P3X GitList

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bin		moved ngs.pl startup script stderr & stdout to go to NGS/logs/deployment.log; made path to debug.txt explicit in NGS::VEP	12 years ago
environments		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	12 years ago
lib		moved ngs.pl startup script stderr & stdout to go to NGS/logs/deployment.log; made path to debug.txt explicit in NGS::VEP	12 years ago
public		needed FindBin in app.pl after update to D2 v0.09; bootstrap 3.0.0 spacelabs theme	12 years ago
script		new vcf analysis script	12 years ago
t		needed FindBin in app.pl after update to D2 v0.09; bootstrap 3.0.0 spacelabs theme	12 years ago
views		added transcription db = refseq option; fix for FLT3-ITD 1 variant; tests for invalid variant format	12 years ago
README.txt	854B	updated README's	12 years ago
config.yml	913B	initial working project	13 years ago
module_build.pl	438B	updated module_build.pl	12 years ago
ngs.sqlite	16kB	renamed vep orphans to non-CDS regions; added new ref entry to sqlite db; results page displays input src filename	12 years ago

README.txt

http://www.ensembl.org/info/docs/variation/vep/vep_script.html Setup/update VEP - delete scripts/variant_effect_predictor dir extract variant_effect_predictor.tar.gz into scripts dir run scripts/variant_effect_predictor/INSTALL.pl - skip cache. Cache manually installed/updated (needs to match VEP version) from: ftp://ftp.ensembl.org/pub/release-<xx>/variation/VEP/ see README.txt in NGS/script dir for more details Cache directory structure: vep dir containing core & refseq dirs, each with homo_sapiens/xx cache * on dev box - symlink /home/raj/.vep -> /media/sf_WIN_DRIVE/vep * on deployment - /home/raj/.vep to run from command-line: perl script/variant_effect_predictor.pl -config=script/vep.ini \ -i=t/data/myeloid_variants.vep -o=output.txt --polyphen=b --sift=b \ --check_existing --coding_only --regulatory --dir=refseq/core