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 <[email protected]> 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 <[email protected]> +Uploaders: Steffen Moeller <[email protected]> +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 <[email protected]> +License: GPL-2.0 + +Files: debian/* +Copyright: 2018 Steffen Moeller <[email protected]> +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 You're receiving this email because of your account on salsa.debian.org.
_______________________________________________ debian-med-commit mailing list [email protected] https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
