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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/sortmerna">Debian Med / sortmerna</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/sortmerna/-/commit/f09615815a7041ba9ec7bc6114012efcbdae608f">f0961581</a></strong>
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<span>by Andreas Tille</span>
<i>at 2022-02-01T13:39:11+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Sort out documentation
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<strong><a href="https://salsa.debian.org/med-team/sortmerna/-/commit/d9b2d7ff6ebf068b5cffc7a147d580a84ef53a1e">d9b2d7ff</a></strong>
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<span>by Andreas Tille</span>
<i>at 2022-02-01T15:31:57+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Sort out doc installation (some of the docs are not part of upstream tarball any more)
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<h4>5 changed files:</h4>
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<a href="#f168b81935360ddcf2dd0f2d4b98b8603829060f">
debian/README_scripts.txt
→
debian/README.Debian
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<a href="#9d9aaaac3f06acf1a05e3b67781afe64b64a22f7">
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−
debian/doc-base
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<li class="file-stats">
<a href="#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32">
debian/docs
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<li class="file-stats">
<a href="#68d8c5c6babbf5cf109b2584c454449dbff75772">
debian/install
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="f168b81935360ddcf2dd0f2d4b98b8603829060f">
<a href="https://salsa.debian.org/med-team/sortmerna/-/compare/5dec8d9ba46763d3e40f04a3cfcadcea16b6008e...d9b2d7ff6ebf068b5cffc7a147d580a84ef53a1e#f168b81935360ddcf2dd0f2d4b98b8603829060f"><strong>debian/README_scripts.txt</strong>
→
<strong>debian/README.Debian</strong>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">sortmerna for Debian</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"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">The Debian package does not come with the large reference files needed to run</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">the pipeline but they can be fetched easily by running the following:</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> $ sudo /usr/share/sortmerna/rRNA_databases/scripts/fetch_rrna_data.sh</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">These files can also be recreated from the original sources. The<span class="idiff left right"> following</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">instructions are provided with the original source release of SortMeRNA<span class="idiff left right">:</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">These files can also be recreated from the original sources. The</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">instructions are provided with the original source release of SortMeRNA</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">(see README.md)</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"> -- Andreas Tille <tille@debian.org> Mon, 31 Jan 2022 13:37:04 +0100</span></pre>
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<a href="https://salsa.debian.org/med-team/sortmerna/-/compare/5dec8d9ba46763d3e40f04a3cfcadcea16b6008e...d9b2d7ff6ebf068b5cffc7a147d580a84ef53a1e#9d9aaaac3f06acf1a05e3b67781afe64b64a22f7"><strong>debian/doc-base</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Document: sortmerna</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">Title: SortMeRNA User Manual</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Author: Evguenia Kopylova <jenya.kopylov@gmail.com></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">Abstract: tool for filtering, mapping and OTU-picking NGS reads</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> SortMeRNA is a biological sequence analysis tool for filtering, mapping and</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> OTU-picking NGS reads. The core algorithm is based on approximate seeds and</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> allows for fast and sensitive analyses of nucleotide sequences. The main</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> application of SortMeRNA is filtering rRNA from metatranscriptomic data.</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> Additional applications include OTU-picking and taxonomy assignation available</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> through QIIME v1.9+ (http://qiime.org - v1.9.0-rc1).</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> SortMeRNA takes as input a file of reads (fasta or fastq format) and one or</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> multiple rRNA database file(s), and sorts apart rRNA and rejected reads into</span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> two files specified by the user. Optionally, it can provide high quality local</span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> alignments of rRNA reads against the rRNA database. SortMeRNA works with</span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> Illumina, 454, Ion Torrent and PacBio data, and can produce SAM and</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> BLAST-like alignments.</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">Section: Science/Biology</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">Format: pdf</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext">Files: /usr/share/doc/sortmerna/SortMeRNA-User-Manual-2.1.pdf</span></pre>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">*.pdf</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">AUTHORS</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">README*</span></pre>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">scripts /usr/share/sortmerna</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">debian/scripts/* /usr/share/sortmerna/rRNA_databases/scripts</span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">rRNA_databases/scripts/* /usr/share/sortmerna/rRNA_databases/scripts</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">tmp/README.txt /usr/share/sortmerna/rRNA_databases</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">sortmerna /usr/bin</span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">indexdb_rna /usr/bin</span></pre>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"># obj-*/src/sortmerna/sortmerna /usr/bin</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">@@ -10,28 +10,9 @@ export CMAKE_PREFIX_PATH=/usr/lib/$(DEB_HOST_MULTIARCH)/cmake/</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> dh $@</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">#override_dh_auto_configure:</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"># dh_auto_configure -- --includedir=/usr/include/sortmerna</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">override_dh_clean:</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> dh_clean</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> rm -f include/memcheck.h</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> rm -rf tmp</span>
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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">override_dh_auto_build:</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"> dh_auto_build</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> mkdir -p tmp</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"> cat debian/README_scripts.txt rRNA_databases/README.txt > tmp/README.txt</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"># Uses old interface of skbio (see README.source)</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext">#override_dh_auto_test:</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext">#ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext"># python3 ./tests/test_sortmerna.py</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext">#endif</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext">override_dh_auto_install:</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext"> #Skip this - do it manually</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext"> true</span>
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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36
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">override_dh_fixperms:</span>
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37
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> dh_fixperms</span>
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