1. NGS.git
  2. t
 RSS Git Download  Clone
..
  data new tests files for scripts 11 years ago
  001_base.t 68B initial working project 13 years ago
  002_index_route.t 737B added new counters for vep input rows and raw src_file rows; patched lab number regex to allow optional letter prefix; fixed test scripts to report vep input row count instead of 'accepted' rows 11 years ago
  003_data.t 2kB moved all db queries to NGS::DB; added download facility for processed data; new MySQL ngs db for download data 11 years ago
  004_data.t 1kB moved NGS::Test function to NGS::Test::Common & moved test-lib.pl functions to NGS::Test, removed all calls to test-lib.pl from tests 11 years ago
  005_data.t 1kB moved NGS::Test function to NGS::Test::Common & moved test-lib.pl functions to NGS::Test, removed all calls to test-lib.pl from tests 11 years ago
  006_data.t 1kB moved NGS::Test function to NGS::Test::Common & moved test-lib.pl functions to NGS::Test, removed all calls to test-lib.pl from tests 11 years ago
  007_data.t 1kB moved NGS::Test function to NGS::Test::Common & moved test-lib.pl functions to NGS::Test, removed all calls to test-lib.pl from tests 11 years ago
  008_data.t 1kB moved NGS::Test function to NGS::Test::Common & moved test-lib.pl functions to NGS::Test, removed all calls to test-lib.pl from tests 11 years ago
  009_data.t 1kB moved NGS::Test function to NGS::Test::Common & moved test-lib.pl functions to NGS::Test, removed all calls to test-lib.pl from tests 11 years ago
  010_data.t 1kB moved NGS::Test function to NGS::Test::Common & moved test-lib.pl functions to NGS::Test, removed all calls to test-lib.pl from tests 11 years ago
  011_data.t 4kB moved NGS::Test function to NGS::Test::Common & moved test-lib.pl functions to NGS::Test, removed all calls to test-lib.pl from tests 11 years ago
  012_data.t 2kB moved NGS::Test function to NGS::Test::Common & moved test-lib.pl functions to NGS::Test, removed all calls to test-lib.pl from tests 11 years ago
  013_data.t 2kB moved NGS::Test function to NGS::Test::Common & moved test-lib.pl functions to NGS::Test, removed all calls to test-lib.pl from tests 11 years ago
  014_data.t 4kB moved NGS::Test function to NGS::Test::Common & moved test-lib.pl functions to NGS::Test, removed all calls to test-lib.pl from tests 11 years ago
  015_data.t 1kB moved NGS::Test function to NGS::Test::Common & moved test-lib.pl functions to NGS::Test, removed all calls to test-lib.pl from tests 11 years ago
  016_data.t 2kB simplified args passed in NGS.pm method calls - src_data & data_file are equivalent so replaced all refs to former with latter; simplified config block in _parse() 11 years ago
  017_data.t 1kB wrapped call to NGS::VEP in try/catch to handle die via 500.tt - works for tests as well; test for invalid filename; display list of valid filenames in upload page 11 years ago
  test-lib.pl 3kB major rewrite of test scripts - adapted for D2 version .154 - replaced D2::Test with Plack::Test; new NGS::Test Import::Base class 11 years ago
  test.t 761B wrapped call to NGS::VEP in try/catch to handle die via 500.tt - works for tests as well; test for invalid filename; display list of valid filenames in upload page 11 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 or: perl script/variant_effect_predictor.pl -config=/home/raj/apps/NGS/script/vep.ini \ -o=output.txt --dir=/home/raj/.vep/refseq --polyphen=b --sift=b --check_existing \ --coding_only --regulatory -i=/tmp/20_06_14.vep PERFORMANCE: a) 4055-row vep input with unsorted chromosome order on 163.160.171.48: fork=0 255 sec fork=2 580 sec fork=4 620 sec b) 1028-row vep input with alpha-numerically sorted chromosome order on 163.160.171.48: fork=0 95 sec fork=2 65 sec (optimal) fork=3 68 sec fork=4 70 sec fork=5 75 sec fork=6 75 sec performance much WORSE on dev server with fork enabled splitting a 1110-row vep input into separate chromosome input files slightly REDUCED performance (77sec vs 66sec) on dev