Yes and i even chmodded it to 777 for testing purposes. When I run it
I get the option overview of the tool. I can't copy that right now
(out of office) but the application works as I also 2bitted a genome.

> On 04 Jan 2014, at 18:37, Jeremy Goecks <jeremy.goe...@emory.edu> wrote:
>
> Can you run the faToTwoBit tool from the command line? It can be difficult to 
> find the right executable for UCSC tools sometimes; if you have the wrong 
> executable (e.g. 32 bit instead of 64 bit), you'll see the misleading 'not 
> found' error.
>
> Best,
> J.
>
> On Jan 3, 2014, at 11:35 AM, Jasper Jan Koehorst 
> <jasper.koeho...@wur.nl<mailto:jasper.koeho...@wur.nl>> wrote:
>
>
> First of all, best wishes!
>
> I was/am trying to visualize a GTF file in galaxy on a local 64 bit ubuntu 
> system. However I stumbled upon an issue were it remained grey. When I did an 
> automaic visualization I saw a line that went up and down over the 
> chromosome. When I switched to pack I got a grey / / / line slashed output.
>
> I contacted dannon and ceberhard on IRC and they told me to add a print 
> statement on line 200 for the tracker. This visualized the following error:
>
> {'kind': 'error', 'message': '/bin/sh: 1: faToTwoBit: not found\n'}
>
> So I downloaded and placed the faToTwoBit file in /usr/bin I even chmodded it 
> to 777 but the error remained. I also started digging into the code on where 
> it calls the application and added /usr/bin/ in front of it but no luck so 
> far.
>
> Anyone has a clue on what is happening? It almost must be an ubuntu related 
> issue as I dont see how galaxy cannot find the path.
>
> $PATH is still properly set when running galaxy as I added echo $path it to a 
> tool and it returned
>
> /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/bin
>
> The IRC chat can be seen here:
>
> http://pastebin.com/9fZrkRDn
>
> Thanks a lot,
>
>
> /home/galaxy/HB27.2bit10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] "GET 
> /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=0&high=320487&mode=Auto&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D
>  HTTP/1.1" 200 - 
> "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda";
>  "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, 
> like Gecko) Chrome/31.0.1650.63 Safari/537.36"
>
> 10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] "GET 
> /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=1602432&high=1894876&mode=Auto&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D
>  HTTP/1.1" 200 - 
> "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda";
>  "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, 
> like Gecko) Chrome/31.0.1650.63 Safari/537.36"
>
> 10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] "GET 
> /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=1281945&high=1602432&mode=Auto&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D
>  HTTP/1.1" 200 - 
> "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda";
>  "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, 
> like Gecko) Chrome/31.0.1650.63 Safari/537.36"
>
> 10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] "GET 
> /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=320486&high=640973&mode=Auto&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D
>  HTTP/1.1" 200 - 
> "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda";
>  "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, 
> like Gecko) Chrome/31.0.1650.63 Safari/537.36"
>
> 10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] "GET 
> /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=961459&high=1281946&mode=Auto&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D
>  HTTP/1.1" 200 - 
> "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda";
>  "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, 
> like Gecko) Chrome/31.0.1650.63 Safari/537.36"
>
> 10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] "GET 
> /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=640972&high=961459&mode=Auto&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D
>  HTTP/1.1" 200 - 
> "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda";
>  "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, 
> like Gecko) Chrome/31.0.1650.63 Safari/537.36"
>
> {'kind': 'error', 'message': '/bin/sh: 1: faToTwoBit: not found\n'}
>
> galaxy.webapps.galaxy.api.datasets ERROR 2014-01-03 17:24:36,418 Error in 
> dataset API at listing contents: 'data': 'data'
>
> Traceback (most recent call last):
>
>  File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", 
> line 46, in show
>
>    rval = self._data( trans, dataset, **kwd )
>
>  File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", 
> line 201, in _data
>
>    ref_seq = data_dict[ 'data' ]
>
> KeyError: 'data'
>
> 10.64.9.118 - - [03/Jan/2014:17:24:35 +0200] "GET 
> /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=320486&high=640973&mode=Pack&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D
>  HTTP/1.1" 500 - 
> "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda";
>  "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, 
> like Gecko) Chrome/31.0.1650.63 Safari/537.36"
>
> {'kind': 'error', 'message': '/bin/sh: 1: faToTwoBit: not found\n'}
>
> galaxy.webapps.galaxy.api.datasets ERROR 2014-01-03 17:24:36,595 Error in 
> dataset API at listing contents: 'data': 'data'
>
> Traceback (most recent call last):
>
>  File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", 
> line 46, in show
>
>    rval = self._data( trans, dataset, **kwd )
>
>  File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", 
> line 201, in _data
>
>    ref_seq = data_dict[ 'data' ]
>
> KeyError: 'data'
>
> 10.64.9.118 - - [03/Jan/2014:17:24:35 +0200] "GET 
> /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=0&high=320487&mode=Pack&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D
>  HTTP/1.1" 500 - 
> "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda";
>  "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, 
> like Gecko) Chrome/31.0.1650.63 Safari/537.36"
>
> {'kind': 'error', 'message': '/bin/sh: 1: faToTwoBit: not found\n'}
>
> {'kind': 'error'galaxy.webapps.galaxy.api.datasets ERROR 2014-01-03 
> 17:24:37,049 Error in dataset API at listing contents: 'data': 'data'
>
> Traceback (most recent call last):
>
>  File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", 
> line 46, in show
>
>    rval = self._data( trans, dataset, **kwd )
>
>  File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", 
> line 201, in _data
>
>    ref_seq = data_dict[ 'data' ]
>
> KeyError: 'data'
>
> , 'message': '/bin/sh: 1: faToTwoBit: not found\n'}
>
> 10.64.9.118 - - [03/Jan/2014:17:24:35 +0200] "GET 
> /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=1602432&high=1894876&mode=Pack&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D
>  HTTP/1.1" 500 - 
> "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda";
>  "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, 
> like Gecko) Chrome/31.0.1650.63 Safari/537.36"
>
> {{'kind': 'error', 'message''kind'galaxy.webapps.galaxy.api.datasets ERROR 
> 2014-01-03 17:24:37,099 Error in dataset API at listing contents: 'data': 
> 'data'
>
> Traceback (most recent call last):
>
>  File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", 
> line 46, in show
>
>    rval = self._data( trans, dataset, **kwd )
>
>  File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", 
> line 201, in _data
>
>    ref_seq = data_dict[ 'data' ]
>
> KeyError: 'data'
>
> : : 'error'10.64.9.118 - - [03/Jan/2014:17:24:35 +0200] "GET 
> /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=961459&high=1281946&mode=Pack&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D
>  HTTP/1.1" 500 - 
> "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda";
>  "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, 
> like Gecko) Chrome/31.0.1650.63 Safari/537.36"
>
> '/bin/sh: 1: faToTwoBit: not found\n', 'message': '/bin/sh: 1: faToTwoBit: 
> not found\n'}
>
> }
>
> galaxy.webapps.galaxy.api.datasets ERROR 2014-01-03 17:24:37,102 Error in 
> dataset API at listing contents: 'data': 'data'
>
> Traceback (most recent call last):
>
>  File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", 
> line 46, in show
>
>    rval = self._data( trans, dataset, **kwd )
>
>  File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", 
> line 201, in _data
>
>    ref_seq = data_dict[ 'data' ]
>
> KeyError: 'data'
>
> 10.64.9.118 - - [03/Jan/2014:17:24:35 +0200] "GET 
> /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=640972&high=961459&mode=Pack&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D
>  HTTP/1.1" 500 - 
> "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda";
>  "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, 
> like Gecko) Chrome/31.0.1650.63 Safari/537.36"
>
> galaxy.webapps.galaxy.api.datasets ERROR 2014-01-03 17:24:37,102 Error in 
> dataset API at listing contents: 'data': 'data'
>
> Traceback (most recent call last):
>
>  File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", 
> line 46, in show
>
>    rval = self._data( trans, dataset, **kwd )
>
>  File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", 
> line 201, in _data
>
>    ref_seq = data_dict[ 'data' ]
>
> KeyError: 'data'
>
> 10.64.9.118 - - [03/Jan/2014:17:24:35 +0200] "GET 
> /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=1281945&high=1602432&mode=Pack&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D
>  HTTP/1.1" 500 - 
> "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ldda=hda";
>  "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, 
> like Gecko) Chrome/31.0.1650.63 Safari/537.36"
>
> ___________________________________________________________
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>
>

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