[ensembl-dev] protein compara pipeline - MAFFT_BINARIES environmental variable

Sharon Wei weix at cshl.edu
Tue Jan 22 17:25:28 GMT 2013


Hi Ensembl Compara developers,

I am trying out the version69 protein compara pipeline and one problem I 
encountered was the mafft_highmem jobs failed because the MAFFT_BINARIES 
environmental variable was set on line67 in
ensembl-compara/modules/Bio/EnsEMBL/Compara/RunnableDB/ProteinTrees/Mafft.pm 


When I comment out this line, all the jobs finished without errors.
I am using MAFFT v7.015b.

I am wondering whether this is due to MAFFT version differences or 
ensembl needs to update the module Mafft.pm.


Thanks,

Sharon




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