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UCSC-LoweLab / tRNAscan-SE

A program for detection of tRNA genes
GNU General Public License v3.0
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Using config file with tRNAscan-SE from conda #29

Closed julie-tooi closed 1 year ago

julie-tooi commented 1 year ago

Hello! Thank you for your work and great tool!

I have a question about config file usage:

I installed the tRNAscan-SE (v2.0.9) with conda It looks like I don't have the original file tRNAscan-SE.conf (at least in env folder)

I tried to copy the config file from tRNAscan-SE repo and use -c command to provide tRNAscan-SE.conf.src

tRNAscan-SE -c tRNAscan-SE.conf.src -o test ~/test.fasta

The annotation failed with this message:

/tscan9759.fpass for writing.  Aborting program.

Do you have any ideas on how to solve this?

Many thanks, Julie

patriciaplchan commented 1 year ago

tRNAscan-SE.conf should be installed in the same directory as tRNAscan-SE executable. Please look for it.

During the installation, new values are inserted into tRNAscan-SE.conf.src for creating tRNAscan-SE.conf. Therefore, directly using tRNAscan-SE.conf.src will not work.

julie-tooi commented 1 year ago

Thank you for the answer!

I found the tRNAscan-SE.conf miniconda3/envs/trnascan_env/bin folder, but not in libs :D

Now everything works, thanks!