Differences

This shows you the differences between two versions of the page.

--- vep-software [2018/04/15 21:00] – aorth
+++ vep-software [2023/05/22 06:10] (current) – aorth
@@ Line 5: / Line 5: @@
 ===== Information =====
-  * Latest Version: 92.1
+  * Latest Version: 109.3
   * Added: February, 2017
-  * Updated: April, 2018
+  * Updated: May, 2023
-  * Link: http://www.ensembl.org/info/docs/tools/vep/index.html
+  * Link: https://github.com/Ensembl/ensembl-vep
-  * Annotations: ''/export/apps/vep/92.1/cache''
+  * Annotations: ''/export/apps/vep/109.3/cache''
 ===== Usage =====
@@ Line 17: / Line 17: @@
 Load one version into your environment and run it:
-<code>$ module load vep/92.1
+<code>$ module load vep/109.3
-$ vep --cache /export/apps/vep/92.1/cache
+$ vep --cache /export/apps/vep/109.3/cache</code>
-</code>
-**N.B.** The VEP cache is installed in ''/export/apps/vep/92.1/cache'', so make sure to
+**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.
 ===== Installation ======
@@ Line 27: / Line 26: @@
 <code>$ cd /tmp
-$ curl -L -O https://github.com/Ensembl/ensembl-vep/archive/release/92.1.zip
+$ curl -L -O https://github.com/Ensembl/ensembl-vep/archive/release/109.3.zip
-$ unzip 92.1.zip
+$ unzip 109.3.zip
-$ sudo yum install perl-DBI perl-DBD-mysql perl-JSON perl-perlIO-gzip
+$ sudo dnf install perl-DBI perl-DBD-mysql perl-JSON perl-perlIO-gzip
-$ module load htslib/1.6
+$ cd ensembl-vep-release-109.3
-$ cd ensembl-vep-release-92.1
 $ 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/92.1
+$ sudo mkdir -p /export/apps/vep/109.3
-$ sudo cp -r * /export/apps/vep/92.1</code>
+$ sudo cp -r * /export/apps/vep/109.3</code>