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:
-noMaskIgnore lower-case masking in fa file.
-stripVersion Strip off
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,
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,
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
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.
--
Jeremy Goecks
Assistant Professor, Computational
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
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 /
