changed script/variant_effect_predictor.pl file to symlink to same file inside variant_effect_predictor dir for ease of updating vep version - now just download, extract & run new v_e_p.tar.gz
moved forking config to config files - dev server faster without forks, deployment optimum with fork = 2; moved hires timer to immediately either side of vep script loop; deleted vep input file from /tmp if exists due to generation using append mode (in case previous run aborted before unlink) event; output format tweaks
11 years ago
README.txt
to update vep:
1) delete variant_effect_predictor dir (leave symlink intact)
2) download latest version from: http://www.ensembl.org/info/docs/tools/vep/index.html
3) run INSTALL.pl - skip cache (done manually below)
4) rename local Bio to eg Bio.v7x, move to ~/perl-lib and update Bio symlink in ~/perl5/lib/perl5
5) download & extract matching databases into ~/.vep/core & ~/.vep/refseq using
ftp://ftp.ensembl.org/pub/release-<xx>/variation/VEP/
*) main difference after upgrade is Bio::EnsEMBL classes - other Bio:: classes same
