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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/ensembl-vep">Debian Med / ensembl-vep</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/ensembl-vep/-/commit/4b1f2bae85fca248e5c4c7f3a1dba2d02faeff7c">4b1f2bae</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-05-28T11:36:04+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add todo
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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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+
debian/install
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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/ensembl-vep/-/commit/4b1f2bae85fca248e5c4c7f3a1dba2d02faeff7c#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">ensembl-vep (100.2-1) 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"> TODO:</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> 1. Can't locate Bio/EnsEMBL/Registry.pm in @INC (you may need to install the Bio::EnsEMBL::Registry module)</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> ---> https://plants.ensembl.org/info/docs/api/registry.html</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> 2. Check install method - probably there is some more elegant way than debian/install</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> 3. Run Build time tests</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Thu, 28 May 2020 09:22:57 +0200</span></pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/ensembl-vep/-/commit/4b1f2bae85fca248e5c4c7f3a1dba2d02faeff7c#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -3,7 +3,9 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.</td>
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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 (= 13)</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13),</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> libmodule-build-perl,</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> perl</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Standards-Version: 4.5.0</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/ensembl-vep</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/ensembl-vep.git</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="14" 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">@@ -12,7 +14,15 @@ Homepage: https://github.com/Ensembl/ensembl-vep/</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Package: ensembl-vep</span>
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13
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Architecture: any</span>
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14
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Depends: ${perl:Depends},</span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> ${misc:Depends}</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> ${misc:Depends},</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> libarchive-zip-perl,</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> libdbi-perl</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">Recommends: libdbd-mariadb-perl,</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> libset-intervaltree-perl,</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> libjson-perl,</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> libperlio-gzip-perl,</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">Suggests: libbio-db-bigfile-perl</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"># Bio::DB::BigFile is not yet packaged: https://metacpan.org/pod/release/LDS/Bio-BigFile-1.07/lib/Bio/DB/BigFile.pm</span>
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16
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">Description: Variant Effect Predictor predicting the functional effects of genomic variants</span>
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17
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> The Ensembl Variant Effect Predictor predicts the functional effects of</span>
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18
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28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> genomic variants. It has three components:</span>
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<a href="https://salsa.debian.org/med-team/ensembl-vep/-/commit/4b1f2bae85fca248e5c4c7f3a1dba2d02faeff7c#68d8c5c6babbf5cf109b2584c454449dbff75772"><strong>debian/install</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">filter_vep usr/bin</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">haplo usr/bin</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">variant_recoder usr/bin</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">vep usr/bin</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">modules/* usr/share/perl5</span></pre>
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<a href="https://salsa.debian.org/med-team/ensembl-vep/-/commit/4b1f2bae85fca248e5c4c7f3a1dba2d02faeff7c#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">@@ -20,6 +20,12 @@ include /usr/share/dpkg/default.mk</td>
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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"> dh $@</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">override_dh_install:</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> dh_install</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> for perlscript in `grep -l '#!/usr/bin/env \+perl' debian/*/usr/bin/*` ; do \</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> sed -i '1s+#!/usr/bin/env perl+#!/usr/bin/perl+' $${perlscript} ; \</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> done</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"></span>
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23
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">#override_dh_auto_test:</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">#ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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