[med-svn] [rapmap] 02/02: Add rudimentary debian/ dir (not working yet)
Andreas Tille
tille at debian.org
Tue Sep 6 19:10:19 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository rapmap.
commit e3e0c61f9d30d7daaab07d85f0b9f1e368218d2d
Author: Andreas Tille <tille at debian.org>
Date: Tue Sep 6 19:45:37 2016 +0200
Add rudimentary debian/ dir (not working yet)
---
debian/changelog | 5 +++++
debian/compat | 1 +
debian/control | 46 ++++++++++++++++++++++++++++++++++++++++++++++
debian/copyright | 14 ++++++++++++++
debian/rules | 27 +++++++++++++++++++++++++++
debian/source/format | 1 +
debian/upstream/metadata | 12 ++++++++++++
debian/watch | 4 ++++
8 files changed, 110 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..2ce2aff
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+rapmap (0.3.0+dfsg-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Tue, 06 Sep 2016 19:16:57 +0200
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..f6033ab
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,46 @@
+Source: rapmap
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 9),
+ cmake,
+ zlib1g-dev,
+ libdivsufsort-dev,
+ libcereal-dev,
+ libjellyfish-2.0-dev,
+ libspdlog-dev,
+ libtclap-dev
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/rapmap.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/rapmap.git
+Homepage: https://github.com/COMBINE-lab/RapMap
+
+Package: rapmap
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Description: rapid sensitive and accurate DNA read mapping via quasi-mapping
+ RapMap is a testing ground for ideas in quasi-mapping / (lightweight /
+ pseudo) transcriptome alignment. That means that, at this point, it is
+ somewhat experimental. The develop branch will have the latest
+ improvements and additions, but is not guaranteed to be stable between
+ commits. Breaking changes to the master branch will be accompanied by a
+ tag to the version before the breaking change. Currently, RapMap is a
+ stand-alone quasi-mapper that can be used with other tools. It is also
+ being used as part of Sailfish and Salmon. Eventually, the hope is to
+ create and stabilize an API so that it can be used as a library from
+ other tools.
+ .
+ Quasi-mapping / (lightweight / pseudo)-alignment is the term we are
+ using here for the type of information required for certain tasks (e.g.
+ transcript quantification) that is less "heavyweight" than what is
+ provided by traditional alignment. For example, one may only need to
+ know the transcripts / contigs to which a read aligns and, perhaps, the
+ position within those transcripts rather than the optimal alignment and
+ base-for-base CIGAR string that aligns the read and substring of the
+ transcript. For details on RapMap (quasi-mapping in particular), please
+ check out the associated paper. Note: RapMap implements both quasi-
+ mapping and pseudo-alignment (originally introduced in Bray et al.
+ 2016), these two are not the same thing. They are distinct concepts, and
+ RapMap simply happens to implement algorithms for computing both.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..6923fe6
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,14 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: RapMap
+Source: https://github.com/COMBINE-lab/RapMap/releases
+Files-Excluded: */external
+ */include/spdlog
+ */include/tclap
+
+Files: *
+Copyright: © 20xx-20yy <upstream>
+License: <license>
+
+Files: debian/*
+Copyright: © 2016 maintainername <maintainer at e.mail>
+License: <license>
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..9dad43d
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,27 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+export LC_ALL=C.UTF-8
+
+# 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.
+
+# for hardening you might like to uncomment this:
+# export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+
+%:
+ dh $@
+
+override_dh_auto_configure:
+ dh_auto_configure -- -DJELLYFISH_ROOT=/usr
+
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..bdcd55d
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,4 @@
+version=3
+
+opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
+ https://github.com/COMBINE-lab/RapMap/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
--
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