<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Hi Robert,</div><div><br></div><div>Yes, the MAKER source code is open under either the Artistic or GNU GPL for academic use. You can download the code here:</div><div><br></div><div><a href="http://yandell.topaz.genetics.utah.edu/cgi-bin/maker_license.cgi">http://yandell.topaz.genetics.utah.edu/cgi-bin/maker_license.cgi</a>.</div><div><br></div><div>Registration allows us to track unique user downloads and create cool geocoded maps for funding purposes :)<br><div><br></div><div>B</div><div><br></div><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(127, 127, 127, 1.0);"><b>From: </b></span><span style="font-family:'Helvetica'; font-size:medium;">Robert Buels <<a href="mailto:rbuels@gmail.com">rbuels@gmail.com</a>><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(127, 127, 127, 1.0);"><b>Subject: </b></span><span style="font-family:'Helvetica'; font-size:medium;"><b>Re: [maker-devel] maker2jbrowse implementation</b><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(127, 127, 127, 1.0);"><b>Date: </b></span><span style="font-family:'Helvetica'; font-size:medium;">July 2, 2013 11:32:40 AM MDT<br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(127, 127, 127, 1.0);"><b>To: </b></span><span style="font-family:'Helvetica'; font-size:medium;"><<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br></span></div><br><br>One of my objectives has been maintaining complete backward compatibility with data formatted from JBrowse 1.2.1 onward. I add capabilities, and the look and feel of the browser improves, but you can still view data in it that was formatted with JBrowse 1.2.1 (released March 17, 2011).<br><br>I would try to have a look at the maker2jbrowse implementation to troubleshoot further, but your source code doesn't seem to be public. Or at least the link to the source browser on the GMOD wiki page (<a href="http://gmod.org/wiki/MAKER#MAKER_Development">http://gmod.org/wiki/MAKER#MAKER_Development</a>) doesn't work, and I can't find any kind of source code links under <a href="http://www.yandell-lab.org/software/maker.html">http://www.yandell-lab.org/software/maker.html</a>. Is the MAKER source code actually open?<br><br>Regarding the 2012 tutorial, the directions in the 2012 tutorial should still work, since I have been keeping backward compatibility with the scripts also.<br><br>Val, Carson, could you elaborate with details on the backward compatibility problems you're seeing? Or could you give me access to the maker2jbrowse source code?<br><br><br>Robert Buels<br>Lead Developer<br>JBrowse - <a href="http://jbrowse.org">http://jbrowse.org</a><br><br>On 07/02/2013 12:27 PM, Carson Holt wrote:<br><blockquote type="cite">The Jbrowse codebase tends to undergo very rapid alteration (much of<br></blockquote><blockquote type="cite">which is not backwards compatible with other Jbrowse versions), as a<br></blockquote><blockquote type="cite">result the script maker2jbrowse has had to evolve with Jbrowse (and will<br></blockquote><blockquote type="cite">not work with all versions). I'm not sure if the script is currently<br></blockquote><blockquote type="cite">behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I can<br></blockquote><blockquote type="cite">have it working with whatever the most current repository is if you were<br></blockquote><blockquote type="cite">to give me a week, or you can try loading the GFF3's using Jbrowse's own<br></blockquote><blockquote type="cite">loader (tutorial here --> <a href="http://gmod.org/wiki/JBrowse_Tutorial_2012">http://gmod.org/wiki/JBrowse_Tutorial_2012</a>).<br></blockquote><blockquote type="cite"> Of course this tutorial is also likely to be somewhat out of date<br></blockquote><blockquote type="cite">:-( But the 2013 version is supposed to be up and running as part of<br></blockquote><blockquote type="cite">this years GMOD summer school in ~3 weeks. They use MAKER generated<br></blockquote><blockquote type="cite">data for the tutorial, so it should be relevant to what you are doing.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Thanks,<br></blockquote><blockquote type="cite">Carson<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">From: V Wong <<a href="mailto:vwong@umn.edu">vwong@umn.edu</a> <<a href="mailto:vwong@umn.edu">mailto:vwong@umn.edu</a>>><br></blockquote><blockquote type="cite">Reply-To: <<a href="mailto:vwong@umn.edu">vwong@umn.edu</a> <<a href="mailto:vwong@umn.edu">mailto:vwong@umn.edu</a>>><br></blockquote><blockquote type="cite">Date: Tuesday, July 2, 2013 11:38 AM<br></blockquote><blockquote type="cite">To: <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a> <<a href="mailto:maker-devel@yandell-lab.org">mailto:maker-devel@yandell-lab.org</a>>><br></blockquote><blockquote type="cite">Subject: [maker-devel] maker2jbrowse implementation<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Hi Maker team,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I'm trying to get Maker output into JBrowse (version 1.9.3) on our<br></blockquote><blockquote type="cite">server, using the -d option for the index.log file. However, I am<br></blockquote><blockquote type="cite">getting this error for each contig:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">ERROR: No track information for source<br></blockquote><blockquote type="cite">'AK_assembly_datastore/22/D4/AK_contig_1/'<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Looking at the perl script, the file locations are getting read, but<br></blockquote><blockquote type="cite">then the tracks aren't getting found in the hash of commands.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Any advice for getting past this will be most appreciated. Thank you!<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Best,<br></blockquote><blockquote type="cite">Val<br></blockquote><blockquote type="cite">_______________________________________________ maker-devel mailing list<br></blockquote><blockquote type="cite"><a href="mailto:maker-devel@box290.bluehost.com">maker-devel@box290.bluehost.com</a> <<a href="mailto:maker-devel@box290.bluehost.com">mailto:maker-devel@box290.bluehost.com</a>><br></blockquote><blockquote type="cite"><a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">_______________________________________________<br></blockquote><blockquote type="cite">maker-devel mailing list<br></blockquote><blockquote type="cite"><a href="mailto:maker-devel@box290.bluehost.com">maker-devel@box290.bluehost.com</a><br></blockquote><blockquote type="cite"><a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a><br></blockquote><blockquote type="cite"><br></blockquote><br><br><br><br><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(127, 127, 127, 1.0);"><b>From: </b></span><span style="font-family:'Helvetica'; font-size:medium;"><<a href="mailto:maker-devel-request@yandell-lab.org">maker-devel-request@yandell-lab.org</a>><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(127, 127, 127, 1.0);"><b>Subject: </b></span><span style="font-family:'Helvetica'; font-size:medium;"><b>confirm 25a5d094a80beae62e51d1f0ee53d38a5d0bfacc</b><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(127, 127, 127, 1.0);"><b>Date: </b></span><span style="font-family:'Helvetica'; font-size:medium;">July 2, 2013 11:32:44 AM MDT<br></span></div><br><br>If you reply to this message, keeping the Subject: header intact,<br>Mailman will discard the held message. Do this if the message is<br>spam. If you reply to this message and include an Approved: header<br>with the list password in it, the message will be approved for posting<br>to the list. The Approved: header can also appear in the first line<br>of the body of the reply.<br><br><br></blockquote></div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div><span class="Apple-style-span" style="font-family: Arial; font-size: 12px; "><div>Barry Moore</div><div>Research Scientist</div><div>Dept. of Human Genetics</div><div>University of Utah</div><div>Salt Lake City, UT 84112</div><div>--------------------------------------------</div><div>(801) 585-3543</div><div><br class="khtml-block-placeholder"></div></span></div><div><br></div></span><br class="Apple-interchange-newline">
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