[galaxy-dev] faToTwoBit: not found / trackster

3 Jan 2014

      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'