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

Cyriac Kandoth kandoth at cbio.mskcc.org
Mon Apr 25 16:33:42 BST 2016


Try separating out the mouse caches from the human caches...

perl convert_cache.pl --species mus_musculus --version 84_GRCm38 --dir
$VEP_DATA
perl convert_cache.pl --species homo_sapiens --version 84_GRCh37,84_GRCh38
--dir $VEP_DATA

If that works, lemme know, I'll update the gist.

~Cyriac

On Sun, Apr 24, 2016 at 12:40 PM, Paul Hatton <P.S.HATTON at bham.ac.uk> wrote:

> When I follow the gist it is fine apart from:
>
>
>
> [variant_effect_predictor 17:28] $ convert_cache.pl --species
> homo_sapiens,mus_musculus --version 84_GRCh37,84_GRCh38,84_GRCm38 --dir
> $VEP_DATA
>
> 2016-04-24 17:29:18 - Processing homo_sapiens
>
> 2016-04-24 17:29:18 - Processing version 84_GRCh38
>
> Can't use an undefined value as an ARRAY reference at ./convert_cache.pl
> line 188.
>
>
>
> Does this look at all familiar? Maybe an error on my part but I have
> followed the gist closely.
>
>
>
> This is using perl 5.20, which is the version that has been recommended to
> me for vcf2maf, in case that is relevant:
>
>
>
> [variant_effect_predictor 17:35] $ which perl
>
> /gpfs/apps/perl/v5.20.0_gcc-v4.7.2/bin/perl
>
>
>
> Many thanks (again)
>
>
>
> --
>
> 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]
>
>
>
> *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>
> 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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