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<font size="-1"><font face="Courier New, Courier, monospace">Thanks
Will,<br>
<br>
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!<br>
<br>
rjs<br>
<br>
<br>
</font></font>
<div class="moz-cite-prefix">On 09/19/2014 02:16 AM, Will McLaren
wrote:<br>
</div>
<blockquote
cite="mid:CAMVEDX1R-BuwRmfUTkqs9osJHgYfSs10VW9xQM1CivpaDEPB4w@mail.gmail.com"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=ISO-8859-1">
<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 $PERL5LIB persist next
time you open a terminal.</div>
<div><br>
</div>
<div>Regards</div>
<div><br>
</div>
<div>Will McLaren</div>
<div>Ensembl Variation</div>
<div><span style="font-family:'Courier New',Courier,monospace"><br>
</span></div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On 18 September 2014 23:25, Rob Sargent
<span dir="ltr"><<a moz-do-not-send="true"
href="mailto:rob.sargent@utah.edu" target="_blank">rob.sargent@utah.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"> <font size="-1"><font
face="Courier New, Courier, monospace">I'm new here so
no doubt I'm missing something obvious. Any help
appreciated.<br>
<br>
I downloaded v76, unzipped and <br>
<br>
</font></font>
<blockquote><font size="-1"><font face="Courier New,
Courier, monospace">stability:~$ 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 moz-do-not-send="true"
href="http://convert_cache.pl" target="_blank">convert_cache.pl</a>
example_GRCh37.vcf example_GRCh38.vcf <a
moz-do-not-send="true" href="http://filter_vep.pl"
target="_blank">filter_vep.pl</a> <a
moz-do-not-send="true" href="http://gtf2vep.pl"
target="_blank">gtf2vep.pl</a> INSTALL.pl
README.txt <a moz-do-not-send="true"
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 moz-do-not-send="true"
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 moz-do-not-send="true"
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 moz-do-not-send="true"
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 moz-do-not-send="true"
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 moz-do-not-send="true"
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 moz-do-not-send="true"
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 moz-do-not-send="true"
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
moz-do-not-send="true"
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
moz-do-not-send="true"
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
moz-do-not-send="true"
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
moz-do-not-send="true"
href="http://variant_effect_predictor.pl"
target="_blank">variant_effect_predictor.pl</a>
line 50.<br>
BEGIN failed--compilation aborted at ./<a
moz-do-not-send="true"
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
moz-do-not-send="true"
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 moz-do-not-send="true"
href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>)<br>
<br>
Help: <a moz-do-not-send="true"
href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a>
, <a moz-do-not-send="true"
href="mailto:helpdesk@ensembl.org" target="_blank">helpdesk@ensembl.org</a><br>
Twitter: @ensembl , @EnsemblWill<br>
<br>
<a moz-do-not-send="true"
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 moz-do-not-send="true"
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 moz-do-not-send="true"
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>
<br>
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</blockquote>
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