User:Lindenb/Notebook/UMR915/2012/04/02: Difference between revisions
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=variant_effect_predictor.pl= | =variant_effect_predictor.pl= | ||
==Fix for proxy== | |||
replace | |||
unless(getstore($url, $target_file) == 200) | |||
by | |||
my $status = system("/usr/bin/curl --proxy 'http://proxy:3128' -o '$target_file' -L '$url'"); | |||
(...) | |||
my $status2 = system("/usr/bin/curl --proxy 'http://proxy:3128' -o '$target_file' -L --create-dirs '$BIOPERL_URL,'"); | |||
some problems with the bioperl install, downloaded the tar.gz and moved the perl modules to the directory 'Bio': | |||
in the directory 'Bio': | |||
<pre>Align | |||
AlignIO | |||
Annotation | |||
Assembly | |||
Biblio | |||
bioperl-1.2.3 | |||
Cluster | |||
ClusterIO | |||
Coordinate | |||
Das | |||
DB | |||
EnsEMBL | |||
Event | |||
Expression | |||
Factory | |||
Graphics | |||
Index | |||
LiveSeq | |||
Location | |||
Map | |||
MapIO | |||
Matrix | |||
Ontology | |||
OntologyIO | |||
Phenotype | |||
Root | |||
Search | |||
SearchIO | |||
Seq | |||
SeqFeature | |||
SeqIO | |||
Structure | |||
Symbol | |||
Taxonomy | |||
tmp | |||
Tools | |||
Tree | |||
TreeIO | |||
Variation</pre> | |||
==Run== | |||
<pre> perl variant_effect_predictor.pl --regulatory --sift=b --polyphen=b --regulatory --input_file 20120327.rs.vcf.gz --format vcf -o 20120402.vcf --vcf</pre> | <pre> perl variant_effect_predictor.pl --regulatory --sift=b --polyphen=b --regulatory --input_file 20120327.rs.vcf.gz --format vcf -o 20120402.vcf --vcf</pre> | ||
Revision as of 05:42, 2 April 2012
 Project name
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Dailyvariant_effect_predictor.plFix for proxyreplace unless(getstore($url, $target_file) == 200) by my $status = system("/usr/bin/curl --proxy 'http://proxy:3128' -o '$target_file' -L '$url'");
(...)
my $status2 = system("/usr/bin/curl --proxy 'http://proxy:3128' -o '$target_file' -L --create-dirs '$BIOPERL_URL,'");
in the directory 'Bio': Align AlignIO Annotation Assembly Biblio bioperl-1.2.3 Cluster ClusterIO Coordinate Das DB EnsEMBL Event Expression Factory Graphics Index LiveSeq Location Map MapIO Matrix Ontology OntologyIO Phenotype Root Search SearchIO Seq SeqFeature SeqIO Structure Symbol Taxonomy tmp Tools Tree TreeIO Variation
Runperl variant_effect_predictor.pl --regulatory --sift=b --polyphen=b --regulatory --input_file 20120327.rs.vcf.gz --format vcf -o 20120402.vcf --vcf
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