<div dir="ltr">You can easily enough add directories to your INC by using:<div><br></div><div>perl -I /path/to/modules <a href="http://variant_effect_predictor.pl">variant_effect_predictor.pl</a></div><div><br></div><div>This is how I maintain various head and branch installations of the Ensembl API when testing code.</div>
<div><br></div><div style>Will</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 15 May 2013 11:31, Duarte Molha <span dir="ltr"><<a href="mailto:duartemolha@gmail.com" target="_blank">duartemolha@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><p><font color="#1f497d" face="Calibri, sans-serif"><span style="font-size:11pt">I much preferred to have a way of </span><span style="font-size:14.44444465637207px">specifying</span><span style="font-size:11pt"> it on the arguments. Yes we could use the PERL5LIB... but I was thinking more in terms of being able to </span><span style="font-size:14.44444465637207px">quickly</span><span style="font-size:11pt"> change from production ready plugins to testing plugins by </span><span style="font-size:14.44444465637207px">specifying</span><span style="font-size:11pt"> a different location.</span></font></p>
<p><font color="#1f497d" face="Calibri, sans-serif"><span style="font-size:11pt">If you wish to maintain </span><span style="font-size:14.44444465637207px">backwards</span><span style="font-size:11pt"> compatibility I suggest that to keep
the –dir argument as an overriding argument (if present the script expects both
cache and plugins in the same directory) and add only 1 additional argument --dir_plugins</span></font></p><p><font color="#1f497d" face="Calibri, sans-serif"><span style="font-size:14.44444465637207px">if you want to specify a different location.</span></font></p>
<p><font color="#1f497d" face="Calibri, sans-serif"><span style="font-size:14.44444465637207px">I personally prefer to to have control over my run environment without having to be dependent on the system path environment and can be different for different users, servers,etc...</span></font></p>
<p><font color="#1f497d" face="Calibri, sans-serif"><span style="font-size:14.44444465637207px">Thanks</span></font></p><span class="HOEnZb"><font color="#888888"><p><font color="#1f497d" face="Calibri, sans-serif"><span style="font-size:14.44444465637207px"><br>
Duarte</span></font></p><p><font color="#1f497d" face="Calibri, sans-serif"><span style="font-size:14.44444465637207px"><br></span></font></p></font></span></div><div class="gmail_extra"><div class="im"><br clear="all"><div>
<font style color="#999999">=========================<br>
Duarte Miguel Paulo Molha <br></font><div><font style color="#999999"> <a href="http://about.me/duarte" target="_blank">http://about.me/duarte</a> <br>=========================</font></div>
</div>
<br><br></div><div><div class="h5"><div class="gmail_quote">On Wed, May 15, 2013 at 11:20 AM, Will McLaren <span dir="ltr"><<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Hi Duarte,<div><br></div><div>It has been pointed out to me that the VEP will actually look for plugins anywhere in $PERL5LIB, so you could simply add you plugins dir (if separate) to $PERL5LIB and then --dir will be used to look up the cache directory.</div>
<div><br></div><div>Would this suit your purposes?</div><div><br></div><div>Cheers</div><span><font color="#888888"><div><br></div><div>Will</div></font></span></div><div><div><div class="gmail_extra">
<br><br><div class="gmail_quote">On 15 May 2013 11:11, Duarte Molha <span dir="ltr"><<a href="mailto:Duarte.Molha@ogt.com" target="_blank">Duarte.Molha@ogt.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div lang="EN-GB" link="blue" vlink="purple"><div><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Much appreciated<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> <a href="mailto:dev-bounces@ensembl.org" target="_blank">dev-bounces@ensembl.org</a> [mailto:<a href="mailto:dev-bounces@ensembl.org" target="_blank">dev-bounces@ensembl.org</a>] <b>On Behalf Of </b>Will McLaren<br>
<b>Sent:</b> 15 May 2013 11:09<br><b>To:</b> Ensembl developers list<br><b>Subject:</b> Re: [ensembl-dev] VEP feature request - different plugin and cache folder locations<u></u><u></u></span></p><div><div><p class="MsoNormal">
<u></u> <u></u></p><div><p class="MsoNormal">Hi Duarte,<u></u><u></u></p><div><p class="MsoNormal"><u></u> <u></u></p></div><div><p class="MsoNormal">Yes, a very reasonable suggestion.<u></u><u></u></p></div><div><p class="MsoNormal">
<u></u> <u></u></p></div><div><p class="MsoNormal">I'll look into it.<u></u><u></u></p></div><div><p class="MsoNormal"><u></u> <u></u></p></div><div><p class="MsoNormal">Will<u></u><u></u></p></div></div><div><p class="MsoNormal" style="margin-bottom:12.0pt">
<u></u> <u></u></p><div><p class="MsoNormal">On 15 May 2013 10:50, Duarte Molha <<a href="mailto:duartemolha@gmail.com" target="_blank">duartemolha@gmail.com</a>> wrote:<u></u><u></u></p><div><div><p class="MsoNormal">
Dear Devs<u></u><u></u></p></div><div><p class="MsoNormal"><u></u> <u></u></p></div><div><p class="MsoNormal">I would like to ask that the vep cache directory and the vep plugin directory be decoupled in the script.<u></u><u></u></p>
</div><div><p class="MsoNormal"><u></u> <u></u></p></div><div><p class="MsoNormal">It doesn't make sense (at least to me) that both these disparate sets of data have to be put in the same folder.<u></u><u></u></p></div>
<div><p class="MsoNormal"><u></u> <u></u></p></div><div><p class="MsoNormal">Sure I can hack the code myself, but I do not want to have to make this change everytime a new version comes out<u></u><u></u></p></div><div><p class="MsoNormal">
<u></u> <u></u></p></div><div><p class="MsoNormal">All I am asking is that you be given options like:<u></u><u></u></p></div><div><p class="MsoNormal"><u></u> <u></u></p></div><div><p class="MsoNormal">--dir_cache /vep_dache<u></u><u></u></p>
</div><div><p class="MsoNormal">--dir_plugins /vep_plugins<u></u><u></u></p></div><div><p class="MsoNormal"><u></u> <u></u></p></div><div><p class="MsoNormal">Is this something you would be willing to change?<u></u><u></u></p>
</div><div><p class="MsoNormal"><u></u> <u></u></p></div><div><p class="MsoNormal">Thanks<u></u><u></u></p></div><div><p class="MsoNormal"><br>Duarte<u></u><u></u></p></div><div><p class="MsoNormal"><u></u> <u></u></p></div>
<div><p class="MsoNormal"><span style="color:#999999">=========================<br> Duarte Miguel Paulo Molha </span><u></u><u></u></p><div><p class="MsoNormal"><span style="color:#999999"> <a href="http://about.me/duarte" target="_blank">http://about.me/duarte</a> <br>
=========================</span><u></u><u></u></p></div></div></div><p class="MsoNormal" style="margin-bottom:12.0pt"><br>_______________________________________________<br>Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
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