I have a script that takes some gene data and runs it through dozens of programs to try to tease out as much information as possible and make me some pretty reports. However, while it seems to work under Windows fine, I can't get it working on Ubuntu 12.10.
It wants to use some software from the tigr-glimmer
package, long-orfs
, extract
, etc. (see below), and it seems like the script provided expects them to be separate binaries. When installed, however, they actually seem to be "sub-programs"(?) of a binary tigr-glimmer
, that need to be run as tigr-glimmer long-orfs
, or the like. I attempted making an alias to turn long-orfs
into tigr-glimmer long-orfs
, but that seems to have no effect.
Can I somehow make a link between the two, or rather, how should I go about fixing this? The Python script is open to me, but I would rather avoid opening that can of worms. It seems to scan through the env. paths for a set of given strings (e.g. long-orfs
...) looking for an executable file, which apparently my alias doesn't qualify as. If I change how that works, then I'll need to change dozens of the calls strewn about several files...
I have nearly no Linux experience, so my sense of how to do this is almost certainly wrong. Please set me straight :P
ubuntu@domU:~$ python run_antismash.py --clusterblast P115_92.gb
ERROR: Failed to locate executable for 'long-orfs'
ERROR: Failed to locate executable for 'extract'
ERROR: Failed to locate executable for 'build-icm'
ERROR: Failed to locate executable for 'glimmer3'
ERROR: Not all prerequisites met
ubuntu@domU:~$ alias long-orfs
alias long-orfs='tigr-glimmer long-orfs'
ubuntu@domU:~$ long-orfs
Starting at Fri Mar 15 22:08:17 2013
USAGE: long-orfs [options] <sequence-file> <output-file>
Read DNA sequence [...]
long-orfs
et. al.