Ok, then it's very likely a PATH issue. There's no magic needed here - faToTwoBit simply needs to be on your path. It seems you've tried debugging this already; one suggestion is to provide the full path to the executable and see if that works.
-- Jeremy Goecks Assistant Professor, Computational Biology Institute George Washington University
On Jan 6, 2014, at 1:49 AM, Jasper Jan Koehorst jasper.koehorst@wur.nl wrote:
To give a better answer, when I enter the command this is what I get:
:~$ faToTwoBit
faToTwoBit - Convert DNA from fasta to 2bit format
usage:
faToTwoBit in.fa [in2.fa in3.fa ...] out.2bit
options:
-noMask Ignore lower-case masking in fa file.
-stripVersion Strip off version number after '.' for GenBank accessions.
-ignoreDups Convert first sequence only if there are duplicate sequence
names. Use 'twoBitDup' to find duplicate sequences.2014/1/4 Jasper Koehorst jasperkoehorst@gmail.com 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.goecks@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.koehorst@wur.nlmailto:jasper.koehorst@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:
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..." "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..." "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..." "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..." "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..." "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..." "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..." "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..." "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..." "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..." "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..." "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..." "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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