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

[Leo Gordon]

Dear Sharon,

We know that older versions of Mafft (6.707 and before) need the MAFFT_BINARIES variable to be set,
but newer versions of Mafft (6.864 and after) need it to be unset.
(I can confirm this having run ProteinFamilies pipeline with different versions already).

So if you are running Mafft 7, please feel free to comment out setting this variable.

We haven't done it in our ProteinTrees pipeline code because
the last time we ran ProteinTrees it was using Mafft version 6.707 which still required the variable to be set.

We will update ensembl-compara code as soon as we run the ProteinTrees with Mafft 7.

Thanks for reminding us about it :)
Best regards,

Leo.


On 22 Jan 2013, at 17:25, Sharon Wei wrote:

> 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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