[med-svn] [Git][med-team/seqmagick][master] 2 commits: Initial packaging, some test suite errors are remainig
Andreas Tille
gitlab at salsa.debian.org
Tue May 15 06:34:12 BST 2018
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 <tille at debian.org> 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 <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+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 <tille at debian.org>
+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
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