<div dir="ltr">Try separating out the mouse caches from the human caches...<div><br></div><div><font face="monospace, monospace">perl <a href="http://convert_cache.pl">convert_cache.pl</a> --species mus_musculus --version 84_GRCm38 --dir $VEP_DATA</font></div><div><font face="monospace, monospace">perl <a href="http://convert_cache.pl">convert_cache.pl</a> --species homo_sapiens --version 84_GRCh37,84_GRCh38 --dir $VEP_DATA</font></div><div><div><br></div><div>If that works, lemme know, I'll update the gist.</div><div><br></div><div>~Cyriac</div></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Sun, Apr 24, 2016 at 12:40 PM, Paul Hatton <span dir="ltr"><<a href="mailto:P.S.HATTON@bham.ac.uk" target="_blank">P.S.HATTON@bham.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<p class="MsoNormal"><a name="m_1715611134870723797__MailEndCompose"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">When I follow the gist it is fine apart from:<u></u><u></u></span></a></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"><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<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">2016-04-24 17:29:18 - Processing homo_sapiens<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">2016-04-24 17:29:18 - Processing version 84_GRCh38<u></u><u></u></span></p>
<p class="MsoNormal"><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.<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"><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.<u></u><u></u></span></p>
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<p class="MsoNormal"><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:<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">[variant_effect_predictor 17:35] $ which perl<u></u><u></u></span></p>
<p class="MsoNormal"><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<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"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Many thanks (again)<u></u><u></u></span></p><span class="">
<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"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">--<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Paul Hatton<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">High Performance Computing and Visualisation Specialist<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">IT Services, The University of Birmingham<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Ph: 0121-414-3994 Mob:07785 977340 Skype:P.S.Hatton<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">[Service Manager, Birmingham Environment for Academic Research]<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">[Also Technical Director, IBM Visual and Spatial Technology Centre]<u></u><u></u></span></p>
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</span><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""> Cyriac Kandoth [mailto:<a href="mailto:kandoth@cbio.mskcc.org" target="_blank">kandoth@cbio.mskcc.org</a>]
<br><span class="">
<b>Sent:</b> 19 April 2016 21:59<br>
<b>To:</b> Ensembl developers list<br>
<b>Cc:</b> Paul Hatton<br>
</span><b>Subject:</b> Re: [ensembl-dev] VEP installation problems - unable to install GRCh37 caches<u></u><u></u></span></p><div><div class="h5">
<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">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"<u></u><u></u></p>
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<p class="MsoNormal">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:<u></u><u></u></p>
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<p class="MsoNormal"><a href="https://github.com/Ensembl/VEP_plugins" target="_blank">https://github.com/Ensembl/VEP_plugins</a><u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">~C<u></u><u></u></p>
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<p class="MsoNormal">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:<u></u><u></u></p>
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<p class="MsoNormal">Hi Paul,<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">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><u></u><u></u></p>
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<p class="MsoNormal">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><u></u><u></u></p>
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<p class="MsoNormal"><span style="color:#888888"><u></u> <u></u></span></p>
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<p class="MsoNormal"><span style="color:#888888">~Cyriac<u></u><u></u></span></p>
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<p class="MsoNormal">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:<u></u><u></u></p>
<p class="MsoNormal" style="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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