<div dir="ltr">Hi Michael,<div><br></div><div>Thanks for the suggestion - I'll add this change to the next VEP version.</div><div><br></div><div>I think it's probably OK for now as most users will run INSTALL.pl from within the VEP directory as per the instructions.</div>
<div><br></div><div>Cheers</div><div><br></div><div>Will McLaren</div><div>Ensembl Variation<br><div class="gmail_extra"><br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word"><div><blockquote type="cite"><div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px"><span style="font-family:'Helvetica';font-size:medium;color:rgba(0,0,0,1.0)"><b>From: </b></span><span style="font-family:'Helvetica';font-size:medium">Michael Yourshaw <<a href="mailto:myourshaw@ucla.edu" target="_blank">myourshaw@ucla.edu</a>><br>
</span></div><div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px"><span style="font-family:'Helvetica';font-size:medium;color:rgba(0,0,0,1.0)"><b>Subject: </b></span><span style="font-family:'Helvetica';font-size:medium"><b>[ensembl-dev] VEP installer fails if run from a different working directory</b><br>
</span></div><div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px"><span style="font-family:'Helvetica';font-size:medium;color:rgba(0,0,0,1.0)"><b>Date: </b></span><span style="font-family:'Helvetica';font-size:medium">10 January 2014 02:14:33 GMT<br>
</span></div><div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px"><span style="font-family:'Helvetica';font-size:medium;color:rgba(0,0,0,1.0)"><b>To: </b></span><span style="font-family:'Helvetica';font-size:medium">Ensembl developers list <<a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a>><br>
</span></div><div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px"><span style="font-family:'Helvetica';font-size:medium;color:rgba(0,0,0,1.0)"><b>Reply-To: </b></span><span style="font-family:'Helvetica';font-size:medium">Ensembl developers list <<a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a>><br>
</span></div><br><div style="word-wrap:break-word">When the VEP installer script is not in the working directory, e.g.,<div><br></div><div><span style="color:rgb(83,48,225);font-family:Monaco;font-size:10px">compute-4-55:~$ </span>perl ~/downloads/variant_effect_predictor/INSTALL.pl --DESTDIR ~/VEP</div>
<div><div><br></div><div>I get this error:</div><div><br></div><div>Testing VEP script<br>ERROR: Testing VEP script failed with the following error<br>Can't open perl script "<a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a>": No such file or directory</div>
<div><br></div><div><div>Maybe something like</div><div><br></div><div>use File::Basename;</div><div>my $dirname = dirname(__FILE__);</div><div>my $test_vep = `perl $dirname/<a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> --help 2>&1`;</div>
<div><br></div><div><br></div><div>Also, I got this, even with --AUTO</div><div><br></div><div>The VEP requires the ensembl, ensembl-variation and optionally ensembl-functgenomics modules<br><br>Skip to the next step (n) to install cache files<br>
<br>Do you want to continue installing the API (y/n)? y</div><div><br></div><div>It would be nice to have complete walk-home-and-ignore for AUTO.<br><br></div><div>
<span style="border-collapse:separate;font-size:12px;border-spacing:0px"><div style="word-wrap:break-word"><span style="border-collapse:separate;font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;border-spacing:0px"><span style="border-collapse:separate;font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;border-spacing:0px"><span style="border-collapse:separate;font-family:'Lucida Grande';font-size:10px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;border-spacing:0px"><p class="MsoNormal">
<font face="'Devanagari MT'" size="7"><span style="font-size:27px"><font face="'Lucida Grande'" size="3"><span style="font-size:12px"><br></span></font><font size="5"><span style="font-size:18px">ॐ</span></font></span></font></p>
</span><div><br></div><p style="margin:0px 0px 6px;font-style:normal;font-variant:normal;font-weight:normal;font-size:16px;line-height:normal;font-family:Helvetica"><span style="font-family:'Lucida Grande';font-size:10px">Michael Yourshaw, PhD</span></p>
<div style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;font-size:10px;line-height:normal;font-family:'Lucida Grande'"><span style="letter-spacing:0px">UCLA Geffen School of Medicine</span></div>
<div style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;font-size:10px;line-height:normal;font-family:'Lucida Grande'"><span style="letter-spacing:0px">Department of Human Genetics, Nelson Lab</span></div>
<div style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;font-size:10px;line-height:normal;font-family:'Lucida Grande'"><span style="letter-spacing:0px">695 Charles E Young Drive S</span></div>
<div style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;font-size:10px;line-height:normal;font-family:'Lucida Grande'"><span style="letter-spacing:0px">Gonda 5554</span></div><p style="margin:0px 0px 3px;font-style:normal;font-variant:normal;font-weight:normal;font-size:10px;line-height:normal;font-family:'Lucida Grande'">
<span style="letter-spacing:0px">Los Angeles CA 90095-8348 USA</span></p><p style="margin:0px 0px 3px;font-style:normal;font-variant:normal;font-weight:normal;font-size:10px;line-height:normal;font-family:'Lucida Grande';color:rgb(0,0,153)">
<span style="text-decoration:underline;letter-spacing:0px"><a href="mailto:myourshaw@ucla.edu" target="_blank">myourshaw@ucla.edu</a></span></p><p style="margin:0px 0px 6px;font-style:normal;font-variant:normal;font-weight:normal;font-size:10px;line-height:normal;font-family:'Lucida Grande'">
<span style="letter-spacing:0px"><a href="tel:970.691.8299" value="+19706918299" target="_blank">970.691.8299</a></span></p><p style="margin:0px 0px 6px;font-style:normal;font-variant:normal;font-weight:normal;font-size:9px;line-height:normal;font-family:'Lucida Grande'">
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