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

[Paul Hatton]

Many thanks for such a helpful response, Cyriac. That gist looks very hopeful; I have been off-campus for the last couple of days but will try that in the next day or so and update this list. Looks very hopeful though.

Thanks and 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]
[    http://www.birmingham.ac.uk/bear ]
[Also Technical Director, IBM Visual and Spatial Technology Centre]

From: Cyriac Kandoth [mailto:kandoth at cbio.mskcc.org]
Sent: 19 April 2016 21:59
To: Ensembl developers list
Cc: Paul Hatton
Subject: Re: [ensembl-dev] VEP installation problems - unable to install GRCh37 caches

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<mailto: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<mailto: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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