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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/fieldbioinformatics">Debian Med / fieldbioinformatics</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/fieldbioinformatics/-/commit/8e699457839447c812f7c371aae63234da9314bf">8e699457</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-06-23T14:10:26+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to new
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<strong><a href="https://salsa.debian.org/med-team/fieldbioinformatics/-/commit/06e1c2a8d8e97d12d83365962cf21a60175f8b12">06e1c2a8</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-06-23T15:12:27+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Shorter synopsis
</pre>
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<strong><a href="https://salsa.debian.org/med-team/fieldbioinformatics/-/commit/42dd48213eb592bbd590dbb71bb0cc76a1f344e7">42dd4821</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-06-23T15:48:51+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix DEP5
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<li>
<strong><a href="https://salsa.debian.org/med-team/fieldbioinformatics/-/commit/b396c4fce7ac9ebbc936bf80bc21181b08fa6710">b396c4fc</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-06-23T15:49:08+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Make sure package fieldbioinformatics will not remain empty
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<h4>4 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/fieldbioinformatics/-/compare/ae338338e9c3435fbdbaa8907f9c7cf4eca5267a...b396c4fce7ac9ebbc936bf80bc21181b08fa6710#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">fieldbioinformatics (1.1.3-1) <span class="idiff left right">unstable</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">fieldbioinformatics (1.1.3-1) <span class="idiff left right">UNRELEASED</span>; 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: #963530)</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> * New upstream release</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"> -- Malihe Asemani <ml.asemani@gmail.com> Tue, 16 Jun 2020 22:25:27 +0430</span></pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/fieldbioinformatics/-/compare/ae338338e9c3435fbdbaa8907f9c7cf4eca5267a...b396c4fce7ac9ebbc936bf80bc21181b08fa6710#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -16,7 +16,7 @@ Package: fieldbioinformatics</td>
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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">Description: pipeline <span class="idiff left right">for working</span> with virus sequencing data sequenced with nanopore</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">Description: pipeline with virus sequencing data sequenced with nanopore</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> This is the ARTIC bioinformatics pipeline for working with virus sequencing</span>
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<td class="diff-line-num old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> data, sequenced with nanopore. Nanopore is a complete bioinformatics</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> protocol to take the output from the sequencing protocol to consensus</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -28,7 +28,7 @@ Architecture: all</td>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">Depends: ${python3:Depends},</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"> ${misc:Depends}</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">Enhances: fieldbioinformatics</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext">Description: pipeline for <span class="idiff left right">working with </span>virus sequencing data sequenced with nanopore (examples)</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">Description: pipeline for virus sequencing data sequenced with nanopore (examples)</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"> This is the ARTIC bioinformatics pipeline for working with virus sequencing</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> data, sequenced with nanopore. Nanopore is a complete bioinformatics</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> protocol to take the output from the sequencing protocol to consensus</span>
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<a href="https://salsa.debian.org/med-team/fieldbioinformatics/-/compare/ae338338e9c3435fbdbaa8907f9c7cf4eca5267a...b396c4fce7ac9ebbc936bf80bc21181b08fa6710#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,6 +8,8 @@ License: MIT</td>
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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 Malihe Asemani <ml.asemani@gmail.com></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">License: MIT</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">License: MIT</span>
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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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<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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -25,4 +27,4 @@ License: MIT</td>
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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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<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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<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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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"> SOFTWARE.</span></pre>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">\ No newline at end of file</td>
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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/fieldbioinformatics/-/compare/ae338338e9c3435fbdbaa8907f9c7cf4eca5267a...b396c4fce7ac9ebbc936bf80bc21181b08fa6710#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -11,6 +11,13 @@ export PYBUILD_NAME=fieldbioinformatics</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> dh $@ --with python3 --buildsystem=pybuild</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">override_dh_auto_install:</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> dh_auto_install</span>
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> # FIXME: Hmmmm, no idea why this dirty hack is needed but files are</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> # installed like into a python3 modules package</span>
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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> mv debian/python3-$(PYBUILD_NAME)/* debian/$(PYBUILD_NAME)</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> rmdir debian/python3-$(PYBUILD_NAME)</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"></span>
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14
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">override_dh_auto_test:</span>
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<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
15
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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16
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> echo "Test is downloading extra data and thus can not be running here"</span>
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