[med-svn] [varmatch] 02/02: Initial packaging
Afif Elghraoui
afif at moszumanska.debian.org
Tue Jul 12 08:22:04 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a commit to branch master
in repository varmatch.
commit 76a44dcaebe02cf8c809a085ae38744754d1f6e9
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 | 25 ++++++++++++++++++++++++
debian/source/format | 1 +
debian/upstream/metadata | 8 ++++++++
11 files changed, 139 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..2f54c47
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,25 @@
+#!/usr/bin/make -f
+# See debhelper(7) (uncomment to enable)
+# output every command that modifies files on the build system.
+#export DH_VERBOSE = 1
+
+
+# see FEATURE AREAS in dpkg-buildflags(1)
+#export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+
+# see ENVIRONMENT in dpkg-buildflags(1)
+# package maintainers to append CFLAGS
+#export DEB_CFLAGS_MAINT_APPEND = -Wall -pedantic
+# package maintainers to append LDFLAGS
+#export DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed
+
+
+%:
+ dh $@
+
+
+# dh_make generated override targets
+# This is example for Cmake (See https://bugs.debian.org/641051 )
+#override_dh_auto_configure:
+# dh_auto_configure -- # -DCMAKE_LIBRARY_PATH=$(DEB_HOST_MULTIARCH)
+
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
--
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