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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-bidi-font-family:"Times New Roman";color:#1F497D">Cyriac,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-bidi-font-family:"Times New Roman";color:#1F497D">I have to send abject apologies - I had omitted the<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-bidi-font-family:"Times New Roman";color:#1F497D">cat $VEP_DATA/*_vep_84_GRC{h37,h38,m38}.tar.gz | tar -izxf - -C $VEP_DATA<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-bidi-font-family:"Times New Roman";color:#1F497D">command, and all is fine now. I had been looking at the instructions for so long that my eyes glazed over. It worked
fine with the combined<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-bidi-font-family:"Times New Roman";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal" style="tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt">
<span style="font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman"">convert_cache.pl --species homo_sapiens,mus_musculus --version 84_GRCh37,84_GRCh38,84_GRCm38 --dir $VEP_DATA<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-bidi-font-family:"Times New Roman";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-bidi-font-family:"Times New Roman";color:#1F497D">command, and the example program on the gist ran absolutely fine.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-bidi-font-family:"Times New Roman";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-bidi-font-family:"Times New Roman";color:#1F497D">Many thanks for pointing me to the gist and apologies again for my error at the final hurdle.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-bidi-font-family:"Times New Roman";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-bidi-font-family:"Times New Roman";color:#1F497D">Regards<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-bidi-font-family:"Times New Roman";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman";color:#1F497D;mso-no-proof:yes">--<span style="mso-spacerun:yes">
</span><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman";color:#1F497D;mso-no-proof:yes">Paul Hatton<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman";color:#1F497D;mso-no-proof:yes">High Performance Computing and Visualisation Specialist<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman";color:#1F497D;mso-no-proof:yes">IT Services, The University of Birmingham<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman";color:#1F497D;mso-no-proof:yes">Ph: 0121-414-3994<span style="mso-spacerun:yes">
</span>Mob: 07785-977340<span style="mso-spacerun:yes"> </span>Skype: P.S.Hatton<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman";color:#1F497D;mso-no-proof:yes">[Service Manager, Birmingham Environment for Academic Research]<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman";color:#1F497D;mso-no-proof:yes">[<span style="mso-spacerun:yes">
</span><a href="http://www.birmingham.ac.uk/bear"><span style="color:blue">http://www.birmingham.ac.uk/bear</span></a> ]<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman";color:#1F497D;mso-no-proof:yes">[Also Technical Director, IBM Visual and Spatial Technology
Centre]<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";mso-bidi-font-family:"Times New Roman";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";mso-fareast-font-family:"Times New Roman";mso-ansi-language:EN-US">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";mso-fareast-font-family:"Times New Roman";mso-ansi-language:EN-US">
Cyriac Kandoth [mailto:kandoth@cbio.mskcc.org] <br>
<b>Sent:</b> 25 April 2016 23:22<br>
<b>To:</b> Paul Hatton<br>
<b>Cc:</b> Ensembl developers list<br>
<b>Subject:</b> Re: [ensembl-dev] VEP installation problems - unable to install GRCh37 caches<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal">I'm unable to reproduce that error. But looking at the code, it appears to happen if you're missing the "info.txt" file in a cache folder. Check for them like this:<o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">$ ll -h $VEP_DATA/{homo_sapiens,mus_musculus}/*/info.txt<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">-rw-r--r-- 1 kandoth pwgmgr 786 Feb 26 16:03 /opt/common/CentOS_6-dev/vep/v84/homo_sapiens/84_GRCh37/info.txt<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">-rw-r--r-- 1 kandoth pwgmgr 1.4K Feb 29 12:31 /opt/common/CentOS_6-dev/vep/v84/homo_sapiens/84_GRCh38/info.txt<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">-rw-r--r-- 1 kandoth pwgmgr 533 Feb 23 10:14 /opt/common/CentOS_6-dev/vep/v84/mus_musculus/84_GRCm38/info.txt<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">If your info.txt files are missing, then one of the steps before "<a href="http://convert_cache.pl">convert_cache.pl</a>" was skipped. E.g. make sure you didn't forget to untar those cache tarballs after rsync-ing them.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">~Cyriac<o:p></o:p></p>
</div>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal">On Mon, Apr 25, 2016 at 1:01 PM, Paul Hatton <<a href="mailto:P.S.HATTON@bham.ac.uk" target="_blank">P.S.HATTON@bham.ac.uk</a>> wrote:<o:p></o:p></p>
<div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><a name="m_895113676860907393__MailEndCompose"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Afraid not:</span></a><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">[vep 17:57] $ perl ./<a href="http://convert_cache.pl" target="_blank">convert_cache.pl</a> --species
mus_musculus --version 84_GRCm38 --dir $VEP_DATA</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">2016-04-25 17:58:10 - Processing mus_musculus</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">2016-04-25 17:58:10 - Processing version 84_GRCm38</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Can't use an undefined value as an ARRAY reference at ./<a href="http://convert_cache.pl" target="_blank">convert_cache.pl</a>
line 188.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Not sure if this helps:</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">[vep 18:00] $ ll -h $VEP_DATA</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">total 13G</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">-rw-r--r-- 1 appmaint appmaint 1.7G Apr 24 17:32 ExAC.r0.3.sites.minus_somatic.vcf.gz</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">-rw-r--r-- 1 appmaint appmaint 800K Apr 24 17:35 ExAC.r0.3.sites.minus_somatic.vcf.gz.tbi</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">drwxr-xr-x 4 appmaint appmaint 512 Apr 24 17:03 homo_sapiens</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">-r-x------ 1 appmaint appmaint 4.8G Apr 24 16:42 homo_sapiens_vep_84_GRCh37.tar.gz</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">-r-x------ 1 appmaint appmaint 4.8G Apr 24 16:42 homo_sapiens_vep_84_GRCh38.tar.gz</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">drwxr-xr-x 3 appmaint appmaint 512 Apr 24 17:17 mus_musculus</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">-r-x------ 1 appmaint appmaint 1.4G Apr 24 16:42 mus_musculus_vep_84_GRCm38.tar.gz</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">drwxr-xr-x 2 appmaint appmaint 512 Apr 24 16:59 Plugins</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Regards</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">--</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Paul Hatton</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">High Performance Computing and Visualisation Specialist</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">IT Services, The University of Birmingham</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Ph: 0121-414-3994 Mob:07785 977340 Skype:P.S.Hatton</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">[Service Manager, Birmingham Environment for Academic Research]</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">[Also Technical Director, IBM Visual and Spatial Technology Centre]</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";mso-ansi-language:EN-US">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";mso-ansi-language:EN-US">
Cyriac Kandoth [mailto:<a href="mailto:kandoth@cbio.mskcc.org" target="_blank">kandoth@cbio.mskcc.org</a>]
<br>
<b>Sent:</b> 25 April 2016 16:34<br>
<b>To:</b> Paul Hatton<br>
<b>Cc:</b> Ensembl developers list</span><o:p></o:p></p>
<div>
<div>
<p class="MsoNormal"><br>
<b>Subject:</b> Re: [ensembl-dev] VEP installation problems - unable to install GRCh37 caches<o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Try separating out the mouse caches from the human caches...<o:p></o:p></p>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-family:"Courier New"">perl
<a href="http://convert_cache.pl" target="_blank">convert_cache.pl</a> --species mus_musculus --version 84_GRCm38 --dir $VEP_DATA</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-family:"Courier New"">perl
<a href="http://convert_cache.pl" target="_blank">convert_cache.pl</a> --species homo_sapiens --version 84_GRCh37,84_GRCh38 --dir $VEP_DATA</span><o:p></o:p></p>
</div>
<div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">If that works, lemme know, I'll update the gist.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">~Cyriac<o:p></o:p></p>
</div>
</div>
</div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">On Sun, Apr 24, 2016 at 12:40 PM, Paul Hatton <<a href="mailto:P.S.HATTON@bham.ac.uk" target="_blank">P.S.HATTON@bham.ac.uk</a>> wrote:<o:p></o:p></p>
<div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><a name="m_895113676860907393_m_17156111348707237"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">When I follow the gist it is fine apart from:</span></a><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">[variant_effect_predictor 17:28] $
<a href="http://convert_cache.pl" target="_blank">convert_cache.pl</a> --species homo_sapiens,mus_musculus --version 84_GRCh37,84_GRCh38,84_GRCm38 --dir $VEP_DATA</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">2016-04-24 17:29:18 - Processing homo_sapiens</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">2016-04-24 17:29:18 - Processing version 84_GRCh38</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Can't use an undefined value as an ARRAY reference at ./<a href="http://convert_cache.pl" target="_blank">convert_cache.pl</a>
line 188.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Does this look at all familiar? Maybe an error on my part but I have followed the gist closely.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">This is using perl 5.20, which is the version that has been recommended to me for vcf2maf, in case
that is relevant:</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">[variant_effect_predictor 17:35] $ which perl</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">/gpfs/apps/perl/v5.20.0_gcc-v4.7.2/bin/perl</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Many thanks (again)</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">--</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Paul Hatton</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">High Performance Computing and Visualisation Specialist</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">IT Services, The University of Birmingham</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Ph: 0121-414-3994 Mob:07785 977340 Skype:P.S.Hatton</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">[Service Manager, Birmingham Environment for Academic Research]</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">[Also Technical Director, IBM Visual and Spatial Technology Centre]</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";mso-ansi-language:EN-US">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";mso-ansi-language:EN-US">
Cyriac Kandoth [mailto:<a href="mailto:kandoth@cbio.mskcc.org" target="_blank">kandoth@cbio.mskcc.org</a>]
<br>
<b>Sent:</b> 19 April 2016 21:59<br>
<b>To:</b> Ensembl developers list<br>
<b>Cc:</b> Paul Hatton<br>
<b>Subject:</b> Re: [ensembl-dev] VEP installation problems - unable to install GRCh37 caches</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I forgot to mention - the order of instructions in that gist is specifically addressing the error you reported - "For technical reasons this installer is unable to install GRCh37
caches alongside others; please install them separately"<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Also, I'd recommend against installing all plugins, it can get messy. Only the ExAC plugin is currently used by vcf2maf. In the future, it may use more. Here is a list of all the
available plugins:<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><a href="https://github.com/Ensembl/VEP_plugins" target="_blank">https://github.com/Ensembl/VEP_plugins</a><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">~C<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">On Tue, Apr 19, 2016 at 4:18 PM, Cyriac Kandoth <<a href="mailto:kandoth@cbio.mskcc.org" target="_blank">kandoth@cbio.mskcc.org</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Hi Paul,<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">It is appropriate to post such a qn to dev@ensembl. If you have an issue specifically with vcf2maf, we (mskcc) can help you at <a href="https://github.com/mskcc/vcf2maf/issues" target="_blank">https://github.com/mskcc/vcf2maf/issues</a><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">The latest readme for vcf2maf includes instructions for installing VEP v83 -
<a href="https://github.com/mskcc/vcf2maf" target="_blank">https://github.com/mskcc/vcf2maf</a> - I will remove these instructions in the next few days in favor of gists. Here's a gist for installing VEP v84 with an offline cache for GRCh37 -
<a href="https://gist.github.com/ckandoth/57d189f018b448774704d3b2191720a6" target="_blank">
https://gist.github.com/ckandoth/57d189f018b448774704d3b2191720a6</a><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#888888"> </span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#888888">~Cyriac</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">On Tue, Apr 19, 2016 at 4:07 AM, Paul Hatton <<a href="mailto:P.S.HATTON@bham.ac.uk" target="_blank">P.S.HATTON@bham.ac.uk</a>> wrote:<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:12.0pt">Apologies if this is the wrong list to post this to, but a search for this problem led me to this list and I can't find any mention of it in the archives (which sort-of suggests that
I'm on the wrong list).<br>
<br>
I look after the applications base on our Linux-based HPC service at the University of Birmingham (UK) and we have recently established a new Centre for Computational Biology and hence I am asked to install much specialist software such as VEP. I have a great
deal of experience in installing applications on a Linux HPC service but limited experience of these specialist applications, so apologies again if this is a naive question posted to the wrong list .... feel free to point me elsewhere if more appropriate ......<br>
<br>
Anyhow, I have been asked to get vcf2maf running, which depends on VEP. I have been unable to get a clean installation of VEP 82, 83 or 84 which I think is having knock-on problems to users running vcf2maf, and so I'd like to get VEP installed cleanly first.
Whilst VEP itself build fine with<br>
<br>
cd ensembl-tools-release-84/scripts/variant_effect_predictor<br>
export PERL5LIB=/gpfs/apps/VEP/84:$PERL5LIB<br>
export PATH=/gpfs/apps/VEP/84/htslib:$PATH<br>
perl INSTALL.pl --DESTDIR /gpfs/apps/VEP/84 --CACHEDIR /gpfs/apps/VEP/84/cache --PLUGINS all<br>
<br>
and installs VEP as expected, when I ask it to download the cache files it fails at the end with<br>
<br>
- downloading <a href="ftp://ftp.ensembl.org/pub/release-84/variation/VEP/xiphophorus_maculatus_vep_84_Xipmac4.4.2.tar.gz" target="_blank">
ftp://ftp.ensembl.org/pub/release-84/variation/VEP/xiphophorus_maculatus_vep_84_Xipmac4.4.2.tar.gz</a><br>
- unpacking xiphophorus_maculatus_vep_84_Xipmac4.4.2.tar.gz<br>
ERROR: For technical reasons this installer is unable to install GRCh37 caches alongside others; please install them separately<br>
<br>
and I can't find any help as to what I should do next. For example, though, /gpfs/apps/VEP/84/cache/homo_sapiens has directories 84_GRCh37 and 84_GRCh38 which seem fully populated, though, so can this be safely ignored?<br>
<br>
If I then repeat the installation asking not to install any cache files and ask it to install all of the FASTA files the third one fails with<br>
<br>
ERROR: Could not change directory to dna<br>
<br>
and the installer then terminates, rather than trying the next one. I think this comes from lines 737 to 739 in INSTALL.pl:<br>
<br>
foreach my $sub(split /\//, $3) {<br>
$ftp->cwd($sub) or die "ERROR: Could not change directory to $sub\n$@\n";<br>
}<br>
<br>
and suggests that there are some missing directories on the download site for these files. Is this the case and, if so, is there any way around this apart from rerunning the installer for each of the 70 options one-by-one, which would take quite a while?<br>
<br>
Apologies again if this is the wrong list and/or these are simplistic questions. Any help is much appreciated.<br>
<br>
Regards<br>
<br>
--<br>
Paul Hatton<br>
High Performance Computing and Visualisation Specialist<br>
IT Services, The University of Birmingham<br>
Ph: 0121-414-3994 Mob:07785 977340 Skype:P.S.Hatton<br>
[Service Manager, Birmingham Environment for Academic Research]<br>
[Also Technical Director, IBM Visual and Spatial Technology Centre]<br>
<br>
<br>
<br>
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Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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