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vep-software [2017/02/06 21:34] – created joguyavep-software [2023/05/22 06:10] (current) – aorth
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-====== Variant Effect Predictor(VEP) ======+====== Variant Effect Predictor (VEP) ======
  
 VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.
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 ===== Information ===== ===== Information =====
  
-  * Latest Version: 87+  * Latest Version: 109.3
   * Added: February, 2017   * Added: February, 2017
-  * Link: http://www.ensembl.org/info/docs/tools/vep/index.html+  * Updated: May, 2023 
 +  * Link: https://github.com/Ensembl/ensembl-vep 
 +  * Annotations: ''/export/apps/vep/109.3/cache''
  
 ===== Usage ===== ===== Usage =====
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 <code>$ module avail vep</code> <code>$ module avail vep</code>
  
-===== Installation ====== +Load one version into your environment and run it: 
-Notes from the sysadmin during installation:+<code>$ module load vep/109.3 
 +$ vep --cache /export/apps/vep/109.3/cache</code>
  
-<code> +**N.B.** The VEP cache is installed in ''/export/apps/vep/109.3/cache'', so make sure to specify this when working with VEP. Contact Alan or Jean-Baka if you need more databases installed.
-- install vep-script +
-$ sudo mkdir -p /export/apps/vep/87/ +
-$ sudo chown -R joguya:joguya /export/apps/vep/87/ +
-$ cd scripts/variant_effect_predictor +
-$ module load perl/5.22.3 +
-$ scl enable devtoolset-3 bash +
-$ cpanm File::Copy::Recursive Archive::Extract LWP::Simple LWP::Protocol::https CGI +
-$ module load htslib/1.3.2 +
-$ mkdir /export/apps/vep/87/cache +
-$ perl INSTALL.pl --DESTDIR /export/apps/vep/87 --NO_HTSLIB  +
-$ PERL5LIB=$PERL5LIB:/export/apps/vep/87 perl INSTALL.pl --DESTDIR /export/apps/vep/87 --NO_HTSLIB +
-$ cp *.pl *.vcf /export/apps/vep/87/ +
-$ sudo chown -R root:root /export/apps/vep/87/+
  
-- download cattle annotation data to /export/data/ for use by VEP in /export/data/bio +===== Installation ====== 
-$ sudo mkdir /export/data/bio/vep +Notes from the sysadmin during installation:
-$ sudo chown joguya:joguya /export/data/bio/vep +
-$ PERL5LIB=$PERL5LIB:/export/apps/vep/87 perl INSTALL.pl --DESTDIR /export/apps/vep/87 --CACHEDIR /export/data/bio/vep --NO_HTSLIB +
-$ sudo chown -R root:root /export/data/bio/vep +
-</code>+
  
 +<code>$ cd /tmp
 +$ curl -L -O https://github.com/Ensembl/ensembl-vep/archive/release/109.3.zip
 +$ unzip 109.3.zip
 +$ sudo dnf install perl-DBI perl-DBD-mysql perl-JSON perl-perlIO-gzip
 +$ cd ensembl-vep-release-109.3
 +$ cpanm -l . Set::IntervalTree
 +$ mkdir cache
 +$ module load htslib/1.9 # use our own, instead of the one installed by INSTALL.pl
 +$ PERL5LIB=lib/perl5 perl INSTALL.pl --NO_HTSLIB --CACHEDIR cache
 +$ sudo mkdir -p /export/apps/vep/109.3
 +$ sudo cp -r * /export/apps/vep/109.3</code>
vep-software.1486416888.txt.gz · Last modified: 2017/02/06 21:34 by joguya