<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; "><div>The Jbrowse codebase tends to undergo very rapid alteration (much of which is not backwards compatible with other Jbrowse versions), as a result the script maker2jbrowse has had to evolve with Jbrowse (and will not work with all versions). I'm not sure if the script is currently behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I can have it working with whatever the most current repository is if you were to give me a week, or you can try loading the GFF3's using Jbrowse's own loader (tutorial here --> <a href="http://gmod.org/wiki/JBrowse_Tutorial_2012">http://gmod.org/wiki/JBrowse_Tutorial_2012</a>). Of course this tutorial is also likely to be somewhat out of date :-( But the 2013 version is supposed to be up and running as part of this years GMOD summer school in ~3 weeks. They use MAKER generated data for the tutorial, so it should be relevant to what you are doing.</div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><div><br></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> V Wong <<a href="mailto:vwong@umn.edu">vwong@umn.edu</a>><br><span style="font-weight:bold">Reply-To: </span> <<a href="mailto:vwong@umn.edu">vwong@umn.edu</a>><br><span style="font-weight:bold">Date: </span> Tuesday, July 2, 2013 11:38 AM<br><span style="font-weight:bold">To: </span> <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] maker2jbrowse implementation<br></div><div><br></div><div dir="ltr"><div style="">Hi Maker team,</div><div style=""><br></div><div style="">I'm trying to get Maker output into JBrowse (version 1.9.3) on our server, using the -d option for the index.log file. However, I am getting this error for each contig:</div><div><br></div>ERROR: No track information for source 'AK_assembly_datastore/22/D4/AK_contig_1/'<br><div><br></div><div style="">Looking at the perl script, the file locations are getting read, but then the tracks aren't getting found in the hash of commands.</div><div><br></div><div style="">Any advice for getting past this will be most appreciated. Thank you!</div><div style=""><br></div><div style="">Best,</div><div style="">Val</div></div>
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