[med-svn] [Git][med-team/parallel-fastq-dump][master] Initial packaging

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / parallel-fastq-dump


Commits:
b4de1c07 by Andreas Tille at 2020-05-13T15:05:49+02:00
Initial packaging

- - - - -


8 changed files:

- + debian/changelog
- + debian/control
- + debian/copyright
- + debian/rules
- + debian/salsa-ci.yml
- + debian/source/format
- + debian/upstream/metadata
- + debian/watch


Changes:

=====================================
debian/changelog
=====================================
@@ -0,0 +1,5 @@
+parallel-fastq-dump (0.6.6-1) UNRELEASED; urgency=medium
+
+  * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org>  Wed, 13 May 2020 14:43:42 +0200


=====================================
debian/control
=====================================
@@ -0,0 +1,30 @@
+Source: parallel-fastq-dump
+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-compat (= 12),
+               dh-python,
+               python3,
+               python3-setuptools
+Standards-Version: 4.5.0
+Vcs-Browser: https://salsa.debian.org/med-team/parallel-fastq-dump
+Vcs-Git: https://salsa.debian.org/med-team/parallel-fastq-dump.git
+Homepage: https://github.com/rvalieris/parallel-fastq-dump
+
+Package: parallel-fastq-dump
+Architecture: all
+Depends: ${python3:Depends},
+         ${misc:Depends},
+         sra-toolkit
+Description: parallel fastq-dump wrapper
+ NCBI fastq-dump can be very slow sometimes, even if you have the
+ resources (network, IO, CPU) to go faster, even if you already
+ downloaded the sra file (see the protip below). This tool speeds up the
+ process by dividing the work into multiple threads.
+ .
+ This is possible because fastq-dump have options (-N and -X) to query
+ specific ranges of the sra file, this tool works by dividing the work
+ into the requested number of threads, running multiple fastq-dump in
+ parallel and concatenating the results back together, as if you had just
+ executed a plain fastq-dump call.


=====================================
debian/copyright
=====================================
@@ -0,0 +1,30 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: parallel-fastq-dump
+Source: https://github.com/rvalieris/parallel-fastq-dump/releases
+
+Files: *
+Copyright: 2017-2020 Renan Valieris
+License: MIT
+
+Files: debian/*
+Copyright: 2020 Andreas Tille <tille at debian.org>
+License: MIT
+
+License: MIT
+ 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/rules
=====================================
@@ -0,0 +1,7 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+export LC_ALL=C.UTF-8
+
+%:
+	dh $@ --with python3 --buildsystem=pybuild


=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+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/upstream/metadata
=====================================
@@ -0,0 +1,3 @@
+Registry:
+ - Name: conda:bioconda
+   Entry: parallel-fastq-dump


=====================================
debian/watch
=====================================
@@ -0,0 +1,4 @@
+version=4
+
+opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE at -$1.tar.gz%" \
+https://github.com/rvalieris/parallel-fastq-dump/releases .*/archive/v?@ANY_VERSION@\.tar\.gz



View it on GitLab: https://salsa.debian.org/med-team/parallel-fastq-dump/-/commit/b4de1c0735586af5106b286357a7b3cb4e2694b6

-- 
View it on GitLab: https://salsa.debian.org/med-team/parallel-fastq-dump/-/commit/b4de1c0735586af5106b286357a7b3cb4e2694b6
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20200513/721d66ba/attachment-0001.html>