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ambj / MuPeXI

MuPeXI: the mutant peptide extractor and informer, a tool for predicting neo-epitopes from tumor sequencing data.
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Variant Effect Predictor version compatibility #14

Closed trishorts closed 5 years ago

trishorts commented 6 years ago

latest version of VEP as of 05/01/2018 is 92. No version requirement is stated on the main MuPeXI git page. MuPeXI doesn't seem immediately compatible with this to start with as the program variant_effect_predictor.pl has been renamed to vep (plus other changes)

In the MuPeXI user manual shows usage of version 85. image

However, this version is no longer available.

Version 87 could possibly work but there are (I believe) 27 releases (87.0-87.27). Not sure if that level matters.

What would help the most would be specification of which latest version is known to function well.

ambj commented 6 years ago

Ensembls VEP version 87 works.

I will test MuPeXI with one of the newest versions.

Best, /AM

isidroc commented 5 years ago

Any updates on this thread? Thanks

ambj commented 5 years ago

Hi Unfortunately I havn't had time to look into this issue the latest version of VEP i have tested is 87. Thank you for reminding me of this issue - hopefully i have time to test the latest version installed on our HPC during November. Best, /AM

ambj commented 5 years ago

Unfortunately not - VEP have changed the general setup and how to run the program since version 90.

ambj commented 5 years ago

To keep this thread clean - I moved it to a now issue see #23

trishorts commented 5 years ago

I moved on.

ambj commented 5 years ago

Dear @trishorts and @isidroc

I have now tested MuPeXI with the lates version of VEP (95.1).

Nothing have changed in the way you run VEP and therefore how MuPeXI calls the command. VEP have changed how they build the tool and isolated VEP from the ensembl-tools-release. If you follow the installation instructions provided by Ensembl (https://www.ensembl.org/info/docs/tools/vep/script/index.html) you will end up with an executable where you just need to call fx "vep --help" when it is loaded in your PATH.

MuPeXI is able to use both the short executable or the full path but either should still be stated in the config.ini file

Sorry for the late respons - hope you found a way out of the problem.

Best, Anne-Mette