[med-svn] [smrtanalysis] 02/02: Initial commit
Afif Elghraoui
afif-guest at moszumanska.debian.org
Sat May 16 22:13:58 UTC 2015
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a commit to branch master
in repository smrtanalysis.
commit 2ba5b2f4df2cf782028d5706e636ae75737ee3fd
Author: Afif Elghraoui <afif at ghraoui.name>
Date: Sat May 16 15:05:32 2015 -0700
Initial commit
---
debian/README.source | 14 ++++++++++++++
debian/changelog | 5 +++++
debian/compat | 1 +
debian/control | 39 +++++++++++++++++++++++++++++++++++++++
debian/copyright | 36 ++++++++++++++++++++++++++++++++++++
debian/docs | 3 +++
debian/get-orig-source | 39 +++++++++++++++++++++++++++++++++++++++
debian/rules | 33 +++++++++++++++++++++++++++++++++
debian/source/format | 1 +
9 files changed, 171 insertions(+)
diff --git a/debian/README.source b/debian/README.source
new file mode 100644
index 0000000..dd8e8c8
--- /dev/null
+++ b/debian/README.source
@@ -0,0 +1,14 @@
+smrtanalysis for Debian
+-----------------------
+
+Pacific Biosciences distributes the SMRT Analysis suite releases on
+<http://www.pacb.com/devnet/>. The components are in various Github
+repositories at <https://github.com/PacificBiosciences>. The top-level
+SMRT Analysis repository there is used as the source for this package,
+but it contains only documentation.
+
+License information is in the main release and also in the subcomponents'
+repositories.
+
+ -- Afif Elghraoui <afif at ghraoui.name>, Sat, 16 May 2015 15:02:05 -0700
+
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..2d131c6
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+smrtanalysis (2.3.0-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #nnnn) <nnnn is the bug number of your ITP>
+
+ -- Afif Elghraoui <afif at ghraoui.name> Sat, 16 May 2015 00:13:48 -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..edf671b
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,39 @@
+Source: smrtanalysis
+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),
+ pandoc
+Standards-Version: 3.9.5
+Homepage: https://github.com/PacificBiosciences/SMRT-Analysis
+Vcs-Git: git://anonscm.debian.org/debian-med/smrtanalysis.git
+Vcs-Browser: http://anonscm.debian.org/cgit/smrtanalysis.git
+
+Package: smrtanalysis
+Architecture: all
+Depends: ${misc:Depends}
+Description: software suite for single molecule, real-time sequencing
+ SMRT® Analysis is a powerful, open-source bioinformatics software suite
+ available for analysis of DNA sequencing data from Pacific Biosciences’
+ SMRT technology.
+ .
+ Users can choose from a variety of analysis protocols that utilize PacBio®
+ and third-party tools. Analysis protocols include de novo genome assembly,
+ cDNA mapping, DNA base-modification detection, and long-amplicon analysis to
+ determine phased consensus sequences.
+ .
+ This is a metapackage that depends on the components of SMRT Analysis
+
+Package: smrtportal
+Architecture: all
+Depends: smrtanalysis,
+ ${misc:Depends}
+Description: web interface for smrtanalysis
+ The browser-based SMRT Portal GUI offers push-button analysis, allowing the
+ user to create, submit, and monitor analysis jobs. The underlying algorithms
+ can be accessed on the command-line for pipeline development with SMRT Pipe,
+ utilizing LIMS-friendly APIs and a large collection of utilities for working
+ with PacBio bas.h5 files and other common file formats. SMRT View is an
+ application for graphical visualization of processed and annotated sequence
+ data, including kinetics data unique to PacBio SMRT technology.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..b215fa0
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,36 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: SMRT Analysis
+Source: https://github.com/PacificBiosciences/SMRT-Analysis
+
+Files: *
+Copyright: 2013-2015 Pacific Biosciences of California, Inc.
+License: BSD-3-Clause
+
+Files: debian/*
+Copyright: 2015 Afif Elghraoui <afif at ghraoui.name>
+License: BSD-3-Clause
+
+License: BSD-3-Clause
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+ 2. 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.
+ 3. Neither the name of the University nor the names of its contributors
+ may be used to endorse or promote products derived from this software
+ without specific prior written permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND 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 THE HOLDERS OR
+ 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..a293306
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1,3 @@
+README.md
+index.html
+docs-html/
diff --git a/debian/get-orig-source b/debian/get-orig-source
new file mode 100755
index 0000000..fcda3aa
--- /dev/null
+++ b/debian/get-orig-source
@@ -0,0 +1,39 @@
+#!/bin/sh
+# if you need to repack for whatever reason you can
+# use this script via uscan or directly
+#
+# FIXME: currently the code is not conform to Debian Policy
+# http://www.debian.org/doc/debian-policy/ch-source.html
+# "get-orig-source (optional)"
+# This target may be invoked in any directory, ...
+# --> currently it is assumed the script is called in the
+# source directory featuring the debian/ dir
+
+COMPRESS=xz
+
+set -e
+NAME=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
+
+if ! echo $@ | grep -q upstream-version ; then
+ VERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 's/\([0-9\.]\+\)-[0-9]\+$/\1/'`
+ git clone --depth 1 --recursive \
+ https://github.com/PacificBiosciences/SMRT-Analysis.git \
+ ../${NAME}-${VERSION}
+else
+ VERSION=`echo $@ | sed "s?^.*--upstream-version \([0-9.]\+\) .*${NAME}.*?\1?"`
+ if echo "$VERSION" | grep -q "upstream-version" ; then
+ echo "Unable to parse version number"
+ exit
+ fi
+fi
+
+TARDIR=${NAME}-${VERSION}
+mkdir -p ../tarballs
+cd ../tarballs
+
+# Remove useless files
+rm -rf ../${TARDIR}/.git*
+rm -rf ../${TARDIR}/docs/.git*
+
+GZIP="--best --no-name" tar --owner=root --group=root --mode=a+rX -caf "$NAME"_"$VERSION".orig.tar.${COMPRESS} "../${TARDIR}"
+rm -rf ../${TARDIR}
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..688932e
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,33 @@
+#!/usr/bin/make -f
+# output every command that modifies files on the build system.
+#DH_VERBOSE = 1
+
+DPKG_EXPORT_BUILDFLAGS = 1
+include /usr/share/dpkg/default.mk
+
+# see FEATURE AREAS in dpkg-buildflags(1)
+#export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+
+%:
+ dh $@
+
+override_dh_auto_build-indep:
+ mkdir -p docs-html
+ for docfile in docs/*.md; do \
+ outfile=$$(basename $${docfile%.md}); \
+ pandoc -f markdown_github -t html $$docfile | \
+ pandoc -f mediawiki --standalone --toc -t html \
+ -o docs-html/$$outfile; \
+ mv docs-html/$$outfile "docs-html/`echo $$outfile | tr '-' ' '`"; \
+ done
+ ln -s docs-html/Home index.html
+
+override_dh_auto_clean:
+ dh_auto_clean
+ rm -rf index.html docs-html
+
+override_dh_compress:
+ dh_compress --exclude=docs-html/
+
+get-orig-source:
+ . debian/get-orig-source
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)
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/smrtanalysis.git
More information about the debian-med-commit
mailing list