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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/busco">Debian Med / busco</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/busco/-/commit/f0a2568e2c2e800779fdfdbc5d5621c3b5b16ce7">f0a2568e</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2021-07-25T14:41:08+00:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">[skip ci] Update manpage
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<h4>1 changed file:</h4>
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<a href="#57eaa34160ba31d4c92ba756672f4d55d8251b60">
debian/busco.1
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<h4>Changes:</h4>
<li id="57eaa34160ba31d4c92ba756672f4d55d8251b60">
<a href="https://salsa.debian.org/med-team/busco/-/commit/f0a2568e2c2e800779fdfdbc5d5621c3b5b16ce7#57eaa34160ba31d4c92ba756672f4d55d8251b60"><strong>debian/busco.1</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">.TH BUSCO "1" "July 2021" "busco 5.2.<span class="idiff left right">0</span>" "User Commands"</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH BUSCO "1" "July 2021" "busco 5.2.<span class="idiff left right">2</span>" "User Commands"</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">busco \- benchmarking sets of universal single-copy orthologs</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">usage: busco \fB\-i\fR [SEQUENCE_FILE] \fB\-l\fR [LINEAGE] \fB\-o\fR [OUTPUT_NAME] \fB\-m\fR [MODE] [OTHER OPTIONS]</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">Welcome to BUSCO 5.2.<span class="idiff left right">0</span>: the Benchmarking Universal Single\-Copy Ortholog assessment tool.</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Welcome to BUSCO 5.2.<span class="idiff left right">2</span>: the Benchmarking Universal Single\-Copy Ortholog assessment tool.</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">For more detailed usage information, please review the README file provided with this distribution and the BUSCO user guide. Visit this page https://gitlab.com/ezlab/busco#how\-to\-cite\-busco to see how to cite BUSCO</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">.SS "optional arguments:"</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">\fB\-i\fR SEQUENCE_FILE, \fB\-\-in\fR SEQUENCE_FILE</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">Input sequence file in FASTA format. Can be an assembled genome or transcriptome (DNA), or protein sequences from an annotated gene set.</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Input sequence file in FASTA format. Can be an assembled genome or transcriptome (DNA), or protein sequences from an annotated gene set.<span class="idiff left right"> Also possible to use a path to a directory containing multiple input files.</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">\fB\-o\fR OUTPUT, \fB\-\-out\fR OUTPUT</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Give your analysis run a recognisable short name. Output folders and files will be labelled with this name. WARNING: do not provide a path</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -97,6 +97,9 @@ Disable the info logs, displays only errors</td>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="plaintext">\fB\-r\fR, \fB\-\-restart\fR</span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="plaintext">Continue a run that had already partially completed.</span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext">\fB\-\-tar\fR</span>
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<td class="new_line diff-line-num new" data-linenumber="101" 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">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext">Compress some subdirectories with many files to save space</span>
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<td class="new_line diff-line-num new" data-linenumber="102" 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">
102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext">.TP</span>
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100
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<td class="new_line diff-line-num" data-linenumber="103" 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">
103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="plaintext">\fB\-\-update\-data\fR</span>
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101
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="plaintext">Download and replace with last versions all lineages datasets and files necessary to their automated selection</span>
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102
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="plaintext">.TP</span>
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