[med-svn] [rockhopper] 02/02: Initial non-wrking packaging

[Andreas Tille]

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tille pushed a commit to branch master
in repository rockhopper.

commit f754c48e65e099698d79f569f9311cbd10d16431
Author: Andreas Tille <tille at debian.org>
Date:   Fri Feb 9 16:57:13 2018 +0100

    Initial non-wrking packaging
---
 debian/changelog         |  5 +++++
 debian/compat            |  1 +
 debian/control           | 35 +++++++++++++++++++++++++++++++++++
 debian/copyright         | 13 +++++++++++++
 debian/rules             |  9 +++++++++
 debian/source/format     |  1 +
 debian/upstream/metadata | 20 ++++++++++++++++++++
 debian/watch             |  6 ++++++
 8 files changed, 90 insertions(+)

diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..79a6590
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+rockhopper (2.0.3+dfsg-1) UNRELEASED; urgency=medium
+
+  * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org>  Mon, 21 Aug 2017 13:12:44 +0200
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..f599e28
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+10
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..3e49483
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,35 @@
+Source: rockhopper
+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 (>= 10)
+Standards-Version: 4.1.3
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/rockhopper.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/rockhopper.git
+Homepage: http://cs.wellesley.edu/~btjaden/Rockhopper/
+
+Package: rockhopper
+Architecture: any
+Depends: ${shlibs:Depends},
+         ${misc:Depends},
+         libhtsjdk-java
+Description: system for analyzing bacterial RNA-seq data
+ Rockhopper is a comprehensive and user-friendly system for
+ computational analysis of bacterial RNA-seq data. As input, Rockhopper
+ takes RNA sequencing reads output by high-throughput sequencing
+ technology (FASTQ, QSEQ, FASTA, SAM, or BAM files). Rockhopper supports
+ the following tasks:
+ .
+  * Reference based transcript assembly (when one or more reference
+    genomes are available)
+    - Aligning reads to genomes
+    - Assembling transcripts
+    - Identifying transcript boundaries and novel transcripts such as
+      small RNAs
+  * De novo transcript assembly (when reference genomes are unavailable)
+  * Normalizing data from different experiments
+  * Quantifying transcript abundance
+  * Testing for differential gene expression
+  * Characterizing operon structures
+  * Visualizing results in a genome browser
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..a66ee4e
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,13 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: Rockhopper
+Source: http://cs.wellesley.edu/~btjaden/Rockhopper/download.html
+Files-Excluded: net/
+                org/broad/tribble
+
+Files: *
+Copyright: 2013 Brian Tjaden
+License: GPL-3+
+
+Files: debian/*
+Copyright: 2018 Andreas Tille <tille at debian.org>
+License: GPL-3+
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..1f1f174
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,9 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+export LC_ALL=C.UTF-8
+
+include /usr/share/dpkg/default.mk
+
+%:
+	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..abacf73
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,20 @@
+Reference:
+ - Author: Brian Tjaden
+   Title: "De novo assembly of bacterial transcriptomes from RNA-seq data"
+   Journal: Genome Biology
+   Year: 2015
+   DOI: 10.1186/s13059-014-0572-2
+   PMID: 25583448
+   URL: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0572-2
+   eprint: https://genomebiology.biomedcentral.com/track/pdf/10.1186/s13059-014-0572-2?site=genomebiology.biomedcentral.com
+ - Author: Ryan McClure and Divya Balasubramanian and Yan Sun and Maksym Bobrovskyy and Paul Sumby and Caroline A. Genco and Carin K. Vanderpool and Brian Tjaden
+   Title: "Computational analysis of bacterial RNA-Seq data"
+   Journal: Nucleic Acids Research
+   Year: 2013
+   Volume: 41
+   Number: 14
+   Pages: e140
+   DOI: 10.1093/nar/gkt444
+   PMID: 23716638
+   URL: https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkt444
+   eprint: https://academic.oup.com/nar/article-pdf/41/14/e140/4919671/gkt444.pdf
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..c9d13de
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,6 @@
+version=4
+
+opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg.*//g,repack,compression=xz" \
+   http://cs.wellesley.edu/~btjaden/Rockhopper/download.html .*/Rockhopper-(\d.+)\.tar\.bz2
+
+# http://cs.wellesley.edu/~btjaden/Rockhopper/download.html download/current/Rockhopper-(\d.+)\.tar\.bz2

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