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TobyBaril / EarlGrey

Earl Grey: A fully automated TE curation and annotation pipeline
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TE Strainer script issue #156

Open saramiller23 opened 1 week ago

saramiller23 commented 1 week ago

Hi,

I am able to run EarlGrey, however once I get to the TE Straining step, I get an error that the program can't locate the TE strainer scripts. 

    <<< Straining TEs and Refining de novo Consensus Sequences >>>

python: can't open file '/data/toby/EarlGrey/scripts/TEstrainer/scripts//splitter.py': [Errno 2] No such file or directory python: can't open file '/data/toby/EarlGrey/scripts/TEstrainer/scripts//indexer.py': [Errno 2] No such file or directory

I talked with our BioHPC and they think this path is likely hardcoded into one of the programs in the package, but cannot find these files in conda installation directory. We are excited to use this program so any suggestions or workarounds that you have would be appreciated!

We installed EarlGrey using conda with the following command: conda create -n earlgrey -c conda-forge -c bioconda earlgrey=5.0.0

TobyBaril commented 1 day ago

Hi @saramiller23 - thanks for pointing this out! This was a bug in the 0 build of version 5 that was fixed in the 1 build. If you purge the environment, then reinstall, it should function as expected. You can then test the specific script is found before committing more jobs by running python $(which earlGrey | sed 's#bin/earlGrey#share/earlgrey-5.0.0-1/scripts/TEstrainer/scripts/splitter.py#g').

If found, you should get the following output:

usage: splitter.py [-h] -i IN_SEQ -o OUT_DIR
splitter.py: error: the following arguments are required: -i/--in_seq, -o/--out_dir