[ensembl-dev] Installing v76 to non-standard dir fails
Rob Sargent
rob.sargent at utah.edu
Mon Sep 22 00:43:30 BST 2014
Thanks Will,
Setting the PERL5LIB prior to running (with -d) got past the test. I'm
a little surprised the cache still defaults to ~/.vep rather that to
somewhere under DESTDIR, but the -c works!
rjs
On 09/19/2014 02:16 AM, Will McLaren wrote:
> 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 $PERL5LIB persist next time you open a
> terminal.
>
> Regards
>
> Will McLaren
> Ensembl Variation
>
>
> On 18 September 2014 23:25, Rob Sargent <rob.sargent at utah.edu
> <mailto:rob.sargent at utah.edu>> wrote:
>
> I'm new here so no doubt I'm missing something obvious. Any help
> appreciated.
>
> I downloaded v76, unzipped and
>
> stability:~$ cd
> tools/ensembl-tools-release-76/scripts/variant_effect_predictor/
> stability:variant_effect_predictor$ ls
> convert_cache.pl <http://convert_cache.pl> example_GRCh37.vcf
> example_GRCh38.vcf filter_vep.pl <http://filter_vep.pl>
> gtf2vep.pl <http://gtf2vep.pl> INSTALL.pl README.txt
> variant_effect_predictor.pl <http://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
> <http://variant_effect_predictor.pl> line 50.
> BEGIN failed--compilation aborted at
> ./variant_effect_predictor.pl
> <http://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
> <http://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
> <http://variant_effect_predictor.pl> line 50.
> BEGIN failed--compilation aborted at
> ./variant_effect_predictor.pl
> <http://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
> <http://variant_effect_predictor.pl>
> #----------------------------------#
> # ENSEMBL VARIANT EFFECT PREDICTOR #
> #----------------------------------#
>
> version 76
> by Will McLaren (wm2 at ebi.ac.uk <mailto:wm2 at ebi.ac.uk>)
>
> Help: dev at ensembl.org <mailto:dev at ensembl.org> ,
> helpdesk at ensembl.org <mailto:helpdesk at ensembl.org>
> Twitter: @ensembl , @EnsemblWill
>
> http://www.ensembl.org/info/docs/tools/vep/script/index.html
>
> Usage:
> perl variant_effect_predictor.pl
> <http://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
>
>
> _______________________________________________
> Dev mailing list Dev at ensembl.org <mailto:Dev at ensembl.org>
> Posting guidelines and subscribe/unsubscribe info:
> http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>
>
>
>
> _______________________________________________
> Dev mailing list Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20140921/054be01e/attachment.html>
More information about the Dev
mailing list