[med-svn] [Git][med-team/trace2dbest][master] 2 commits: Initial packaging.

Tue May 22 21:27:06 BST 2018

Andreas Tille pushed to branch master at Debian Med / trace2dbest


Commits:
bf144414 by Steffen Möller at 2018-05-22T21:21:47+02:00
Initial packaging.

- - - - -
d3874fe5 by Steffen Möller at 2018-05-22T21:58:28+02:00
First round of improvements.

- - - - -


10 changed files:

- + debian/changelog
- + debian/compat
- + debian/control
- + debian/copyright
- + debian/rules
- + debian/source/format
- + debian/trace2dbest-doc.doc-base
- + debian/trace2dbest-doc.docs
- + debian/trace2dbest.install
- + debian/upstream/metadata


Changes:

=====================================
debian/changelog
=====================================

--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+trace2dbest (3.0.1-1) unstable; urgency=medium
+
+  * Initial release (closes: #899322)
+
+ -- Steffen Moeller <moeller at debian.org>  Tue, 22 May 2018 19:23:13 +0200


=====================================
debian/compat
=====================================
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+10


=====================================
debian/control
=====================================
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,35 @@
+Source: trace2dbest
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Steffen Moeller <moeller at debian.org>
+Build-Depends: debhelper (>= 10)
+Standards-Version: 4.1.4
+Homepage: http://www.nematodes.org/bioinformatics/trace2dbEST/
+Vcs-Git: https://salsa.debian.org/med-team/trace2dbest.git
+Vcs-Browser: https://salsa.debian.org/med-team/trace2dbest
+
+Package: trace2dbest
+Architecture: all
+Depends: ${misc:Depends}, perl
+Description: bulk submission of chromatogram data to dbEST
+ ESTs are short sequences derived from reverse-transcribed RNA.
+ Their abundances yield insights in the expression of genes across
+ tissues, support the discovery of new genes and allow one to assess
+ the coverage of whole genome sequencing projects. Public databases
+ like dbEST at the NCBI collect this data.
+ .
+ trace2dbEST process raw sequenceing chromatograph trace files from
+ EST projects into quality-checked sequences, ready for submission to
+ dbEST. trace2dbEST guides you through the creation of all the necessary
+ files for submission of ESTs to dbEST. trace2dbest makes use of other
+ software (available free under academic licence) that you will need to
+ have installed, namely phred, cross_match and (optionally) BLAST.
+
+Package: trace2dbest-doc
+Architecture: all
+Depends: ${misc:Depends}
+Recommends: pdf-viewer|xpdf
+Description: Documentation and sample files for trace2dbest
+ Sequence files and user guide to trace2dbEST.
+


=====================================
debian/copyright
=====================================
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,27 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: trace2dbest
+Source: http://www.nematodes.org/downloads/software/trace2dbest/trace2dbest_3.0.1.tar.gz
+
+Files: *
+Copyright: 2005 Alasdair Anthony, Ralf Schmid <nematode.bioinf at ed.ac.uk>
+License: GPL-2.0
+
+Files: debian/*
+Copyright: 2018 Steffen Moeller <moeller at debian.org>
+License: GPL-2.0
+
+License: GPL-2.0
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; version 2 of the License.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <https://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".


=====================================
debian/rules
=====================================
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,7 @@
+#!/usr/bin/make -f
+
+%:
+	dh $@
+
+override_dh_compress:
+	dh_compress -X.pdf -X.gz


=====================================
debian/source/format
=====================================
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)


=====================================
debian/trace2dbest-doc.doc-base
=====================================
--- /dev/null
+++ b/debian/trace2dbest-doc.doc-base
@@ -0,0 +1,8 @@
+Document: trace2dbest
+Title: User Guide to trace2dbest
+Author: Alasdair Anthony, Ralf Schmid, John Parkinson, Mark Blaxter
+Abstract: Guided tour to submitting bulk EST data
+Section: Science/Biology
+
+Format: PDF
+Files: /usr/share/doc/trace2dbest-doc/trace2dbest3.0_UG.pdf


=====================================
debian/trace2dbest-doc.docs
=====================================
--- /dev/null
+++ b/debian/trace2dbest-doc.docs
@@ -0,0 +1,3 @@
+*.pdf
+*.seq
+example_traces.tar.gz


=====================================
debian/trace2dbest.install
=====================================
--- /dev/null
+++ b/debian/trace2dbest.install
@@ -0,0 +1 @@
+*.pl	usr/bin


=====================================
debian/upstream/metadata
=====================================
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,34 @@
+Reference:
+ - Author: John Parkinson and Alasdair Anthony and James Wasmuth and
+    Ralf Schmid and Ann Hedley and Mark Blaxter
+   Title: PartiGene—constructing partial genomes
+   Journal: Bioinformatics
+   Volume: 20
+   Issue: 9
+   Day: 12
+   Month: 6
+   Year: 2004
+   Pages: 1398–1404
+   URL: https://academic.oup.com/bioinformatics/article/20/9/1398/195483
+   DOI: 10.1093/bioinformatics/bth101
+   ePrint: "https://academic.oup.com/bioinformatics/article-pdf/\
+    20/9/1398/490254/bth101.pdf"
+ - Author: Ralf Schmid and Mark Blaxter
+   Year: 2009
+   Type: Book chapter
+   Title: >
+    EST Processing: From Trace to Sequence
+   Editor: John Parkinson
+   Booktitle: Expressed Sequence Tags (ESTs)
+   Series: Methods in Molecular Biology (Methods and Protocols)
+   Volume: 533
+   Publisher: Humana Press
+   ISBN: 978-1-58829-759-4
+   DOI: 10.1007/978-1-60327-136-3_9
+Registry:
+ - Name: OMICtools
+   Entry: NA
+ - Name: SciCrunch
+   Entry: NA
+ - Name: bio.tools
+   Entry: NA



View it on GitLab: https://salsa.debian.org/med-team/trace2dbest/compare/c41da461abcc9e4a310030c2c4c55754f12c5beb...d3874fe5d4ff5daf664cebee10fa5c60d19845d9

-- 
View it on GitLab: https://salsa.debian.org/med-team/trace2dbest/compare/c41da461abcc9e4a310030c2c4c55754f12c5beb...d3874fe5d4ff5daf664cebee10fa5c60d19845d9
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