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
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
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 [...]