Question: Help with running gi2taxonomy.py
0
gravatar for ibis
3.4 years ago by
ibis0
United Kingdom
ibis0 wrote:

Hello,

I have been trying to run the gi2taxonomy.py script (see link), but I m getting an error and I dont know exactly what is wrong.

https://toolshed.g2.bx.psu.edu/repos/devteam/gi2taxonomy/rev/7b1b03c4465d

Anybody can help please?

I am running it on a cluster and my input file lookes like this (txt):

1    320336089
2    320336089

That's how I tried to run it:

module load http-proxy

./gi2taxonomy.py -i gi_example.txt -o results.txt

And got this error:

import: unable to open X server `'.

import: unable to open X server `'.

import: unable to open X server `'.

import: unable to open X server `'.

./gi2taxonomy.py: line 6: from: command not found

./gi2taxonomy.py: line 10: syntax error near unexpected token `('

./gi2taxonomy.py: line 10: `def stop_err(msg):'

I m new with using python so any help is welcome!

Thanks,

Ibis

ADD COMMENTlink modified 3.4 years ago by Bjoern Gruening5.1k • written 3.4 years ago by ibis0
0
gravatar for Bjoern Gruening
3.4 years ago by
Bjoern Gruening5.1k
Germany
Bjoern Gruening5.1k wrote:

It seems you are running it without Galaxy from your command line, is this true?

If so execute the script in the following way:

python ./gi2taxonomy.py -i gi_example.txt -o results.txt

Hope this helps,

Bjoern

ADD COMMENTlink written 3.4 years ago by Bjoern Gruening5.1k
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