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 <[email protected]> Wed, 13 May 2020 14:43:42 +0200 ===================================== debian/control ===================================== @@ -0,0 +1,30 @@ +Source: parallel-fastq-dump +Maintainer: Debian Med Packaging Team <[email protected]> +Uploaders: Andreas Tille <[email protected]> +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 <[email protected]> +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@-$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.
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