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
Hello Olivia,
Great, thanks for the clarification! It took me a little bit, but I
have caught up. First - you don't need to justify using bioblend over
the provided scripts in galaxy distribution. Anything non-trivial
should be using bioblend (if it weren't going to make me very
unpopular I would
Thanks Greg. I'd followed the online local install instructions which I see
leaves the install in the default branch. I think I read somewhere that
default gets the various updates on a monthly basis? So a pull/update will get
the fix sooner or later.
Damion
Hey Greg,
Sorry about the delay on this over the holidays. I see what you're working
with now. If you install your customizations in a portable manner in
/mnt/galaxyData that should be safe and we'll make sure to provide a smooth
migration path going forward should that change. Only 'galaxy'
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,
Perfect thanks!
On Mon, Jan 6, 2014 at 1:16 PM, Dannon Baker dannon.ba...@gmail.com wrote:
Hey Greg,
Sorry about the delay on this over the holidays. I see what you're working
with now. If you install your customizations in a portable manner in
/mnt/galaxyData that should be safe and we'll
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,
