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

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(DJANGO)
(DJANGO)
Line 83: Line 83:
   sudo apt-get install python-django
   sudo apt-get install python-django
-
start a project
+
start a new project
   $ django-admin startproject gene2pubmed
   $ django-admin startproject gene2pubmed
Line 93: Line 93:
gene2pubmed/manage.py
gene2pubmed/manage.py
gene2pubmed/settings.py</pre>
gene2pubmed/settings.py</pre>
 +
 +
testing the development server:
 +
 +
<pre>O$ python gene2pubmed/manage.py  runserver
 +
Validating models...
 +
 +
0 errors found
 +
Django version 1.3, using settings 'gene2pubmed.settings'
 +
Development server is running at http://127.0.0.1:8000/
 +
Quit the server with CONTROL-C.
 +
[02/Apr/2012 07:57:11] "GET / HTTP/1.1" 200 2061</pre>
__NOTOC__
__NOTOC__

Revision as of 07:59, 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



DJANGO

install ubuntu:

  sudo apt-get install python-django

start a new project

  $ django-admin startproject gene2pubmed
$ find gene2pubmed/
gene2pubmed/
gene2pubmed/urls.py
gene2pubmed/__init__.py
gene2pubmed/manage.py
gene2pubmed/settings.py

testing the development server:

O$ python gene2pubmed/manage.py  runserver
Validating models...

0 errors found
Django version 1.3, using settings 'gene2pubmed.settings'
Development server is running at http://127.0.0.1:8000/
Quit the server with CONTROL-C.
[02/Apr/2012 07:57:11] "GET / HTTP/1.1" 200 2061



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