: https://github.com/PacificBiosciences/FALCON/tree/v0.1.3
+
+Files: *
+Copyright: 2011-2014 Pacific Biosciences of California, Inc.
+License: PacBio-BSD-3-Clause
+
+Files: debian/*
+Copyright: 2015 Afif Elghraoui <afif at ghraoui.name>
+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:
+ * Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+ * 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.
+ * 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.
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..eedc49d
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1,2 @@
+README.md
+doc/*.md
diff --git a/debian/examples b/debian/examples
new file mode 100644
index 0000000..63f5742
--- /dev/null
+++ b/debian/examples
@@ -0,0 +1,2 @@
+examples/*
+test_data
diff --git a/debian/falconkit.1 b/debian/falconkit.1
new file mode 100644
index 0000000..b1571dc
--- /dev/null
+++ b/debian/falconkit.1
@@ -0,0 +1,38 @@
+.TH FALCONKIT 1 "December 2015" 0.1.3
+.SH NAME
+falconkit \- genome assembly toolkit
+.PP
+falcon_asm \- assemble a contig using overlapping information
+.br
+falcon_asm_dev
+.br
+falcon_dedup
+.br
+falcon_fixasm \- break contigs on potential misassembly points
+.br
+falcon_overlap
+.br
+falcon_overlap2
+.br
+falcon_qrm \- simple multi-processor overlapper for sequence reads
+.br
+falcon_sense \- simple multi-processor consensus sequence generator
+.br
+falcon_ucns_data
+.br
+falcon_utgcns
+.br
+get_rdata
+.br
+remove_dup_ctg \- remove duplicate contigs
+.SH DESCRIPTION
+Falcon is a set of tools for fast aligning long reads for consensus and
+assembly. It is a simple code collection for efficient assembly of
+haploid and diploid genomes.
+.SH OPTIONS
+A summary of options is included below.
+For a complete description, see the programs' individual help menus
+or the documentation in /usr/share/doc/falconkit/
+.TP
+.B \-h, \-\-help
+Show summary of options.
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..654ff0d
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/falconkit.1
diff --git a/debian/patches/add-shebang-lines.patch b/debian/patches/add-shebang-lines.patch
new file mode 100644
index 0000000..bd934d5
--- /dev/null
+++ b/debian/patches/add-shebang-lines.patch
@@ -0,0 +1,12 @@
+Description: Add shebang lines to executable scripts
+Author: Afif Elghraoui <afif at ghraoui.name>
+Forwarded: no
+Last-Update: 2015-12-20
+--- falconkit.orig/src/py_scripts/falcon_dedup.py
++++ falconkit/src/py_scripts/falcon_dedup.py
+@@ -1,3 +1,5 @@
++#!/usr/bin/python
++
+ import subprocess
+ from pbcore.io import FastaReader
+
diff --git a/debian/patches/python-multiarch.patch b/debian/patches/python-multiarch.patch
new file mode 100644
index 0000000..a1a157b
--- /dev/null
+++ b/debian/patches/python-multiarch.patch
@@ -0,0 +1,77 @@
+Description: Account for multiarch component in module path name
+ Some of the scripts encode the path to the compiled module. The
+ original code does not take into account Debian's multiarch renaming.
+Author: Afif Elghraoui <afif at ghraoui.name>
+Forwarded: not-needed
+Last-Update: 2015-12-19
+--- falconkit.orig/src/py_scripts/falcon_sense.py
++++ falconkit/src/py_scripts/falcon_sense.py
+@@ -41,11 +41,13 @@
+ import sys
+ from multiprocessing import Pool
+ import os
++import sysconfig
+ import falcon_kit
+
+ module_path = falcon_kit.__path__[0]
+
+-falcon = CDLL(os.path.join(module_path, "falcon.so"))
++falcon = CDLL(
++ module_path+os.path.sep+"falcon."+sysconfig.get_config_var('MULTIARCH')+".so")
+
+ falcon.generate_consensus.argtypes = [ POINTER(c_char_p), c_uint, c_uint, c_uint, c_uint, c_uint, c_double ]
+ falcon.generate_consensus.restype = POINTER(falcon_kit.ConsensusData)
+--- falconkit.orig/src/py_scripts/falcon_utgcns.py
++++ falconkit/src/py_scripts/falcon_utgcns.py
+@@ -41,11 +41,13 @@
+ import sys
+ from multiprocessing import Pool
+ import os
++import sysconfig
+ import falcon_kit
+
+ module_path = falcon_kit.__path__[0]
+
+-falcon = CDLL(os.path.join(module_path, "falcon.so"))
++falcon = CDLL(
++ module_path + os.path.sep + "falcon." + sysconfig.get_config_var('MULTIARCH') + ".so")
+ """
+ consensus_data * generate_utg_consensus( char ** input_seq,
+ seq_coor_t *offset,
+--- falconkit.orig/src/py/falcon_kit.py
++++ falconkit/src/py/falcon_kit.py
+@@ -39,6 +39,8 @@
+
+ from ctypes import *
+ import os
++import sysconfig
++multiarch = sysconfig.get_config_var('MULTIARCH')
+ module_path = os.path.split(__file__)[0]
+
+
+@@ -66,7 +68,7 @@
+ _fields_ = [ ("sequence", c_char_p),
+ ("eff_cov", POINTER(c_uint)) ]
+
+-kup = CDLL(os.path.join(module_path, "kmer_lookup.so"))
++kup = CDLL(os.path.join(module_path, "kmer_lookup."+multiarch+".so"))
+
+ kup.allocate_kmer_lookup.argtypes = [seq_coor_t]
+ kup.allocate_kmer_lookup.restype = POINTER(KmerLookup)
+@@ -121,14 +123,14 @@
+ ("t_aln_str", c_char_p)]
+
+
+-DWA = CDLL(os.path.join(module_path, "DW_align.so"))
++DWA = CDLL(os.path.join(module_path, "DW_align."+multiarch+".so"))
+ DWA.align.argtypes = [ POINTER(c_char), c_long, POINTER(c_char), c_long, c_long, c_int ]
+ DWA.align.restype = POINTER(Alignment)
+ DWA.free_alignment.argtypes = [POINTER(Alignment)]
+
+
+
+-falcon = CDLL(os.path.join(module_path,"falcon.so"))
++falcon = CDLL(os.path.join(module_path,"falcon."+multiarch+".so"))
+
+ falcon.generate_consensus.argtypes = [POINTER(c_char_p), c_uint, c_uint, c_uint, c_uint, c_uint, c_double ]
+ falcon.generate_consensus.restype = POINTER(ConsensusData)
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..bf91044
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,2 @@
+add-shebang-lines.patch
+python-multiarch.patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..5c0423b
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,28 @@
+#!/usr/bin/make -f
+
+#DH_VERBOSE = 1
+
+include /usr/share/dpkg/default.mk
+
+define link-man =
+ln -s $2 \
+$(CURDIR)/debian/$1/usr/share/man/man1/`basename $3`
+endef
+
+%:
+ LC_ALL=C.UTF-8 dh $@ --with python2 --buildsystem=pybuild
+
+override_dh_install:
+ dh_install
+ rename 's/\.py//' $(CURDIR)/debian/falconkit/usr/bin/*
+
+override_dh_link:
+ for script in $(CURDIR)/debian/falconkit/usr/bin/*; \
+ do \
+ $(call link-man,falconkit,falconkit.1,$$script.1); \
+ done
+ dh_link
+
+override_dh_fixperms:
+ chmod -x debian/$(DEB_SOURCE)/usr/share/doc/$(DEB_SOURCE)/examples/HBAR.cfg
+ dh_fixperms
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/tests/control b/debian/tests/control
new file mode 100644
index 0000000..723fdfd
--- /dev/null
+++ b/debian/tests/control
@@ -0,0 +1,7 @@
+Test-Command:
+ cp -r test test_data $ADTTMP && cd $ADTTMP && nosetests -v test/
+Depends:
+ python-falconkit,
+ python-nose,
+Restrictions:
+ allow-stderr,
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..763d56c
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=3
+
+# There are no formal upstream releases
--
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