<div dir="ltr">Hi Carson,<div><br></div><div style>Ah, great! After moving the contents of <span style="font-family:arial,sans-serif;font-size:13.333333969116211px">../JBrowse/data/ to our browser directory, </span>the Maker tracks are now on view. </div>
<div style><br></div><div style>However, I'm having some trouble getting our older tracks (bam alignments and coverage tracks) into the same browser. N<span style="font-size:13.333333969116211px;font-family:arial,sans-serif">either 1. copying and pasting the tracks from the previous trackList.json to the new one nor 2. running</span> <a href="http://add-track-json.pl">add-track-json.pl</a><font face="arial, sans-serif"> is doing the job. Is it possible to merge these tracks into one browser?</font></div>
<div style><font face="arial, sans-serif"><br></font></div><div style><font face="arial, sans-serif">Best,</font></div><div style><font face="arial, sans-serif">Val</font></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">
On Thu, Jul 11, 2013 at 6:44 AM, Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word"><div><font face="Calibri,sans-serif">You next put the entire </font>JBrowse directory into the /var/www/html/ directory or wherever you have apache set up to load from (if it's not already there). Then it will be accessible as a webpage (browser is inside the <font face="Calibri,sans-serif">JBrowse directory</font>).</div>
<div style="font-size:14px;font-family:Calibri,sans-serif"><br></div><div style="font-size:14px;font-family:Calibri,sans-serif">Example /var/www/html/Jbrowse/</div><div style="font-size:14px;font-family:Calibri,sans-serif">
Webpage --> <a href="http://localhost/Jbrowse/" target="_blank">http://localhost/Jbrowse/</a></div><div style="font-size:14px;font-family:Calibri,sans-serif"><br></div><div style="font-size:14px;font-family:Calibri,sans-serif">
--Carson</div><div style="font-size:14px;font-family:Calibri,sans-serif"><br></div><span style="font-size:14px;font-family:Calibri,sans-serif"><div style="border-right:medium none;padding-right:0in;padding-left:0in;padding-top:3pt;text-align:left;font-size:11pt;border-bottom:medium none;font-family:Calibri;border-top:#b5c4df 1pt solid;padding-bottom:0in;border-left:medium none">
<div class="im"><span style="font-weight:bold">From: </span> V Wong <<a href="mailto:vwong@umn.edu" target="_blank">vwong@umn.edu</a>><br><span style="font-weight:bold">Reply-To: </span> <<a href="mailto:vwong@umn.edu" target="_blank">vwong@umn.edu</a>><br>
</div><span style="font-weight:bold">Date: </span> Thursday, July 11, 2013 1:10 AM<br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>>, Ignazio Carbone <<a href="mailto:icarbon@ncsu.edu" target="_blank">icarbon@ncsu.edu</a>><br>
<span style="font-weight:bold">Cc: </span> <<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>>, Robert Buels <<a href="mailto:rbuels@gmail.com" target="_blank">rbuels@gmail.com</a>><div class="im">
<br><span style="font-weight:bold">Subject: </span> Re: [maker-devel] maker2jbrowse implementation<br></div></div><div><div class="h5"><div><br></div><div dir="ltr">Hi Carson,<div><br></div><div>Thanks! I followed your instructions, and maker2jbrowse, and it successfully populated the ../JBrowse/data/tracks directory with RepeatMasker, Augustus, and GeneMark predictions.</div>
<div><br></div><div>I'm not entirely sure how to get these numerous tracks into the browser, but that may be something to work out with JBrowse rather than Maker.</div><div><br></div><div>Best,</div><div>Val</div></div>
<div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Jul 9, 2013 at 10:57 AM, Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Val,<br><br>
I've attached new files for you to test. These will be bundled in the<br>
next maker release pending successful tests (~ 1 week).<br><br>
Instructions:<br>
1. Place maker2jbrowse in your .../maker/bin/ directory and<br>
.../maker/src/bin/ directory (this is just to ensure you don't<br>
accidentally overwrite it if you reinstall at any time).<br>
2. Place maker.css in the .../maker/GMOD/Jbrowse/ directory.<br>
3. You must be in the jbrowse installation directory when running<br>
maker2jbrowse. Run the script with the -d flag and the datastore index<br>
file.<br><br>
This new version will assign colors by copying maker.css to the jbrowse<br>
installation as apposed to replacing the genome.css file, and it will also<br>
edit the genome.css file to add the import call for maker.css. In<br>
addition I have updated command line flags in the wrapper to do what is<br>
currently expected by <a href="http://flatfile-to-json.pl" target="_blank">flatfile-to-json.pl</a>.<br><br>
Could you test it out and let me know how it goes.<br><br>
Thanks,<br>
Carson<br><div><div><br><br><br>
On 7/3/13 3:26 PM, "Carson Holt" <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>> wrote:<br><br>
>Like I said that css file is ~1 year old. Once upon a time the Jbrowse<br>
>documentation had you modify the genome.css file to create your own<br>
>tracks. Version 1.2.1 looks like it is the last version where the<br>
>genome.css file that maker provided works. I can still get simple test<br>
>GFF3 tracks to load with current Jbrowse and the maker2jbrowse script.<br>
>But I need to fix some things, because they are all indistinguishable from<br>
>each other (so it is not the desired behavior).<br>
><br>
>Indepent of that issue though, to regenerate the original error, I do the<br>
>following --><br>
> maker2jbrowse<br>
>~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_dat<br>
>a<br>
>store_index.log<br>
> ERROR: No track information for source<br>
>'dpp_contig_datastore/05/1F/contig-dpp-500-500/'<br>
><br>
>Basically you are missing the '-d' flag (whiteout that the script is<br>
>expecting a list of GFF3 files).<br>
><br>
>So this works --><br>
> maker2jbrowse -d<br>
>~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_dat<br>
>a<br>
>store_index.log<br>
><br>
><br>
>Of course all tracks look the same though per the original issue I<br>
>mentioned.<br>
><br>
>Thanks,<br>
>Carson<br>
><br>
><br>
><br>
>Some versions of Jbrowse still load fine with the script as is Jbrowse<br>
>1.3,<br>
><br>
>On 7/3/13 12:39 PM, "Robert Buels" <<a href="mailto:rbuels@gmail.com" target="_blank">rbuels@gmail.com</a>> wrote:<br>
><br>
>>Regarding the genome.css file that's in GMOD/JBrowse, I'm not sure what<br>
>>you're doing with that, but it appears to be a fork of a very old<br>
>>JBrowse main css file. If that's overriding or being copied over the<br>
>>JBrowse released CSS, it will break pretty much everything. It would be<br>
>>like me randomly replacing one of MAKER's Perl modules with my own old<br>
>>forked copy.<br>
>><br>
>>If what you're trying to accomplish is to add some custom styles, the<br>
>>best way to do that would be to do one of:<br>
>><br>
>>* add just your custom feature styles on the <a href="http://flatfile-to-json.pl" target="_blank">flatfile-to-json.pl</a> command<br>
>>line<br>
>>* add a "css": { "url": "<a href="http://url/of/your/custom.css" target="_blank">http://url/of/your/custom.css</a>" } to the<br>
>> JBrowse trackList.json someplace in the workflow (easy to add<br>
>> things to JSON files with JSON.pm) that loads your custom CSS<br>
>> (containing only your custom feature styles!)<br>
>>* add all of the custom styles to the trackList.json as a<br>
>> string: "css": "string { of: lots and lots of; css: properties; }"<br>
>><br>
>><br>
>>Robert Buels<br>
>>Lead Developer<br>
>>JBrowse - <a href="http://jbrowse.org" target="_blank">http://jbrowse.org</a><br>
>><br>
>>On 07/03/2013 12:02 PM, Carson Holt wrote:<br>
>>> I think you may not have it set up right. If you run the example data,<br>
>>> you can then use that. For me it populates the JSON data tracks<br>
>>> information, but nothing displays. I think the problem is with the<br>
>>>maker<br>
>>> genome.css. It is very out of date. I'll do some work on it and then<br>
>>>get<br>
>>> your feedback.<br>
>>><br>
>>> Thanks,<br>
>>> Carson<br>
>>><br>
>>><br>
>>><br>
>>> On 7/3/13 11:45 AM, "Robert Buels" <<a href="mailto:rbuels@gmail.com" target="_blank">rbuels@gmail.com</a>> wrote:<br>
>>><br>
>>>> After looking at the maker2jbrowse source (thanks for giving me<br>
>>>>access),<br>
>>>> there seems to be some kind of problem with the way maker2jbrowse is<br>
>>>> parsing the MAKER datastore index, leading to the script complaining<br>
>>>>of<br>
>>>> 'no track information'.<br>
>>>><br>
>>>> This would probably be easier for a MAKER developer to look into.<br>
>>>><br>
>>>><br>
>>>> Robert Buels<br>
>>>> Lead Developer<br>
>>>> JBrowse - <a href="http://jbrowse.org" target="_blank">http://jbrowse.org</a><br>
>>>><br>
>>>> On 07/02/2013 12:27 PM, Carson Holt wrote:<br>
>>>>> The Jbrowse codebase tends to undergo very rapid alteration (much of<br>
>>>>> which is not backwards compatible with other Jbrowse versions), as a<br>
>>>>> result the script maker2jbrowse has had to evolve with Jbrowse (and<br>
>>>>>will<br>
>>>>> not work with all versions). I'm not sure if the script is currently<br>
>>>>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I can<br>
>>>>> have it working with whatever the most current repository is if you<br>
>>>>>were<br>
>>>>> to give me a week, or you can try loading the GFF3's using Jbrowse's<br>
>>>>>own<br>
>>>>> loader (tutorial here --><br>
>>>>><a href="http://gmod.org/wiki/JBrowse_Tutorial_2012" target="_blank">http://gmod.org/wiki/JBrowse_Tutorial_2012</a>).<br>
>>>>> Of course this tutorial is also likely to be somewhat out of date<br>
>>>>> :-( But the 2013 version is supposed to be up and running as part of<br>
>>>>> this years GMOD summer school in ~3 weeks. They use MAKER generated<br>
>>>>> data for the tutorial, so it should be relevant to what you are<br>
>>>>>doing.<br>
>>>>><br>
>>>>> Thanks,<br>
>>>>> Carson<br>
>>>>><br>
>>>>><br>
>>>>><br>
>>>>> From: V Wong <<a href="mailto:vwong@umn.edu" target="_blank">vwong@umn.edu</a> <mailto:<a href="mailto:vwong@umn.edu" target="_blank">vwong@umn.edu</a>>><br>
>>>>> Reply-To: <<a href="mailto:vwong@umn.edu" target="_blank">vwong@umn.edu</a> <mailto:<a href="mailto:vwong@umn.edu" target="_blank">vwong@umn.edu</a>>><br>
>>>>> Date: Tuesday, July 2, 2013 11:38 AM<br>
>>>>> To: <<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a><br>
>>>>><mailto:<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>>><br>
>>>>> Subject: [maker-devel] maker2jbrowse implementation<br>
>>>>><br>
>>>>> Hi Maker team,<br>
>>>>><br>
>>>>> I'm trying to get Maker output into JBrowse (version 1.9.3) on our<br>
>>>>> server, using the -d option for the index.log file. However, I am<br>
>>>>> getting this error for each contig:<br>
>>>>><br>
>>>>> ERROR: No track information for source<br>
>>>>> 'AK_assembly_datastore/22/D4/AK_contig_1/'<br>
>>>>><br>
>>>>> Looking at the perl script, the file locations are getting read, but<br>
>>>>> then the tracks aren't getting found in the hash of commands.<br>
>>>>><br>
>>>>> Any advice for getting past this will be most appreciated. Thank<br>
>>>>>you!<br>
>>>>><br>
>>>>> Best,<br>
>>>>> Val<br>
>>>>> _______________________________________________ maker-devel mailing<br>
>>>>>list<br>
>>>>> <a href="mailto:maker-devel@box290.bluehost.com" target="_blank">maker-devel@box290.bluehost.com</a><br>
>>>>><mailto:<a href="mailto:maker-devel@box290.bluehost.com" target="_blank">maker-devel@box290.bluehost.com</a>><br>
>>>>><br>
>>>>><a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or" target="_blank">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or</a><br>
>>>>>g<br>
>>>>><br>
>>>>><br>
>>>>> _______________________________________________<br>
>>>>> maker-devel mailing list<br>
>>>>> <a href="mailto:maker-devel@box290.bluehost.com" target="_blank">maker-devel@box290.bluehost.com</a><br>
>>>>><br>
>>>>><a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or" target="_blank">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or</a><br>
>>>>>g<br>
>>>>><br>
>>><br>
>>><br>
>>><br>
><br>
><br><br></div></div></blockquote></div><br></div></div></div></span></div>
</blockquote></div><br></div>