[med-svn] [varmatch] 01/01: Initial packaging

Tue Jul 12 08:27:39 UTC 2016

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afif pushed a commit to branch master
in repository varmatch.

commit cb7de27682f35d4702e3d57330f02ea5c8dfcc60
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Tue Jul 12 01:19:54 2016 -0700

    Initial packaging
---
 debian/changelog             |  5 +++++
 debian/compat                |  1 +
 debian/control               | 30 +++++++++++++++++++++++++++++
 debian/copyright             | 45 ++++++++++++++++++++++++++++++++++++++++++++
 debian/docs                  |  1 +
 debian/install               |  6 ++++++
 debian/patches/libexec.patch | 16 ++++++++++++++++
 debian/patches/series        |  1 +
 debian/rules                 |  6 ++++++
 debian/source/format         |  1 +
 debian/upstream/metadata     |  8 ++++++++
 11 files changed, 120 insertions(+)

diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..eef71b1
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+varmatch (0+20160708+dfsg-1) UNRELEASED; urgency=medium
+
+  * Initial release (Closes: #nnnn)
+
+ -- Afif Elghraoui <afif at debian.org>  Tue, 12 Jul 2016 00:39:51 -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..40ea0e1
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,30 @@
+Source: varmatch
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Build-Depends:
+	debhelper (>=9),
+	libtclap-dev,
+Standards-Version: 3.9.8
+Homepage: https://github.com/medvedevgroup/varmatch
+Vcs-Git: https://anonscm.debian.org/git/debian-med/varmatch.git
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/varmatch.git
+
+Package: varmatch
+Architecture: any
+Depends:
+	${shlibs:Depends},
+	${misc:Depends},
+	python,
+	python-matplotlib,
+Description: robust matching of small genomic variant datasets
+ Small variant calling is an important component of many analyses, and, in
+ many instances, it is important to determine the set of variants which appear
+ in multiple callsets. Variant matching is complicated by variants that have
+ multiple equivalent representations. Normalization and decomposition
+ algorithms have been proposed, but are not robust to different
+ representation of complex variants. The VarMatch algorithm is robust to
+ different representation of complex variants and is particularly effective
+ in low complexity regions or those dense in variants. VarMatch also provides
+ summary statistics, annotations, and visualizations that are useful for
+ understanding callers' performance.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..ad5eb82
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,45 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: varmatch
+Upstream-Contact: Chen Sun <chensun at cse.psu.edu>
+Source: https://github.com/medvedevgroup/varmatch
+Files-Excluded:
+	include/tclap
+	**/*.pyc
+	vm-core
+	vm
+	src/vm-core
+	src/vm
+	src/filter_cv
+	src/filter_hc
+
+Files: *
+Copyright:
+	2016 Chen Sun <chensun at cse.psu.edu>
+	2016 Paul Medvedev
+License: GPL-3.0+
+
+Files: debian/*
+Copyright: 2016 Afif Elghraoui <afif at debian.org>
+License: GPL-3.0+
+
+License: GPL-3.0+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <https://www.gnu.org/licenses/>.
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".
+
+# Please also look if there are files or directories which have a
+# different copyright/license attached and list them here.
+# Please avoid picking licenses with terms that are more restrictive than the
+# packaged work, as it may make Debian's contributions unacceptable upstream.
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..b43bf86
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1 @@
+README.md
diff --git a/debian/install b/debian/install
new file mode 100644
index 0000000..18a96ca
--- /dev/null
+++ b/debian/install
@@ -0,0 +1,6 @@
+varmatch	/usr/bin
+purify	/usr/lib/varmatch
+filter	/usr/lib/varmatch
+vm-core	/usr/lib/varmatch
+src/filter_hc	/usr/lib/varmatch
+src/filter_cv	/usr/lib/varmatch
diff --git a/debian/patches/libexec.patch b/debian/patches/libexec.patch
new file mode 100644
index 0000000..5d7fdc5
--- /dev/null
+++ b/debian/patches/libexec.patch
@@ -0,0 +1,16 @@
+Description: Set path for private executables to /usr/lib/varmatch
+Author: Afif Elghraoui <afif at debian.org>
+Forwarded: no
+Last-Update: 2016-07-12
+
+--- varmatch.orig/varmatch
++++ varmatch/varmatch
+@@ -556,7 +556,7 @@
+ 
+     check_compare_command = True
+ 
+-    script_path = sys.path[0]
++    script_path = "/usr/lib/varmatch"
+     compare_tool = script_path + '/vm-core'
+     output_dir = ''
+     temp_dir = ''
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..29dab71
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+libexec.patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..cd37a16
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,6 @@
+#!/usr/bin/make -f
+
+#export DH_VERBOSE = 1
+
+%:
+	dh $@ 
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/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..2ff414b
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,8 @@
+Reference:
+  Author: Chen Sun and Paul Medvedev
+  Title: "VarMatch: robust matching of small variant datasets using flexible scoring schemes"
+  Journal: bioRxiv
+  Year: 2016
+  Number: 062943
+  DOI: 10.1101/062943
+  URL: http://biorxiv.org/content/early/2016/07/08/062943

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/varmatch.git

