[ensembl-dev] Installing v76 to non-standard dir fails

[Will McLaren]

Hi Rob,

Thanks for the heads up on this; the test script is not using perl -I as it
should. I'll add a fix to the GitHub repo.

If you want to continue with the installer past the test, you can add your
dir to PERL5LIB with something like:

setenv PERL5LIB $PERL5LIB:/usr/sup/applications/vep

for csh/tcsh, or

export PERL5LIB=$PERL5LIB:/usr/sup/applications/vep

for a bash shell. If you rerun the installer (asking it not to install the
API) then it should pass the test OK.

Note that you should add these lines to your ~/.cshrc or ~/.bashrc files to
make the changes to $PERL5LIB persist next time you open a terminal.

Regards

Will McLaren
Ensembl Variation


On 18 September 2014 23:25, Rob Sargent <rob.sargent at utah.edu> wrote:

>  I'm new here so no doubt I'm missing something obvious.  Any help
> appreciated.
>
> I downloaded v76, unzipped and
>
>  stability:~$ cd
> tools/ensembl-tools-release-76/scripts/variant_effect_predictor/
> stability:variant_effect_predictor$ ls
> convert_cache.pl  example_GRCh37.vcf  example_GRCh38.vcf  filter_vep.pl
> gtf2vep.pl  INSTALL.pl  README.txt  variant_effect_predictor.pl
> stability:variant_effect_predictor$ perl  INSTALL.pl -d
> /usr/sup/applications/vep
> Using non-default installation directory /usr/sup/applications/vep - you
> will probably need to add /usr/sup/applications/vep to your PERL5LIB
>
> Hello! This installer is configured to install v76 of the Ensembl API for
> use by the VEP.
> It will not affect any existing installations of the Ensembl API that you
> may have.
>
> It will also download and install cache files from Ensembl's FTP server.
>
> Checking for installed versions of the Ensembl API...done
> It looks like you have an older version (v69) of the API installed.
> This installer will install a limited set of the API v76 for use by the
> VEP only
>
> Skip to the next step (n) to install cache files
>
> Do you want to continue installing the API (y/n)? y
>
> Setting up directories
>
> Downloading required files
>  - fetching ensembl
> ** GET https://github.com/Ensembl/ensembl/archive/release/76.zip ==> 302
> Found
> ** GET https://codeload.github.com/Ensembl/ensembl/zip/release/76 ==> 200
> OK (8s)
>  - unpacking /usr/sup/applications/vep/Bio/tmp/ensembl.zip
>  - moving files
>  - fetching ensembl-variation
> ** GET https://github.com/Ensembl/ensembl-variation/archive/release/76.zip
> ==> 302 Found (1s)
> ** GET
> https://codeload.github.com/Ensembl/ensembl-variation/zip/release/76 ==>
> 200 OK (4s)
>  - unpacking /usr/sup/applications/vep/Bio/tmp/ensembl-variation.zip
>  - moving files
>  - fetching ensembl-funcgen
> ** GET https://github.com/Ensembl/ensembl-funcgen/archive/release/76.zip
> ==> 302 Found (1s)
> ** GET https://codeload.github.com/Ensembl/ensembl-funcgen/zip/release/76
> ==> 200 OK (2s)
>  - unpacking /usr/sup/applications/vep/Bio/tmp/ensembl-funcgen.zip
>  - moving files
>  - fetching BioPerl
> ** GET http://bioperl.org/DIST/BioPerl-1.6.1.tar.gz ==> 200 OK (1s)
>  - unpacking /usr/sup/applications/vep/Bio/tmp/BioPerl-1.6.1.tar.gz
>  - moving files
>
> Testing VEP script
> ERROR: Testing VEP script failed with the following error
> "@EXTRA_HEADERS" is not exported by the
> Bio::EnsEMBL::Variation::Utils::VEP module
>  "%COL_DESCS" is not exported by the Bio::EnsEMBL::Variation::Utils::VEP
> module
> Can't continue after import errors at ./variant_effect_predictor.pl line
> 50.
> BEGIN failed--compilation aborted at ./variant_effect_predictor.pl line
> 68.
>
> Heading the note about PERL5LIB I tried to run the test by hand as follows:
>
> stability:variant_effect_predictor$ perl -I /usr/sup/applications/vep/Bio
> ./variant_effect_predictor.pl
> "@EXTRA_HEADERS" is not exported by the
> Bio::EnsEMBL::Variation::Utils::VEP module
>  "%COL_DESCS" is not exported by the Bio::EnsEMBL::Variation::Utils::VEP
> module
> Can't continue after import errors at ./variant_effect_predictor.pl line
> 50.
> BEGIN failed--compilation aborted at ./variant_effect_predictor.pl line
> 68.
>
>  Not sure is I was one directory off:
>
> stability:variant_effect_predictor$ perl -I /usr/sup/applications/vep ./
> variant_effect_predictor.pl
> #----------------------------------#
> # ENSEMBL VARIANT EFFECT PREDICTOR #
> #----------------------------------#
>
> version 76
> by Will McLaren (wm2 at ebi.ac.uk)
>
> Help: dev at ensembl.org , helpdesk at ensembl.org
> Twitter: @ensembl , @EnsemblWill
>
> http://www.ensembl.org/info/docs/tools/vep/script/index.html
>
> Usage:
> perl variant_effect_predictor.pl [--cache|--offline|--database]
> [arguments]
>
> Basic options
> =============
>
> --help                 Display this message and quit
>
> -i | --input_file      Input file
> -o | --output_file     Output file
> --force_overwrite      Force overwriting of output file
> --species [species]    Species to use [default: "human"]
>
> --everything           Shortcut switch to turn on commonly used options.
> See web
>                        documentation for details [default:
> off]
> --fork [num_forks]     Use forking to improve script runtime
>
> For full option documentation see:
> http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html
>
> rjs
>
>
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