Difference between revisions of "User:Lindenb/Notebook/UMR915/2012/04/02"

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(variant_effect_predictor.pl)
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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 04:42, 2 April 2012

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Daily

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':

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


Run

 perl variant_effect_predictor.pl  --regulatory --sift=b  --polyphen=b  --regulatory --input_file 20120327.rs.vcf.gz  --format vcf -o  20120402.vcf --vcf