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cariann09cariann09
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v4.0.5 update
Fix GO download
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‎docs/Docs.html‎

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<table style="width: 100%; padding: 0; border-spacing:0; border-collapse:collapse;">
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<tr>
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<td style="background-color: #666666; padding-bottom:4px;">
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<a href="https://csoderlund.github.io" class="white">AGCoL</a> <mark class="white">|</mark>
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<a href="https://csoderlund.github.io/TCW" class="white">TCW Home</a> <mark class="white">|</mark>
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<a href="https://github.com/csoderlund/TCW/releases" class="white">Download</a> <mark class="white">|</mark>
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<a href="./Docs.html" class="current">Docs</a> <mark class="white">|</mark>

‎docs/Install.html‎

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<table style="width: 100%; padding: 0; border-spacing:0; border-collapse:collapse;">
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<tr>
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<td style="background-color: #666666; padding-bottom:4px;">
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<a href="https://csoderlund.github.io" class="white">AGCoL</a> <mark class="white">|</mark>
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<a href="https://csoderlund.github.io/TCW" class="white">TCW Home</a> <mark class="white">|</mark>
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<a href="https://github.com/csoderlund/TCW/releases" class="white">Download</a> <mark class="white">|</mark>
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<a href="./Docs.html" class="white">Docs</a> <mark class="white">|</mark>
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</table>
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<a id="test"></a>
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<p>&nbsp;<p><u>TCW v4.0.5 (July 2025)</u>: Test <i>all</i> TCW programs using the demo files, plus downloaded a UniProt database and GO
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<p><u>TCW v4.0.5 (July 2025)</u>: All TCW programs were tested using the demo files, plus downloaded a UniProt database and GO
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with <ttp>runAS</ttp> and verified it worked. <ttp>RunDE</ttp> was tested with <ttp>edgeR</ttp> and <ttp>goSeq</ttp>.
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<table class="ty" style="font-family: Verdana, Arial, Helvetica, sans-serif; font-size:9pt">
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<tr><td>&nbsp;&nbsp;3. <a href="http://linode.com" class="ext" target="_blank"><ttl>Linode</ttl><sup>2</sup></a> (Ubuntu 22.04.2 LTS)
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<td>MySQL 8.0.33<td>17<td>Nanode<td>&nbsp;&nbsp;1Gb<td>2023
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</table>
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<sup>1</sup><small>MacOS M4: Cap3, OrthoMCL and Muscle are not supplied for this machine.
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<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
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The user can supply cap3 in the <tt>Ext/macM4/CAP3</tt> directory if they want assembly to work.</small>
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<br><sup>2</sup><small>Linux/Linode: <tt>rJava</tt> did not install successfully,
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so the <ttp>runDE</ttp> could not be tested.</small>
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<p><sup>1</sup>MacOS M4: Cap3, OrthoMCL and Muscle are not supplied for this machine.
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<ul><li>
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<ttp>runSingleTCW</ttp>: The user can supply cap3 in the <tt>Ext/macM4/CAP3</tt> directory if they want assembly to work.
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<li>
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<ttp>runMultiTCW</ttp>: Muscle is not necessary since MAFFTA can be used for the MSA.
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<li>
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The user can download and run OrthoMCL and input the results to <ttp>runMultiTCW</ttp>, though
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TCW provides other clustering methods.
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</ul>
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<sup>2</sup>Linux/Linode: <tt>rJava</tt> was installed on Feb2026 and <ttp>runDE</ttp> tested.
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<br><ttp>runAS</ttp> has not been tested on Linode, but was used extensively on the Linux listed below.
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<p><u>TCW v4.0.4 (July 2022)</u>: Used to create multiple large TCW comparative projects with expression levels.
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<p><u>TCW v4.0.4 (July 2022)</u>: The following was used to create multiple large TCW comparative projects with expression levels.
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<table class="ty" style="font-family: Verdana, Arial, Helvetica, sans-serif; font-size:9pt">
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<tr><td><b>Machine</b><td><b>MySQL</b><td><b>Java</b><td><b>Core (CPU)</b><td><b>Memory</b><td><b>Purchased</b>
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<tr><td>Linux x86.64 (Centos 7)
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<td>128Gb
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<td style="text-align: center">2011
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</table>
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<br>See <a href="Summary.html#time" class="ext" target="_blank">Summary</a> for timings.
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<p><u>TCW v4.0.5 (Feb 2026)</u>: All programs and UniProt/GO downloads were tested again with versions
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of Java, MySQL and R less than a year old.
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<p>See <a href="Summary.html#time" class="ext" target="_blank">Summary</a> for timings.
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<a id="install"></a>
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<table style="width: 100%"><tr><td style="text-align: left">

‎docs/Mac-OSX.html‎

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a.ext {font-weight: bold;}
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mark.white {font-family:verdana; font-size:12px; color:white;background:none;}
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ttp {font-family: Arial, monospace; font-size: 14px; font-weight: 600; color: #556B2F; }
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ttl {font-family: 'Lucida Console', monospace; font-size: 14px; font-weight: 600; color: DarkSlateGrey;}
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tt {font-size:13px}
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body {font-family: Verdana, Arial, Helvetica, sans-serif; font-size: 14px; }
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<h3>
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Running /Ext/mac external programs
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</h3>
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<font color=red>Since the release of MacOS 10.15, it is difficult to run programs downloaded from the web unless its been
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authenticated by Apple.</font> Running external programs from TCW,
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you will either get popup that states "xxx cannot be opened because developer cannot be verified", or
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the program will just fail. Do the following:
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<font color=green>Since the release of MacOS 10.15, it is impossible to run programs downloaded
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from the web unless they have been authenticated.</font> Using MacOS Sequoia 15.7.3, I authenticated <tt>diamond</tt> as follows:
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<ol>
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<li>Using the Finder, select the program and Open With "Terminal" or "iTerm".
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<li>You will get a pop-up, select "Open".
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<li>After that, you will be able to run it via TCW.
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<li>Bring up the <ttl>System Setting</ttl>, select <ttl>Privacy&amp;Security</ttl>.
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<li>Run TCW <ttl>Annotate</ttl>. It will popup a window with '<tt>diamond Not Open</tt>'; select <b>Done</b>.
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<li>On the <ttl>Privacy</ttl> window,
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it will now show '<tt>diamond was blocked to protect your Mac.</tt>';
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select <b>Allow Anyway</b>.
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<li>Run TCW <ttl>Annotate</ttl>. It will popup '<tt>Open diamond?</tt>'; select <b>Open Anyway</b>.
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<li>It will then popup
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a window asking for your password. Finally, <tt>diamond</tt> will run.
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</ol>
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I did not have to do this for <ttp>Blast</ttp>, but I did need to do it for the other <ttx>/Ext/mac</ttx> programs.
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All were straight-forward except for <ttp>mafft</ttp>; I had to authenticate all the following in the <ttx>mafftdir</ttx>
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<a href="./img/macOS.png">
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<img src="./img/macOS.png" alt="MacOS" title="macOS authenticate" style="width: 700px; border:1px solid black"></a>
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<p>I had to do the same for <tt>makeblastdb</tt>, <tt>blast</tt> and <tt>tblastx</tt> for the <ttp>runSingleTCW</ttp> pair alignment.
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It was easiest to just keep running Annotate until they were all authenticated.
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<p>
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For <ttp>runMultiTCW</ttp> MSA computations, I had to authenticate all the following in the <ttx>mafftdir</ttx>
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directory:
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<pre>
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bin/
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dvtditr
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f2cl
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</pre>
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Supposedly, there is a way to allow any downloaded program to execute by using:
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<pre>
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sudo spctl --master-disable
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</pre>
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Then in Preferences, Security&amp;Privacy, General, select 'anywhere'. I did not try this.
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I could move the <tt>/Ext</tt> directory around and it would stay authenticated. But when I downloaded a
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new TCW_4.tar.gz, I would have to re-authenticate it. Therefore, if you download an updated TCW, use your
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previous authenticated <tt>/Ext</tt> directory.
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<p>
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There may be an easier way to do this, but this works.
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<!---- END BODY -->
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<p><a href="#top">Go to top</a>
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</td></tr>

‎docs/Release.html‎

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<table style="width: 100%; padding: 0; border-spacing:0; border-collapse:collapse;">
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<td style="background-color: #666666; padding-bottom:4px;">
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<a href="https://csoderlund.github.io" class="white">AGCoL</a> <mark class="white">|</mark>
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<a href="https://csoderlund.github.io/TCW" class="white">TCW Home</a> <mark class="white">|</mark>
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<a href="https://github.com/csoderlund/TCW/releases" class="white">Download</a> <mark class="white">|</mark>
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<a href="./Docs.html" class="white">Docs</a> <mark class="white">|</mark>
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You must have Java v17.0.11 or later, starting with TCW v4.0.5.
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<a id=v405></a>
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<h4>v4.0.5 27-July-2025</h4>
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<h4>v4.0.5 1-March-2025</h4>
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1-March-2026 release:
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<ul>
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<li>The GO database no longer would download. This was fixed by adding the <tt>-L</tt> argument to <tt>curl</tt>.
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</ul>
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27-July-2025 release:
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<li>Building some of the GO tables on MariaDB was very slow; this has been fixed.

‎docs/Summary.html‎

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<table style="width: 100%; padding: 0; border-spacing:0; border-collapse:collapse;">
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<td style="background-color: #666666; padding-bottom:4px;">
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<a href="https://csoderlund.github.io" class="white">AGCoL</a> <mark class="white">|</mark>
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<a href="https://csoderlund.github.io/TCW" class="white">TCW Home</a> <mark class="white">|</mark>
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<a href="https://github.com/csoderlund/TCW/releases" class="white">Download</a> <mark class="white">|</mark>
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<a href="./Docs.html" class="white">Docs</a> <mark class="white">|</mark>

‎docs/img/macOS.png‎

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‎docs/index.html‎

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TCW uses Java, mySQL, optionally R, and various <a href="./External.html">External</a> packages.
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It has been tested on Linux and Mac.
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<ul>
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<li>Last release: TCW v4.0.5 (27-July-25). See <a href="./Release.html">Release Notes</a>.
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<li>Last release: TCW v4.0.5 (1-March-26). See <a href="./Release.html">Release Notes</a>.
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Published in <a href="https://doi.org/10.1101/733311" class="ext" target="_blank">BioRxiv</a> (02-May-2022).
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</table>
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<b>Funding</b>
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<p>All upgrades starting with TCW v1.3 have been developed by CAS without funding.
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<p>All upgrades starting with TCW v1.3 (Sept 2014) have been developed by Cari Soderlund without funding.
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<p>This project was funded in part by National Science Foundation grant <a href="http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1044821" class="ext" target="_blank">IOS-1044821</a>.
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<p><font face="Verdana, Arial, Helvetica, sans-serif" size="2">NSF Disclaimer:

‎docs/tour/index.html‎

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<table style="width: 100%; padding: 0; border-spacing:0; border-collapse:collapse;">
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<td style="background-color: #666666; padding-bottom:4px;">
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<a href="https://csoderlund.github.io" class="white">AGCoL</a> <mark class="white">|</mark>
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<a href="https://csoderlund.github.io/TCW" class="white">TCW Home</a> <mark class="white">|</mark>
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<a href="https://github.com/csoderlund/TCW/releases" class="white">Download</a> <mark class="white">|</mark>
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<a href="../Docs.html" class="white">Docs</a> <mark class="white">|</mark>

‎java/src/sng/runAS/ASMain.java‎

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// download
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String cmd = "curl " + url + inFile + " -o " + outPath;
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String cmd = "curl -L " + url + inFile + " -o " + outPath; // CAS405c follow redirects
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System.err.println(cmd);
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exitVal = rcd.run(cmd, null); // current directory, print stderr
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‎java/src/sng/runAS/DoOBO.java‎

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/** Header lines **/
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// format-version: 1.2
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line = inFH.readLine();
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if (line==null) {
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Out.PrtErr("OBO file is empty. " + goDir+"/"+goFile); // CAS405c
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return false;
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}
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String [] tok = line.split(":");
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if (tok.length!=2 || !tok[0].contains("format-version")) {
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Out.PrtErr("Incorrect OBO file: " + line);

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