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mattb112885 / clusterDbAnalysis

ITEP - Integrated Toolkit for Exploration of microbial Pan-genomes
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generateOrganismFileFromGbk.sh not running #61

Closed jcthrash closed 10 years ago

jcthrash commented 10 years ago

Hello, I'm trying to set up organism sub groups, so I attempted to run generateOrganismFileFromGbk.sh, but it does not run:

Comand: $ ./generateOrganismFileFromGbk.sh

Error: ./generateOrganismFileFromGbk.sh: line 58: makeTabDelimitedRow.py: command not found

This error is repeated for all 17 genomes in my genbank file.

However, I did find the script it's asking about, makeTabDelimitedRow.py, in src/utilities/, so I know it's there.

Suggestions?

Thanks for your time.

jcthrash commented 10 years ago

Nevermind- hacked the bash script and added a fully referenced path to that python script. Works fine now.

mattb112885 commented 10 years ago

If you source the "SourceMe.sh" file it should take care of all of these things for you (for future reference, you should always source that before running ITEP scripts so it can find everything). You don't need to call generateOrganismFile.sh explicitly, it is automatically called as part of setup_step1.sh.

Matt

jcthrash commented 10 years ago

Thanks- I've added the source line to my .bashrc file, but still having trouble getting ITEP to see proper paths. Although all the dependencies are installed, ITEP can't see a lot of the scripts or programs, for example in src/external or src/internal. Working with my sys admin right now to see if it's a problem on our end.

mattb112885 commented 10 years ago

Did you source the .bashrc file?

jcthrash commented 10 years ago

Yes, and now it does so automatically with each login as well.

mattb112885 commented 10 years ago

I might know why this is happening. Do you have spaces in the path you saved ITEP in?

If that's the problem I am fixing it now.

Matt

mattb112885 commented 10 years ago

I attempted a fix on this and pushed it up (I think it would be more of a problem if the PATH variable for your machine had spaces in it). If that doesn't work, I'm not sure what it could be but let me know if your sysadmins find something that I can work around on my end.

Matt

jcthrash commented 10 years ago

No spaces in my paths unfortunately. Thanks for your help however. I'll let you know what I discover.

jcthrash commented 10 years ago

Looks like it was a path issue, although I'm not entirely sure where. My sys admin fixed this and ITEP appears to be running fine now. Thanks for your help, and apologies for taking up your time.

jcthrash commented 10 years ago

Ah, just to follow up, it was a path issue in my SourceMe.sh script, which occurred because I moved the ITEP directory.

mattb112885 commented 10 years ago

Thanks for tracking this down. I will make a note in the docs on this (if you move the directory you will need to source the SourceMe file again \ update the .bashrc).

Best

Matt