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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/transdecoder">Debian Med / transdecoder</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/transdecoder/commit/43407e09c8e15370aa3fdbaf7bcbfe345c09b431">43407e09</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-30T11:54:04Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Point Vcs fields to salsa.debian.org
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/transdecoder/commit/c2f12ce39b236059e03f71dbd5a9ea61082812ca">c2f12ce3</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-30T11:54:04Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.2.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/transdecoder/commit/bc8205e311243681f86c4bfad91c413f11dc7119">bc8205e3</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-30T11:54:48Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/transdecoder/commit/1cbad50d244eb736fada1fde7a7c86456909e809">1cbad50d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-30T11:54:49Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove trailing whitespace in debian/changelog
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/transdecoder/commit/2c5730492014444067f078819afdfd3bf1885ba8">2c573049</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-30T11:54:49Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove trailing whitespace in debian/copyright
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/transdecoder/commit/e355f30befbf20fa2fae5de697458e3032a2cc89">e355f30b</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-30T13:23:25Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix Perl path
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/transdecoder/commit/e82ac8a8ea0768c86dec18f37e9914a7579e6622">e82ac8a8</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-30T13:24:09Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove unused patch
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/transdecoder/commit/3eeef9bab576feb4e392e04a460053010899c4b9">3eeef9ba</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-30T13:25:10Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">May be broken Perl pathes are also in docs - fix path after doc is installed
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/transdecoder/commit/079ee4b070931c3eb4f8210c4cf1acb8f64debfc">079ee4b0</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-30T13:41:32Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
</a>
</li>
<li class="file-stats">
<a href="#3f0ac3aa4f6ad89b3a128470f581cba25e11fae2">
<span class="deleted-file">
−
debian/patches/fix-test
</span>
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/transdecoder/compare/786e4524851fc18eb6f44d685acac7e5564e822a...079ee4b070931c3eb4f8210c4cf1acb8f64debfc#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">transdecoder (5.0.1-2) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="3" 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="LC3" class="line" lang="plaintext"> * Point Vcs fields to salsa.debian.org</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="4" 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="LC4" class="line" lang="plaintext"> * Standards-Version: 4.2.1</span>
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<td class="diff-line-num new new_line" data-linenumber="5" 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="LC5" class="line" lang="plaintext"> * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target</span>
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<td class="diff-line-num new new_line" data-linenumber="6" 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="LC6" class="line" lang="plaintext"> * Remove trailing whitespace in debian/changelog</span>
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<td class="diff-line-num new new_line" data-linenumber="7" 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="LC7" class="line" lang="plaintext"> * Remove trailing whitespace in debian/copyright</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Fix Perl path</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Tue, 30 Oct 2018 14:25:40 +0100</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>
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1
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<td class="diff-line-num new_line" data-linenumber="12" 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="LC12" class="line" lang="plaintext">transdecoder (5.0.1-1) unstable; urgency=medium</span>
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2
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<td class="diff-line-num new_line" data-linenumber="13" 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="LC13" class="line" lang="plaintext"></span>
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<td class="diff-line-num 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">
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> * New upstream version (no need to repackage since binary files are now</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="82" 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="93" 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">@@ -82,4 +93,4 @@ transdecoder (2.0.1+dfsg-1) unstable; urgency=low</td>
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<td class="diff-line-num new_line" data-linenumber="93" 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="LC93" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="83" 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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<td class="diff-line-num new_line" data-linenumber="94" 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="LC94" class="line" lang="plaintext"> * Initial release (Closes: #778300)</span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="plaintext"> -- Michael R. Crusoe <mcrusoe@msu.edu> Fri, 13 Feb 2015 06:26:24 -0500<span class="idiff left right"> </span></span></pre>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext"> -- Michael R. Crusoe <mcrusoe@msu.edu> Fri, 13 Feb 2015 06:26:24 -0500</span></pre>
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<a href="https://salsa.debian.org/med-team/transdecoder/compare/786e4524851fc18eb6f44d685acac7e5564e822a...079ee4b070931c3eb4f8210c4cf1acb8f64debfc#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">@@ -6,9 +6,9 @@ Section: science</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper (>= 11~),</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> liburi-perl</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">1.3</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">Vcs-Browser: https://<span class="idiff left right">anonscm.debian.org/cgit/debian-med/transdecoder.git</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">Vcs-Git: https://<span class="idiff left right">anonscm.debian.org/git/debian-med</span>/transdecoder.git</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">2.1</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Vcs-Browser: https://<span class="idiff left right">salsa.debian.org/med-team/transdecoder</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Vcs-Git: https://<span class="idiff left right">salsa.debian.org/med-team</span>/transdecoder.git</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Homepage: https://transdecoder.github.io/</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">Package: transdecoder</span>
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<a href="https://salsa.debian.org/med-team/transdecoder/compare/786e4524851fc18eb6f44d685acac7e5564e822a...079ee4b070931c3eb4f8210c4cf1acb8f64debfc#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">@@ -20,9 +20,9 @@ License: BSD-3-clause</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> · Neither the name of the Broad Institute nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.**</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"> THIS SOFTWARE IS PROVIDED BY THE BROAD INSTITUTE ''AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"> THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE BROAD INSTITUTE<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES(INCLUDING, BUT NOT LIMITED TO,<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE BROAD INSTITUTE</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext"> WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span></pre>
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<a href="https://salsa.debian.org/med-team/transdecoder/compare/786e4524851fc18eb6f44d685acac7e5564e822a...079ee4b070931c3eb4f8210c4cf1acb8f64debfc#3f0ac3aa4f6ad89b3a128470f581cba25e11fae2"><strong>debian/patches/fix-test</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff">Author: Michael R. Crusoe <michael.crusoe@gmail.com></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff">Description: Fix tests</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- transdecoder.orig/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ transdecoder/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -8,6 +8,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"> cd ./sample_data && ./cleanme.pl</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"> test:</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cd ./sample_data/ && ./runMe.sh</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cd sample_data/cufflinks_example && ./runMe.sh</span></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cd sample_data/pasa_example && ./runMe.sh</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cd sample_data/simple_transcriptome_target && ./runMe.sh</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"> </span></pre>
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<a href="https://salsa.debian.org/med-team/transdecoder/compare/786e4524851fc18eb6f44d685acac7e5564e822a...079ee4b070931c3eb4f8210c4cf1acb8f64debfc#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">@@ -13,8 +13,10 @@ override_dh_auto_clean:</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">override_dh_auto_build:</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">override_dh_auto_test:</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> dh_auto_test</span>
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17
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> cd ./sample_data && for script in ./*/cleanme.pl; do $$($$script); done</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">endif</span>
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18
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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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19
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">override_dh_install:</span>
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20
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> dh_install</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="39" 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="41" 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">@@ -39,3 +41,9 @@ override_dh_fixperms:</td>
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39
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41
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext">override_dh_clean:</span>
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42
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext"> # generated man pages</span>
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41
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext"> dh_clean debian/TransDecoder.LongOrfs.1 debian/TransDecoder.Predict.1</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">override_dh_installdocs:</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> dh_installdocs</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> for pl in `grep -Rl '#![[:space:]]*/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> sed -i '1s?^#![[:space:]]*/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' $${pl} ; \</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> done</span></pre>
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