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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/parallel-fastq-dump">Debian Med / parallel-fastq-dump</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/parallel-fastq-dump/-/commit/b4de1c0735586af5106b286357a7b3cb4e2694b6">b4de1c07</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-05-13T15:05:49+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Initial packaging
</pre>
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<h4>8 changed files:</h4>
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debian/changelog
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debian/control
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debian/copyright
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debian/rules
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debian/salsa-ci.yml
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debian/source/format
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debian/upstream/metadata
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debian/watch
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/parallel-fastq-dump/-/commit/b4de1c0735586af5106b286357a7b3cb4e2694b6#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">parallel-fastq-dump (0.6.6-1) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Initial release (Closes: #<bug>)</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Wed, 13 May 2020 14:43:42 +0200</span></pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/parallel-fastq-dump/-/commit/b4de1c0735586af5106b286357a7b3cb4e2694b6#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Source: parallel-fastq-dump</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 12),</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> dh-python,</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> python3,</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> python3-setuptools</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Standards-Version: 4.5.0</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/parallel-fastq-dump</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/parallel-fastq-dump.git</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Homepage: https://github.com/rvalieris/parallel-fastq-dump</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Package: parallel-fastq-dump</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Depends: ${python3:Depends},</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> sra-toolkit</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">Description: parallel fastq-dump wrapper</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> NCBI fastq-dump can be very slow sometimes, even if you have the</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> resources (network, IO, CPU) to go faster, even if you already</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> downloaded the sra file (see the protip below). This tool speeds up the</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> process by dividing the work into multiple threads.</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> This is possible because fastq-dump have options (-N and -X) to query</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> specific ranges of the sra file, this tool works by dividing the work</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> into the requested number of threads, running multiple fastq-dump in</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> parallel and concatenating the results back together, as if you had just</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> executed a plain fastq-dump call.</span></pre>
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<a href="https://salsa.debian.org/med-team/parallel-fastq-dump/-/commit/b4de1c0735586af5106b286357a7b3cb4e2694b6#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Upstream-Name: parallel-fastq-dump</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Source: https://github.com/rvalieris/parallel-fastq-dump/releases</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Files: *</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Copyright: 2017-2020 Renan Valieris</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">License: MIT</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Files: debian/*</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Copyright: 2020 Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">License: MIT</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">License: MIT</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> Permission is hereby granted, free of charge, to any person obtaining a copy</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> of this software and associated documentation files (the "Software"), to deal</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> in the Software without restriction, including without limitation the rights</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> to use, copy, modify, merge, publish, distribute, sublicense, and/or sell</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> copies of the Software, and to permit persons to whom the Software is</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> furnished to do so, subject to the following conditions:</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> .</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> The above copyright notice and this permission notice shall be included in all</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> copies or substantial portions of the Software.</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> .</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> SOFTWARE.</span></pre>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/parallel-fastq-dump/-/commit/b4de1c0735586af5106b286357a7b3cb4e2694b6#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">#!/usr/bin/make -f</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"># DH_VERBOSE := 1</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">export LC_ALL=C.UTF-8</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> dh $@ --with python3 --buildsystem=pybuild</span></pre>
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<li id="b1dbf22e88351ec0d5d1d1a7f53295504b480e61">
<a href="https://salsa.debian.org/med-team/parallel-fastq-dump/-/commit/b4de1c0735586af5106b286357a7b3cb4e2694b6#b1dbf22e88351ec0d5d1d1a7f53295504b480e61"><strong>debian/salsa-ci.yml</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="nn" style="color: #555;">---</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">include</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml</span></span></pre>
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<li id="53399f7f2dd7535c43cdcfa511a9c06044a9c238">
<a href="https://salsa.debian.org/med-team/parallel-fastq-dump/-/commit/b4de1c0735586af5106b286357a7b3cb4e2694b6#53399f7f2dd7535c43cdcfa511a9c06044a9c238"><strong>debian/source/format</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">3.0 (quilt)</span></pre>
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<li id="f5606a935d95a2f20059a7ac1136f47b2edadbf6">
<a href="https://salsa.debian.org/med-team/parallel-fastq-dump/-/commit/b4de1c0735586af5106b286357a7b3cb4e2694b6#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Registry:</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> - Name: conda:bioconda</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> Entry: parallel-fastq-dump</span></pre>
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<a href="https://salsa.debian.org/med-team/parallel-fastq-dump/-/commit/b4de1c0735586af5106b286357a7b3cb4e2694b6#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">version=4</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE@-$1.tar.gz%" \</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">https://github.com/rvalieris/parallel-fastq-dump/releases .*/archive/v?@ANY_VERSION@\.tar\.gz</span></pre>
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