[ensembl-dev] VEP installation problems - unable to install GRCh37 caches

[Cyriac Kandoth]

I forgot to mention - the order of instructions in that gist is
specifically addressing the error you reported - "For technical reasons
this installer is unable to install GRCh37 caches alongside others; please
install them separately"

Also, I'd recommend against installing all plugins, it can get messy. Only
the ExAC plugin is currently used by vcf2maf. In the future, it may use
more. Here is a list of all the available plugins:
https://github.com/Ensembl/VEP_plugins

~C

On Tue, Apr 19, 2016 at 4:18 PM, Cyriac Kandoth <kandoth at cbio.mskcc.org>
wrote:

> Hi Paul,
>
> It is appropriate to post such a qn to dev at ensembl. If you have an issue
> specifically with vcf2maf, we (mskcc) can help you at
> https://github.com/mskcc/vcf2maf/issues
>
> The latest readme for vcf2maf includes instructions for installing VEP v83
> - https://github.com/mskcc/vcf2maf - I will remove these instructions in
> the next few days in favor of gists. Here's a gist for installing VEP v84
> with an offline cache for GRCh37 -
> https://gist.github.com/ckandoth/57d189f018b448774704d3b2191720a6
>
> ~Cyriac
>
> On Tue, Apr 19, 2016 at 4:07 AM, Paul Hatton <P.S.HATTON at bham.ac.uk>
> wrote:
>
>> Apologies if this is the wrong list to post this to, but a search for
>> this problem led me to this list and I can't find any mention of it in the
>> archives (which sort-of suggests that I'm on the wrong list).
>>
>> I look after the applications base on our Linux-based HPC service at the
>> University of Birmingham (UK) and we have recently established a new Centre
>> for Computational Biology and hence I am asked to install much specialist
>> software such as VEP. I have a great deal of experience in installing
>> applications on a Linux HPC service but limited experience of these
>> specialist applications, so apologies again if this is a naive question
>> posted to the wrong list .... feel free to point me elsewhere if more
>> appropriate ......
>>
>> Anyhow, I have been asked to get vcf2maf running, which depends on VEP. I
>> have been unable to get a clean installation of VEP 82, 83 or 84 which I
>> think is having knock-on problems to users running vcf2maf, and so I'd like
>> to get VEP installed cleanly first. Whilst VEP itself build fine with
>>
>> cd ensembl-tools-release-84/scripts/variant_effect_predictor
>> export PERL5LIB=/gpfs/apps/VEP/84:$PERL5LIB
>> export PATH=/gpfs/apps/VEP/84/htslib:$PATH
>> perl INSTALL.pl --DESTDIR /gpfs/apps/VEP/84 --CACHEDIR
>> /gpfs/apps/VEP/84/cache --PLUGINS all
>>
>> and installs VEP as expected, when I ask it to download the cache files
>> it fails at the end with
>>
>>  - downloading
>> ftp://ftp.ensembl.org/pub/release-84/variation/VEP/xiphophorus_maculatus_vep_84_Xipmac4.4.2.tar.gz
>> - unpacking xiphophorus_maculatus_vep_84_Xipmac4.4.2.tar.gz
>> ERROR: For technical reasons this installer is unable to install GRCh37
>> caches alongside others; please install them separately
>>
>> and I can't find any help as to what I should do next. For example,
>> though, /gpfs/apps/VEP/84/cache/homo_sapiens has directories 84_GRCh37 and
>> 84_GRCh38 which seem fully populated, though, so can this be safely ignored?
>>
>> If I then repeat the installation asking not to install any cache files
>> and ask it to install all of the FASTA files the third one fails with
>>
>> ERROR: Could not change directory to dna
>>
>> and the installer then terminates, rather than trying the next one. I
>> think this comes from lines 737 to 739 in INSTALL.pl:
>>
>>  foreach my $sub(split /\//, $3) {
>>       $ftp->cwd($sub) or die "ERROR: Could not change directory to
>> $sub\n$@\n";
>>     }
>>
>> and suggests that there are some missing directories on the download site
>> for these files. Is this the case and, if so, is there any way around this
>> apart from rerunning the installer for each of the 70 options one-by-one,
>> which would take quite a while?
>>
>> Apologies again if this is the wrong list and/or these are simplistic
>> questions. Any help is much appreciated.
>>
>> Regards
>>
>> --
>> Paul Hatton
>> High Performance Computing and Visualisation Specialist
>> IT Services, The University of Birmingham
>> Ph: 0121-414-3994  Mob:07785 977340  Skype:P.S.Hatton
>> [Service Manager, Birmingham Environment for Academic Research]
>> [Also Technical Director, IBM Visual and Spatial Technology Centre]
>>
>>
>>
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>>
>
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