[med-svn] [Git][med-team/catfishq][master] Initial packaging.
Steffen Möller (@moeller)
gitlab at salsa.debian.org
Sun May 23 17:15:29 BST 2021
Steffen Möller pushed to branch master at Debian Med / catfishq
Commits:
664e1be6 by Steffen Moeller at 2021-05-23T18:15:21+02:00
Initial packaging.
- - - - -
12 changed files:
- + debian/README.source
- + debian/catfishq.1
- + debian/changelog
- + debian/control
- + debian/copyright
- + debian/manpages
- + debian/rules
- + debian/salsa-ci.yml
- + debian/source/format
- + debian/source/options
- + debian/upstream/metadata
- + debian/watch
Changes:
=====================================
debian/README.source
=====================================
@@ -0,0 +1,4 @@
+The license was stated on the github page
+(https://github.com/philres/catfishq) but apparently did not make it
+into the PyPI archive.
+Informed upstream via https://github.com/philres/catfishq/issues/10
=====================================
debian/catfishq.1
=====================================
@@ -0,0 +1,66 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.48.1.
+.TH CATFISHQ "1" "May 2021" "catfishq 1.1.3+ds" "User Commands"
+.SH NAME
+catfishq \- concatenates fastq files
+.SH DESCRIPTION
+usage: catfishq [\-h]
+.IP
+[\-\-log {DEBUG,INFO,WARNING,ERROR,CRITICAL,debug,info,warning,error,critical}]
+[\-o OUT] [\-l MIN_LEN] [\-q MIN_QSCORE]
+[\-\-max\-sequencing\-time MAX_SEQ_TIME]
+[\-\-min\-sequencing\-time MIN_SEQ_TIME] [\-\-start\-time START_TIME]
+[\-\-print\-start\-time] [\-n MAX_N] [\-b MAX_BP] [\-r] [\-d]
+FASTQ [FASTQ ...]
+.PP
+Cat long lists of FASTQ files
+.SS "positional arguments:"
+.TP
+FASTQ
+FASTQ files or folders containing FASTQ files
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-\-log\fR {DEBUG,INFO,WARNING,ERROR,CRITICAL,debug,info,warning,error,critical}
+Print debug information
+.TP
+\fB\-o\fR OUT, \fB\-\-output\fR OUT
+Output file. (default: stdout)
+.TP
+\fB\-l\fR MIN_LEN, \fB\-\-min\-length\fR MIN_LEN
+Minimum read length
+.TP
+\fB\-q\fR MIN_QSCORE, \fB\-\-min\-qscore\fR MIN_QSCORE
+Minimum q\-score
+.TP
+\fB\-\-max\-sequencing\-time\fR MAX_SEQ_TIME
+Only output reads that where sequenced up to the given
+time (minutes).
+.TP
+\fB\-\-min\-sequencing\-time\fR MIN_SEQ_TIME
+Only output reads that where sequenced after the given
+time (minutes).
+.TP
+\fB\-\-start\-time\fR START_TIME
+Starttime of the run as guppy time stamp (only
+required with \fB\-\-sequencing\-time\fR). If 'min' is given as
+argument the minimal time is detected automatically.
+.TP
+\fB\-\-print\-start\-time\fR
+Print the minimal start_time of all fastq files
+.TP
+\fB\-n\fR MAX_N, \fB\-\-max_n\fR MAX_N
+Stop after <max_n> reads
+.TP
+\fB\-b\fR MAX_BP, \fB\-\-max_mbp\fR MAX_BP
+Stop after <max_bp> mega base pairs
+.TP
+\fB\-r\fR, \fB\-\-recursive\fR
+Search folders recursively
+.TP
+\fB\-d\fR, \fB\-\-dedup\fR
+Remove duplicated reads.
+.SH AUTHOR
+ This manpage was written by Steffen Moeller for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/changelog
=====================================
@@ -0,0 +1,5 @@
+catfishq (1.1.3+ds-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #989015).
+
+ -- Steffen Moeller <moeller at debian.org> Sun, 23 May 2021 16:48:44 +0200
=====================================
debian/control
=====================================
@@ -0,0 +1,28 @@
+Source: catfishq
+Section: science
+Priority: optional
+Maintainer: Steffen Moeller <moeller at debian.org>
+Build-Depends: debhelper-compat (= 13),
+ dh-python,
+ python3-setuptools,
+ python3-all
+# help2man # used only once
+Standards-Version: 4.5.1
+Homepage: https://github.com/philres/catfishq
+Vcs-Browser: https://salsa.debian.org/med-team/catfishq
+Vcs-Git: https://salsa.debian.org/med-team/catfishq.git
+#Testsuite: autopkgtest-pkg-python
+Rules-Requires-Root: no
+
+Package: catfishq
+Architecture: all
+Depends: ${python3:Depends}, ${misc:Depends}
+Description: concatenates fastq files
+ FASTQ is the most common format to store the reads from high-throughput
+ biological sequencing. This tool takes paths to an arbritary number
+ of zipped and unzipped FASTQ files and/or folders containing zipped or
+ unzipped FASTQ files, concatenates them and prints them to standard out
+ (default) or an unzipped output file.
+ .
+ Supported file extensions are: '*.fastq', '*.fastq.gz', '*.fasta',
+ '*.fasta.gz', '*.fa', '*.fa.gz', '*.fq', '*.fq.gz'
=====================================
debian/copyright
=====================================
@@ -0,0 +1,37 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: catfishq
+Upstream-Contact: @philres (github)
+Source: https://github.com/philres/catfishq
+Files-Excluded: catfishq.egg-info/SOURCES.txt
+
+Files: *
+Copyright: 2020 philres
+License: MIT
+
+Files: debian/*
+Copyright: 2021 Steffen Moeller <moeller at debian.org>
+License: MIT
+
+License: MIT
+ The license information is clearly stated by upstream in its github
+ repository, but got lost while expoerting to PyPI. Upstream is
+ informated via https://github.com/philres/catfishq/issues/10
+ .
+ Permission is hereby granted, free of charge, to any person obtaining a
+ copy of this software and associated documentation files (the "Software"),
+ to deal in the Software without restriction, including without limitation
+ the rights to use, copy, modify, merge, publish, distribute, sublicense,
+ and/or sell copies of the Software, and to permit persons to whom the
+ Software is furnished to do so, subject to the following conditions:
+ .
+ The above copyright notice and this permission notice shall be included
+ in all copies or substantial portions of the Software.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+ OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+ IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
+ CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
+ TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+ SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
=====================================
debian/manpages
=====================================
@@ -0,0 +1 @@
+debian/*.1
=====================================
debian/rules
=====================================
@@ -0,0 +1,14 @@
+#!/usr/bin/make -f
+export DH_VERBOSE = 1
+export PYBUILD_NAME=catfishq
+
+%:
+ dh $@ --with python3 --buildsystem=pybuild
+
+override_dh_python3:
+ dh_python3
+ chmod -x debian/catfishq/usr/lib/python3/dist-packages/catfishq-*.egg-info/*
+
+override_dh_auto_clean:
+ dh_auto_clean
+ rm -f catfishq.egg-info/SOURCES.txt
=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,11 @@
+# For more information on what jobs are run see:
+# https://salsa.debian.org/salsa-ci-team/pipeline
+#
+# To enable the jobs, go to your repository (at salsa.debian.org)
+# and click over Settings > CI/CD > Expand (in General pipelines).
+# In "Custom CI config path" write debian/salsa-ci.yml and click
+# in "Save Changes". The CI tests will run after the next commit.
+---
+include:
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
=====================================
debian/source/format
=====================================
@@ -0,0 +1 @@
+3.0 (quilt)
=====================================
debian/source/options
=====================================
@@ -0,0 +1 @@
+extend-diff-ignore = "^[^/]*[.]egg-info/"
=====================================
debian/upstream/metadata
=====================================
@@ -0,0 +1,14 @@
+---
+Registry:
+ - Name: conda:bioconda
+ Entry: NA
+ Checked: 2021-05-23
+ - Name: bio.tools
+ Entry: NA
+ Checked: 2021-05-23
+ - Name: guix
+ Entry: NA
+ Checked: 2021-05-23
+ - Name: SciCrunch
+ Entry: NA
+ Checked: 2021-05-23
=====================================
debian/watch
=====================================
@@ -0,0 +1,3 @@
+version=4
+opts="repack,repacksuffix=+ds,compression=xz,dversionmangle=auto" \
+https://pypi.debian.net/catfishq/catfishq-(.+)\.(?:zip|tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz)))
View it on GitLab: https://salsa.debian.org/med-team/catfishq/-/commit/664e1be605ab61e812d553f8ad283a4a5a83bf4e
--
View it on GitLab: https://salsa.debian.org/med-team/catfishq/-/commit/664e1be605ab61e812d553f8ad283a4a5a83bf4e
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