Andreas Tille pushed to branch master at Debian Med / seqmagick
Commits: a50ad8d6 by Andreas Tille at 2018-05-14T21:11:31+02:00 Initial packaging, some test suite errors are remainig - - - - - 06dc2157 by Andreas Tille at 2018-05-14T21:49:25+02:00 Test suite has issues - reported upstream - - - - - 10 changed files: - + debian/changelog - + debian/compat - + debian/control - + debian/copyright - + debian/createmanpages - + debian/manpages - + debian/rules - + debian/seqmagick.1 - + debian/source/format - + debian/watch Changes: ===================================== debian/changelog ===================================== --- /dev/null +++ b/debian/changelog @@ -0,0 +1,6 @@ +seqmagick (0.7.0-1) UNRELEASED; urgency=medium + + * Initial release (Closes: #<bug>) + TODO: https://github.com/fhcrc/seqmagick/issues/73 + + -- Andreas Tille <[email protected]> Thu, 22 Jun 2017 12:03:20 +0200 ===================================== debian/compat ===================================== --- /dev/null +++ b/debian/compat @@ -0,0 +1 @@ +11 ===================================== debian/control ===================================== --- /dev/null +++ b/debian/control @@ -0,0 +1,41 @@ +Source: seqmagick +Maintainer: Debian Med Packaging Team <[email protected]> +Uploaders: Andreas Tille <[email protected]> +Section: science +Priority: optional +Build-Depends: debhelper (>= 11~), + dh-python, + python3-all, + python3-setuptools, + python3-nose, + python3-biopython +Standards-Version: 4.1.4 +Vcs-Browser: https://salsa.debian.org/med-team/seqmagick +Vcs-Git: https://salsa.debian.org/med-team/seqmagick.git +Homepage: https://github.com/fhcrc/seqmagick/ + +Package: seqmagick +Architecture: all +Depends: ${python3:Depends}, + ${misc:Depends}, + python3-biopython +Description: imagemagick-like frontend to Biopython SeqIO + Seqmagick is a little utility to expose the file format conversion + in BioPython in a convenient way. + . + Features include: + . + * Modifying sequences: + - Remove gaps + - Reverse & reverse complement + - Trim to a range of residues + - Change case + - Sort by length or ID + * Displaying information about sequence files + * Subsetting sequence files by: + - Position + - ID + - Deduplication + * Filtering sequences by quality score + * Trimming alignments to a region of interest defined by the forward + and reverse primers ===================================== debian/copyright ===================================== --- /dev/null +++ b/debian/copyright @@ -0,0 +1,24 @@ +Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Source: https://github.com/fhcrc/seqmagick/releases + +Files: * +Copyright: 2014-2017 Matsen Group +License: GPL-3+ + +Files: debian/* +Copyright: 2017 Andreas Tille <[email protected]> +License: GPL-3+ + +License: GPL-3+ + This program 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, either version 3 of the License, or + (at your option) any later version. + . + This program 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. + . + On Debian systems you can find a copy of the full text of the GNU General + Public License version 3 at /usr/share/common-licenses/GPL-3. ===================================== debian/createmanpages ===================================== --- /dev/null +++ b/debian/createmanpages @@ -0,0 +1,22 @@ +#!/bin/sh +MANDIR=debian +mkdir -p $MANDIR + +VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'` + +AUTHOR=".SH AUTHOR\nThis manpage was written by $DEBFULLNAME for the Debian distribution and +can be used for any other usage of the program. +" + +progname=seqmagick +help2man --no-info --no-discard-stderr \ + --name='Manipulate sequence files' \ + --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1 +echo $AUTHOR >> $MANDIR/${progname}.1 + +cat <<EOT +Please enhance the help2man output. +The following web page might be helpful in doing so: + http://liw.fi/manpages/ +EOT + ===================================== debian/manpages ===================================== --- /dev/null +++ b/debian/manpages @@ -0,0 +1 @@ +debian/*.1 ===================================== debian/rules ===================================== --- /dev/null +++ b/debian/rules @@ -0,0 +1,7 @@ +#!/usr/bin/make -f + +# DH_VERBOSE := 1 +export LC_ALL=C.UTF-8 + +%: + dh $@ --with python3 --buildsystem=pybuild ===================================== debian/seqmagick.1 ===================================== --- /dev/null +++ b/debian/seqmagick.1 @@ -0,0 +1,60 @@ +.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4. +.TH SEQMAGICK "1" "June 2017" "seqmagick 0.6.1" "User Commands" +.SH NAME +seqmagick \- Manipulate sequence files +.SH SYNOPSIS +usage: seqmagick [\-h] [\-V] [\-v] [\-q] +.IP +{help,convert,info,mogrify,primer\-trim,quality\-filter,extract\-ids,backtrans\-align} +\&... +.SH DESCIPTION +Seqmagick is a little utility to expose the file format conversion +in BioPython in a convenient way. +.SH OPTIONS +.SS "positional arguments:" +.IP +{help,convert,info,mogrify,primer\-trim,quality\-filter,extract\-ids,backtrans\-align} +.TP +help +Detailed help for actions using help <action> +.TP +convert +Convert between sequence formats +.TP +info +Info action +.TP +mogrify +Modify sequence file(s) in place. +.TP +primer\-trim +Find a primer sequence in a gapped alignment, trim to +amplicon +.TP +quality\-filter +Filter reads based on quality scores +.TP +extract\-ids +Extract the sequence IDs from a file +.TP +backtrans\-align +Given a protein alignment and unaligned nucleotides, +align the nucleotides using the protein alignment. +Protein and nucleotide sequence files must contain the +same number of sequences, in the same order, with the +same IDs. +.SS "optional arguments:" +.TP +\fB\-h\fR, \fB\-\-help\fR +show this help message and exit +.TP +\fB\-V\fR, \fB\-\-version\fR +Print the version number and exit +.TP +\fB\-v\fR, \fB\-\-verbose\fR +Be more verbose. Specify \fB\-vv\fR or \fB\-vvv\fR for even more +.TP +\fB\-q\fR, \fB\-\-quiet\fR +Suppress output +.SH AUTHOR +This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. ===================================== debian/source/format ===================================== --- /dev/null +++ b/debian/source/format @@ -0,0 +1 @@ +3.0 (quilt) ===================================== debian/watch ===================================== --- /dev/null +++ b/debian/watch @@ -0,0 +1,3 @@ +version=4 + +https://github.com/fhcrc/seqmagick/releases .*/archive/(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz) View it on GitLab: https://salsa.debian.org/med-team/seqmagick/compare/44293af7d8be49dfc985f88f1c5f779a51df68ba...06dc2157fd006b25d11866542f03012368df3b16 --- View it on GitLab: https://salsa.debian.org/med-team/seqmagick/compare/44293af7d8be49dfc985f88f1c5f779a51df68ba...06dc2157fd006b25d11866542f03012368df3b16 You're receiving this email because of your account on salsa.debian.org.
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