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

[Rob Sargent]

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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