/workspace/EarlGrey/earlGrey: line 83: famdb.py: command not found

[spoonbender76]

Hi,

Thank you for making earlGrey. I tried to use it through gitpod and wanted to include RepBase. I uploaded RMRBSeqs.embl and RMRBSeqs.embl in /workspace/conda/envs/earlGrey/share/RepeatMasker/Libraries and run perl ./configure

(earlGrey) gitpod /workspace/conda/envs/earlGrey/share/RepeatMasker $  perl ./configure

Enter Selection: 5
Building FASTA version of RepeatMasker.lib ........................................
Building RMBlast frozen libraries..
The program is installed with a the following repeat libraries:
File: /workspace/conda/envs/earlGrey/share/RepeatMasker/Libraries/RepeatMaskerLib.h5
FamDB Generator: famdb.py v0.4.2
FamDB Format Version: 0.5
FamDB Creation Date: 2023-01-08 10:42:05.645898

Database: Dfam withRBRM
Version: 3.7
Date: 2023-01-11

Dfam - A database of transposable element (TE) sequence alignments and HMMs.
RBRM - RepBase RepeatMasker Edition - version 20181026

Total consensus sequences: 64595
Total HMMs: 19730

Further documentation on the program may be found here:
  /workspace/conda/envs/earlGrey/share/RepeatMasker/repeatmasker.help

It changed RMBlast: [ Configured, Default ] and leaving others unconfigured

and I run the command nohup /usr/bin/time -v earlGrey -g /workspace/ne_1019.fa -s v1019 -o ./repeatAnnotation -r insecta -t 4 > 1.log 2>2.err & I noticed in logfile it reported /workspace/EarlGrey/earlGrey: line 83: famdb.py: command not found

Is it a bug or it's ok to ignore? Am I doing the configuration/running right?

1.log

[TobyBaril]

Hi,

Thanks for checking out Earl Grey!

The Gitpod was initially made to demonstrate the basic Earl Grey pipeline, so some changes might need to be made to run other parts of the pipeline.

In this case, run this line and it should add the script to the gitpod enviroment path:

export PATH=$PATH:/workspace/conda/envs/earlGrey/share/RepeatMasker/

[spoonbender76]

Hi,

Thank you for the quick reply. I tried the line you suggested and rerun the same command in gitpod. export PATH=$PATH:/workspace/conda/envs/earlGrey/share/RepeatMasker/ nohup /usr/bin/time -v earlGrey -g /workspace/ne_1019.fa -s v1019 -o ./repeatAnnotation -r insecta -t 4 > 1.log 2>2.err &

There goes another error

ERROR:__main__:Error reading file: [Errno 2] Unable to synchronously open file (unable to open file: name = '/workspace/conda/envs/earlGrey/bin/Libraries/RepeatMaskerLib.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

1 (1).log

[TobyBaril]

I've just pushed a fix for this. This was a bug arising in the transition to a conda environment which did not arise with local installs. Release 3.2.1 will fix this. If you do not want to reconfigure the gitpod environment, you can replace the main earlGrey script with the updated one in this repository. Alternatively, you should be able to pull the changes:

cd /workspace/EarlGrey/
git stash
git pull
chmod +x ./configure
./configure

[TobyBaril]

Closing as fixed, but feel free to reopen if this is still bugged for you and I can look for further solutions