<div dir="ltr">Hi Rob,<div><br></div><div>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.</div><div><br></div><div>If you want to continue with the installer past the test, you can add your dir to PERL5LIB with something like:</div><div><br></div><div>setenv PERL5LIB $PERL5LIB:/usr/sup/applications/vep <br><br>for csh/tcsh, or<br><br>export PERL5LIB=$PERL5LIB:/usr/sup/applications/vep<br><br>for a bash shell. If you rerun the installer (asking it not to install the API) then it should pass the test OK.</div><div><br></div><div>Note that you should add these lines to your ~/.cshrc or ~/.bashrc files to make the changes to $PERL5LIB persist next time you open a terminal.</div><div><br></div><div>Regards</div><div><br></div><div>Will McLaren</div><div>Ensembl Variation</div><div><span style="font-family:'Courier New',Courier,monospace"><br></span></div></div><div class="gmail_extra"><br><div class="gmail_quote">On 18 September 2014 23:25, Rob Sargent <span dir="ltr"><<a href="mailto:rob.sargent@utah.edu" target="_blank">rob.sargent@utah.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<font size="-1"><font face="Courier New, Courier, monospace">I'm new
here so no doubt I'm missing something obvious. Any help
appreciated.<br>
<br>
I downloaded v76, unzipped and <br>
<br>
</font></font>
<blockquote><font size="-1"><font face="Courier New, Courier,
monospace">stability:~$ cd
tools/ensembl-tools-release-76/scripts/variant_effect_predictor/</font></font><br>
<font size="-1"><font face="Courier New, Courier, monospace">stability:variant_effect_predictor$
ls</font></font><br>
<font size="-1"><font face="Courier New, Courier, monospace"><a href="http://convert_cache.pl" target="_blank">convert_cache.pl</a>
example_GRCh37.vcf example_GRCh38.vcf <a href="http://filter_vep.pl" target="_blank">filter_vep.pl</a>
<a href="http://gtf2vep.pl" target="_blank">gtf2vep.pl</a> INSTALL.pl README.txt
<a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a></font></font><br>
<font size="-1"><font face="Courier New, Courier, monospace">stability:variant_effect_predictor$
perl INSTALL.pl -d /usr/sup/applications/vep</font></font><br>
<font size="-1"><font face="Courier New, Courier, monospace">Using
non-default installation directory /usr/sup/applications/vep -
you will probably need to add /usr/sup/applications/vep to
your PERL5LIB</font></font><br>
<br>
<font size="-1"><font face="Courier New, Courier, monospace">Hello!
This installer is configured to install v76 of the Ensembl API
for use by the VEP.</font></font><br>
<font size="-1"><font face="Courier New, Courier, monospace">It
will not affect any existing installations of the Ensembl API
that you may have.</font></font><br>
<br>
<font size="-1"><font face="Courier New, Courier, monospace">It
will also download and install cache files from Ensembl's FTP
server.</font></font><br>
<br>
<font size="-1"><font face="Courier New, Courier, monospace">Checking
for installed versions of the Ensembl API...done</font></font><br>
<font size="-1"><font face="Courier New, Courier, monospace">It
looks like you have an older version (v69) of the API
installed.</font></font><br>
<font size="-1"><font face="Courier New, Courier, monospace">This
installer will install a limited set of the API v76 for use by
the VEP only</font></font><br>
<br>
<font size="-1"><font face="Courier New, Courier, monospace">Skip
to the next step (n) to install cache files</font></font><br>
<br>
<font size="-1"><font face="Courier New, Courier, monospace">Do
you want to continue installing the API (y/n)? y</font></font><br>
<br>
<font size="-1"><font face="Courier New, Courier, monospace">Setting
up directories</font></font><br>
<br>
<font size="-1"><font face="Courier New, Courier, monospace">Downloading
required files</font></font><br>
<font size="-1"><font face="Courier New, Courier, monospace"> -
fetching ensembl</font></font><br>
<font size="-1"><font face="Courier New, Courier, monospace">**
GET <a href="https://github.com/Ensembl/ensembl/archive/release/76.zip" target="_blank">https://github.com/Ensembl/ensembl/archive/release/76.zip</a>
==> 302 Found</font></font><br>
<font size="-1"><font face="Courier New, Courier, monospace">**
GET <a href="https://codeload.github.com/Ensembl/ensembl/zip/release/76" target="_blank">https://codeload.github.com/Ensembl/ensembl/zip/release/76</a>
==> 200 OK (8s)</font></font><br>
<font size="-1"><font face="Courier New, Courier, monospace"> -
unpacking /usr/sup/applications/vep/Bio/tmp/ensembl.zip</font></font><br>
<font size="-1"><font face="Courier New, Courier, monospace"> -
moving files</font></font><br>
<font size="-1"><font face="Courier New, Courier, monospace"> -
fetching ensembl-variation</font></font><br>
<font size="-1"><font face="Courier New, Courier, monospace">**
GET
<a href="https://github.com/Ensembl/ensembl-variation/archive/release/76.zip" target="_blank">https://github.com/Ensembl/ensembl-variation/archive/release/76.zip</a>
==> 302 Found (1s)</font></font><br>
<font size="-1"><font face="Courier New, Courier, monospace">**
GET
<a href="https://codeload.github.com/Ensembl/ensembl-variation/zip/release/76" target="_blank">https://codeload.github.com/Ensembl/ensembl-variation/zip/release/76</a>
==> 200 OK (4s)</font></font><br>
<font size="-1"><font face="Courier New, Courier, monospace"> -
unpacking
/usr/sup/applications/vep/Bio/tmp/ensembl-variation.zip</font></font><br>
<font size="-1"><font face="Courier New, Courier, monospace"> -
moving files</font></font><br>
<font size="-1"><font face="Courier New, Courier, monospace"> -
fetching ensembl-funcgen</font></font><br>
<font size="-1"><font face="Courier New, Courier, monospace">**
GET
<a href="https://github.com/Ensembl/ensembl-funcgen/archive/release/76.zip" target="_blank">https://github.com/Ensembl/ensembl-funcgen/archive/release/76.zip</a>
==> 302 Found (1s)</font></font><br>
<font size="-1"><font face="Courier New, Courier, monospace">**
GET
<a href="https://codeload.github.com/Ensembl/ensembl-funcgen/zip/release/76" target="_blank">https://codeload.github.com/Ensembl/ensembl-funcgen/zip/release/76</a>
==> 200 OK (2s)</font></font><br>
<font size="-1"><font face="Courier New, Courier, monospace"> -
unpacking
/usr/sup/applications/vep/Bio/tmp/ensembl-funcgen.zip</font></font><br>
<font size="-1"><font face="Courier New, Courier, monospace"> -
moving files</font></font><br>
<font size="-1"><font face="Courier New, Courier, monospace"> -
fetching BioPerl</font></font><br>
<font size="-1"><font face="Courier New, Courier, monospace">**
GET <a href="http://bioperl.org/DIST/BioPerl-1.6.1.tar.gz" target="_blank">http://bioperl.org/DIST/BioPerl-1.6.1.tar.gz</a> ==> 200 OK
(1s)</font></font><br>
<font size="-1"><font face="Courier New, Courier, monospace"> -
unpacking
/usr/sup/applications/vep/Bio/tmp/BioPerl-1.6.1.tar.gz</font></font><br>
<font size="-1"><font face="Courier New, Courier, monospace"> -
moving files</font></font><br>
<br>
<font size="-1"><font face="Courier New, Courier, monospace">Testing
VEP script</font></font><br>
<font size="-1"><font face="Courier New, Courier, monospace">ERROR:
Testing VEP script failed with the following error</font></font><br>
<font size="-1"><font face="Courier New, Courier, monospace">"@EXTRA_HEADERS"
is not exported by the Bio::EnsEMBL::Variation::Utils::VEP
module</font></font><br>
<font size="-1"><font face="Courier New, Courier, monospace"> "%COL_DESCS"
is not exported by the Bio::EnsEMBL::Variation::Utils::VEP
module</font></font><br>
<font size="-1"><font face="Courier New, Courier, monospace">Can't
continue after import errors at ./<a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a>
line 50.</font></font><br>
<font size="-1"><font face="Courier New, Courier, monospace">BEGIN
failed--compilation aborted at ./<a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a>
line 68.</font></font><br>
</blockquote>
<font size="-1"><font face="Courier New, Courier, monospace">Heading
the note about PERL5LIB I tried to run the test by hand as
follows:<br>
</font></font>
<blockquote><font size="-1"><font face="Courier New, Courier,
monospace">stability:variant_effect_predictor$ perl -I
/usr/sup/applications/vep/Bio ./<a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> <br>
"@EXTRA_HEADERS" is not exported by the
Bio::EnsEMBL::Variation::Utils::VEP module<br>
"%COL_DESCS" is not exported by the
Bio::EnsEMBL::Variation::Utils::VEP module<br>
Can't continue after import errors at
./<a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> line 50.<br>
BEGIN failed--compilation aborted at
./<a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> line 68.<br>
<br>
</font></font></blockquote>
<font size="-1"><font face="Courier New, Courier, monospace">Not
sure is I was one directory off:<br>
</font></font>
<blockquote><font size="-1"><font face="Courier New, Courier,
monospace">stability:variant_effect_predictor$ perl -I
/usr/sup/applications/vep ./<a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> <br>
#----------------------------------#<br>
# ENSEMBL VARIANT EFFECT PREDICTOR #<br>
#----------------------------------#<br>
<br>
version 76<br>
by Will McLaren (<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>)<br>
<br>
Help: <a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a> , <a href="mailto:helpdesk@ensembl.org" target="_blank">helpdesk@ensembl.org</a><br>
Twitter: @ensembl , @EnsemblWill<br>
<br>
<a href="http://www.ensembl.org/info/docs/tools/vep/script/index.html" target="_blank">http://www.ensembl.org/info/docs/tools/vep/script/index.html</a><br>
<br>
Usage:<br>
perl <a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a>
[--cache|--offline|--database] [arguments]<br>
<br>
Basic options<br>
=============<br>
<br>
--help Display this message and quit<br>
<br>
-i | --input_file Input file<br>
-o | --output_file Output file<br>
--force_overwrite Force overwriting of output file<br>
--species [species] Species to use [default: "human"]<br>
<br>
--everything Shortcut switch to turn on commonly
used options. See web<br>
documentation for details [default:
off] <br>
--fork [num_forks] Use forking to improve script runtime<br>
<br>
For full option documentation see:<br>
<a href="http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html" target="_blank">http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html</a><br>
</font></font></blockquote>
<small><font face="Courier New, Courier, monospace">rjs</font></small><br>
<br>
</div>
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<br></blockquote></div><br></div>