User:Lindenb/Notebook/UMR915/2012/04/02

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
(DJANGO)
(Run)
Line 76: Line 76:
<!-- ##### DO NOT edit below this line unless you know what you are doing. ##### -->
<!-- ##### DO NOT edit below this line unless you know what you are doing. ##### -->
|}
|}
 +
 +
 +
=DJANGO=
 +
install ubuntu:
 +
 +
  sudo apt-get install python-django
 +
 +
start a project
 +
 +
  $ django-admin startproject gene2pubmed
 +
__NOTOC__
__NOTOC__

Revision as of 07:55, 2 April 2012

Project name Main project page
Previous entry      Next entry

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



DJANGO

install ubuntu:

  sudo apt-get install python-django

start a project

  $ django-admin startproject gene2pubmed


Personal tools