This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository rockhopper.
commit f754c48e65e099698d79f569f9311cbd10d16431 Author: Andreas Tille <ti...@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 <ti...@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-packag...@lists.alioth.debian.org> +Uploaders: Andreas Tille <ti...@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 <ti...@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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/rockhopper.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit