[med-svn] [snap-aligner] 02/02: initial packaging
Michael Crusoe
misterc-guest at moszumanska.debian.org
Sun Sep 20 04:08:22 UTC 2015
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch master
in repository snap-aligner.
commit f4d2833850f2f10205e4d17f39d7b560b5850020
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date: Sat Sep 19 20:26:41 2015 -0700
initial packaging
---
debian/changelog | 5 +++++
debian/compat | 1 +
debian/control | 24 ++++++++++++++++++++++++
debian/copyright | 31 +++++++++++++++++++++++++++++++
debian/install | 2 ++
debian/rules | 23 +++++++++++++++++++++++
debian/source/format | 1 +
debian/upstream/metadata | 12 ++++++++++++
debian/watch | 17 +++++++++++++++++
9 files changed, 116 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..3e3d932
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+snap-aligner (0.18~1.0~beta.18-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #<bug>)
+
+ -- Michael R. Crusoe <crusoe at ucdavis.edu> Sat, 19 Sep 2015 20:20:26 -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..6de3937
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,24 @@
+Source: snap-aligner
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Michael R. Crusoe <crusoe at ucdavis.edu>
+Build-Depends: debhelper (>= 9)
+Standards-Version: 3.9.6
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/<pkg>/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/<pkg>/trunk/
+Homepage: http://snap.cs.berkeley.edu/
+
+Package: snap-aligner
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: Scalable Nucleotide Alignment Program
+ SNAP is a new sequence aligner that is 3-20x faster and just as accurate as
+ existing tools like BWA-mem, Bowtie2 and Novoalign. It runs on commodity x86
+ processors, and supports a rich error model that lets it cheaply match reads
+ with more differences from the reference than other tools. This gives SNAP up
+ to 2x lower error rates than existing tools (in some cases) and lets it match
+ larger mutations that they may miss. SNAP also natively reads BAM, FASTQ, or
+ gzipped FASTQ, and natively writes SAM or BAM, with built-in sorting,
+ duplicate marking, and BAM indexing.
+
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..72f1be8
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,31 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: SNAP
+Source: https://github.com/amplab/snap
+Files-Excluded: import/z*,
+ tests/bin/*.exe
+ tests/bin/*.dll
+
+Files: *
+Copyright: 2012, Regents of the University of California.
+License: Apache-2.0
+
+Files: debian/*
+Copyright: © 2015 Michael R. Crusoe <crusoe at ucdavis.edu>
+License: Apache-2.0
+
+License: Apache-2.0
+ Licensed under the Apache License, Version 2.0 (the "License");
+ you may not use this file except in compliance with the License.
+ You may obtain a copy of the License at
+ .
+ . http://www.apache.org/licenses/LICENSE-2.0
+ .
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
+ .
+ On Debian systems, the full text of the Apache License, Version 2.0 can be
+ found in the file `/usr/share/common-licenses/Apache-2.0'.
+
diff --git a/debian/install b/debian/install
new file mode 100644
index 0000000..8f4ce48
--- /dev/null
+++ b/debian/install
@@ -0,0 +1,2 @@
+snap-aligner usr/bin/
+SNAPCommand usr/bin/
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..55d0c84
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,23 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+# some helpful variables - uncomment them if needed
+# shamelessly stolen from http://jmtd.net/log/awk/
+#DEBVERS := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}')
+#VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//')
+#DEBFLAVOR := $(shell dpkg-parsechangelog | awk '/^Distribution:/ {print $$2}')
+#DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
+#DEBIAN_BRANCH := $(shell awk 'BEGIN{FS="[= ]+"} /debian-branch/ {print $$2}' debian/gbp.conf)
+#GIT_TAG := $(subst ~,_,$(VERSION))
+
+# alternatively to manually set those variables, you can
+# include /usr/share/dpkg/default.mk
+# and use what is set there.
+
+%:
+ dh $@
+
+override_dh_auto_test:
+ dh_auto_test
+ ./unit_tests
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..d8b5812
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+ Author:
+ Title:
+ Journal:
+ Year:
+ Volume:
+ Number:
+ Pages:
+ DOI:
+ PMID:
+ URL:
+ eprint:
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..b608c3e
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,17 @@
+version=3
+
+#upstrea uses GitHub but numbers their release in a way that I don't know how
+#to de-mangle
+#
+#Example version number: 0.14, 0.15, 1.0beta.18, 1.0beta.19
+
+# Uncomment to find new files on Github
+# - when using releases:
+# https://github.com/#GITHUBUSER#/#PACKAGE#/releases .*/archive/#PREFIX#(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
+# - when using tags
+# https://github.com/#GITHUBUSER#/#PACKAGE#/tags .*/#PREFIX#(\d.*)\.(?:tgz|tbz2|txz|tar\.(?:gz|bz2|xz))
+# Remark: frequently you can do s/#PREFIX#/v?/ since 'v' or nothing is quite common but there are other prefixes possible
+
+# if you need to repack and choose +dfsg prefix
+# opts=dversionmangle=s/[~\+]dfsg[0-9]*// \
+#
--
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