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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/mummer">Debian Med / mummer</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/mummer/-/commit/b672108676d6225bcaee0458d0e487b44f8da047">b6721086</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-07-23T20:32:33+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removing csh dependency
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mummer/-/commit/087f106eed0bce2924e082aaa27f5286e119cd40">087f106e</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-07-23T21:49:18+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added patch to suppress csh related errors
While all is in place already to not depend on csh, there are still
a few checks that are done in two Makefiles and which are causing
error messages during package construction, such as "csh not found"
or an ugly ERROR message during the check (which actually is a
check for availability of build dependencies, and not a real test
suite after compilation.)
This patch removes the unnecessary checks on the now missing csh.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mummer/-/commit/92c67297a4af491111cb4dd64ff01a619b89c455">92c67297</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-07-24T09:13:11+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove csh from docs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mummer/-/commit/1fa199755cf149c6f8b82b910e1c5efb981c2dc3">1fa19975</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-07-24T09:16:08+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debhelper-compat (= 13)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mummer/-/commit/c4c79444f140f59f27e623866e49ccecffcb9b3e">c4c79444</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-07-24T09:22:18+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
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<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="#1c628c5ffcb916d0bc16845567d9660b470141d2">
<span class="new-file">
+
debian/patches/remove-csh-dependency.patch
</span>
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</li>
<li class="file-stats">
<a href="#b79fa61de45b4776d1f9d3d1d3e093effdb63b83">
<span class="new-file">
+
debian/patches/remove-csh-from-doc.patch
</span>
</a>
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/mummer/-/compare/72fbe1757b4933638964f60a947372b2eecb6774...c4c79444f140f59f27e623866e49ccecffcb9b3e#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">mummer (3.23+dfsg-6) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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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"> [ Étienne Mollier ]</span>
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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"> * Team upload.</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"> * Removed dependency to C-Shell.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
</pre>
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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"> [ Andreas Tille ]</span>
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<td class="diff-line-num new new_line" data-linenumber="8" 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="LC8" class="line" lang="plaintext"> * Remove csh from docs</span>
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<td class="diff-line-num new new_line" data-linenumber="9" 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="LC9" class="line" lang="plaintext"> * debhelper-compat (= 13)</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="11" 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="LC11" class="line" lang="plaintext"> -- Étienne Mollier <etienne.mollier@mailoo.org> Thu, 23 Jul 2020 20:31:54 +0200</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">mummer (3.23+dfsg-5) unstable; urgency=medium</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"> [ Charles Plessy ]</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/mummer/-/compare/72fbe1757b4933638964f60a947372b2eecb6774...c4c79444f140f59f27e623866e49ccecffcb9b3e#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5" 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">@@ -5,11 +5,10 @@ Uploaders: Steffen Moeller <moeller@debian.org>,</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> Charles Plessy <plessy@debian.org></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">2</span>),</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">3</span>),</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> texlive-latex-base,</span>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> texlive-latex-recommended,</span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> texlive-fonts-recommended,</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> csh | c-shell <!nocheck></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Standards-Version: 4.5.0</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/mummer</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/mummer.git</span>
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<li id="1c628c5ffcb916d0bc16845567d9660b470141d2">
<a href="https://salsa.debian.org/med-team/mummer/-/compare/72fbe1757b4933638964f60a947372b2eecb6774...c4c79444f140f59f27e623866e49ccecffcb9b3e#1c628c5ffcb916d0bc16845567d9660b470141d2"><strong>debian/patches/remove-csh-dependency.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: remove checks for csh</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> While the package can safely be built without csh, there are still a few</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> checks that are causing various error messages at build time. This patch</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> removes them.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Author: Étienne Mollier <etienne.mollier@mailoo.org></span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">Forwarded: no</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">Last-Update: 2020-07-23</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">---</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">This patch header follows DEP-3: http://dep.debian.net/deps/dep3/</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;">--- mummer.orig/Makefile</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;">+++ mummer/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="p">@@ -38,7 +38,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> CC := $(filter /%,$(shell /bin/sh -c 'type gcc'))</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> CXX := $(filter /%,$(shell /bin/sh -c 'type g++'))</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> SED := $(filter /%,$(shell /bin/sh -c 'type sed'))</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CSH := $(filter /%,$(shell /bin/sh -c 'type csh'))</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> PERL := $(filter /%,$(shell /bin/sh -c 'type perl'))</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> AR := $(filter /%,$(shell /bin/sh -c 'type ar'))</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="p">@@ -76,9 +75,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> ifndef SED</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> @echo "ERROR: 'sed' StreamEDitor not found"</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> endif</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ifndef CSH</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @echo "ERROR: 'csh' C-shell not found"</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-endif</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> ifndef PERL</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> @echo "ERROR: 'perl' PERL not found"</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> endif</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- mummer.orig/scripts/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ mummer/scripts/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="p">@@ -18,7 +18,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> endif</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> SED := $(filter /%,$(shell /bin/sh -c 'type sed'))</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CSH := $(filter /%,$(shell /bin/sh -c 'type csh'))</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> PERL := $(filter /%,$(shell /bin/sh -c 'type perl'))</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> VPATH := $(BIN_DIR)</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> </span></pre>
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<li id="b79fa61de45b4776d1f9d3d1d3e093effdb63b83">
<a href="https://salsa.debian.org/med-team/mummer/-/compare/72fbe1757b4933638964f60a947372b2eecb6774...c4c79444f140f59f27e623866e49ccecffcb9b3e#b79fa61de45b4776d1f9d3d1d3e093effdb63b83"><strong>debian/patches/remove-csh-from-doc.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Description: Remove csh from docs</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Last-Update: Thu, 23 Jul 2020 20:31:54 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">--- a/README</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/README</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -68,7 +68,7 @@</span> format (qry.seq) type the following at t</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> or</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- './run-mummer3.csh ref.seq qry.seq <prefix>'</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ './run-mummer3 ref.seq qry.seq <prefix>'</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> To produce the following files:</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> <prefix>.out</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/docs/run-mummer1.README</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/docs/run-mummer1.README</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="p">@@ -38,10 +38,10 @@</span> it crashes for that reason, that's not a</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> required.</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> To use this system, first compile it by typing 'make' at the</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-command line. There is a script, 'run-mummer1.csh', that runs all</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+command line. There is a script, 'run-mummer1', that runs all</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> the steps of aligning two genomes. The script takes these arguments:</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- run-mummer1.csh <genome1> <genome2> <tag> [-r]</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ run-mummer1 <genome1> <genome2> <tag> [-r]</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> The two genomes must DNA sequences in FASTA format. Multi-FASTA</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> files don't work. The tag is used to create 4 output files,</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="p">@@ -60,7 +60,7 @@</span> not performed.</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> IMPORTANT: the performance of the program can critically depend on the</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> minimum MUM length you use. The default is 20bp. If you want to </span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-change it, do the following: edit the file run-mummer1.csh. Add a new</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+change it, do the following: edit the file run-mummer1. Add a new</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> length switch to the 'mummer' call.</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> The other file - one that we often spend lots of time analyzing - is</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="p">@@ -90,8 +90,8 @@</span> Files in this directory:</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> gaps.cc Finds longest consistent set of matches in list</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> produced by mummer1 program.</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- run-mummer1.csh Script to run alignment programs. Format is:</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- run-mummer1.csh <genome1> <genome2> <tag> [-flip]</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ run-mummer1 Script to run alignment programs. Format is:</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ run-mummer1 <genome1> <genome2> <tag> [-flip]</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> <tag> will be used to make output files: <tag>.out , <tag>.gaps</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> and <tag>.align . -r will reverse complement <genome2></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/docs/web/manual/index.html</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/docs/web/manual/index.html</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="p">@@ -516,7 +516,6 @@</span> td {</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> <li><code>make (GNU make 3.79.1)</code></li></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> <li><code>perl (PERL 5.6.0)</code></li></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> <li><code>sh (GNU sh 1.14.7)</code></li></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <li><code>csh (tcsh 6.10.00)</code></li></span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> <li><code>g++ (GNU gcc 2.95.3)</code></li></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> <li><code>sed (GNU sed 3.02)</code></li></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> <li><code>awk (GNU awk 3.0.4)</code></li></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="p">@@ -647,7 +646,7 @@</span> td {</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> can also be viewed with the same utility programs (see above). Refer to the </span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> <a href="#promer">PROmer</a> section for a list of options and output descriptions.</p></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> <h5>run-mummer1 and run-mummer3</h5></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-<p><code>run-mummer1</code> and <code>run-mummer3</code> are cshell script pipelines </span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+<p><code>run-mummer1</code> and <code>run-mummer3</code> are shell script pipelines </span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> for the general alignment of two sequences. They follow the same three steps </span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> of NUCmer and PROmer, in that they match, cluster and extend, however they handle </span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> any input sequence, not just nucleotide. This non-discrimination can be useful, </span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="p">@@ -1192,7 +1191,7 @@</span> Long Exact Matches:</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> repeat positions are denoted by an <code>'r'</code> following the Start2 position, </span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> and are relative to the forward strand of the sequence.</p></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> <h4><a name="exact"></a>5.1.3. exact-tandems</h4></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-<p><code>exact-tandems</code> is a wrapper cshell script for the <code>repeat-match</code> </span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+<p><code>exact-tandems</code> is a wrapper shell script for the <code>repeat-match</code> </span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> program. It provides a list of exact tandem repeats within a single input sequence.</p></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> <h5>Command line syntax</h5></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> <p><code>exact-tandems <sequence file> <min length></code></p></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="p">@@ -1910,7 +1909,7 @@</span> PROMER</span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> and the reverse strand of the query.</p></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> <h5>Program options</h5></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"> <p>There are no available command line options for <code>run-mummer1</code>. Instead, </span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- the user must directly edit the <code>csh</code> script to alter the command </span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ the user must directly edit the <code>sh</code> script to alter the command </span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> line values passed to the individual pipeline programs. The only available tweak </span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"> is changing the minimum match length value for <code>mummer</code>, set with </span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> the <code>-l</code> option within the script. Decreasing this value may increase </span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"><span class="p">@@ -2008,7 +2007,7 @@</span> S: tagctgtcggggcgatcccctcggtagtga</span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> requires hand editing the script.</p></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> <h5>Program options</h5></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"> <p>There are no available command line options for <code>run-mummer3</code>. Instead, </span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- the user must directly edit the <code>csh</code> script to alter the command </span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ the user must directly edit the <code>sh</code> script to alter the command </span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> line values passed to the individual pipeline programs. Altering these parameters </span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"> is suggested for most applications, as the default values may not always produce </span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> the best output. Parameter values may be added or changed for <code>mummer</code>, </span></pre>
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<a href="https://salsa.debian.org/med-team/mummer/-/compare/72fbe1757b4933638964f60a947372b2eecb6774...c4c79444f140f59f27e623866e49ccecffcb9b3e#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</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">@@ -9,3 +9,5 @@ addition_from_mugsy.patch</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"># most probably broken see bug #843621</span>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"># addition_from_report_duplicates.patch</span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">mummerplot.patch</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">remove-csh-dependency.patch</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">remove-csh-from-doc.patch</span></pre>
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