Differences

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--- vep-software [2017/09/28 11:57] – [Variant Effect Predictor(VEP)] aorth
+++ vep-software [2023/05/22 06:10] (current) – aorth
@@ Line 5: / Line 5: @@
 ===== Information =====
-  * Latest Version: 87
+  * Latest Version: 109.3
   * Added: February, 2017
-  * Link: http://www.ensembl.org/info/docs/tools/vep/index.html
+  * Updated: May, 2023
-  * Annotations: ''/export/data/bio/vep/''
+  * Link: https://github.com/Ensembl/ensembl-vep
+  * Annotations: ''/export/apps/vep/109.3/cache''
 ===== Usage =====
@@ Line 15: / Line 16: @@
 <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>