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

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(DJANGO)
(DJANGO)
Line 96: Line 96:
testing the development server:
testing the development server:
-
<pre>O$ python gene2pubmed/manage.py  runserver
+
<pre>$ python gene2pubmed/manage.py  runserver
Validating models...
Validating models...
Line 105: Line 105:
[02/Apr/2012 07:57:11] "GET / HTTP/1.1" 200 2061</pre>
[02/Apr/2012 07:57:11] "GET / HTTP/1.1" 200 2061</pre>
 +
<div style="background-color:yellow; margin:20px;">
 +
  <h1>It worked!</h1>
 +
  <h2>Congratulations on your first Django-powered page.</h2>
 +
  <p>Of course, you haven't actually done any work yet. Here's what to do next:</p>
 +
  <ul>
 +
    <li>If you plan to use a database, edit the <code>DATABASES</code> setting in <code>gene2pubmed/settings.py</code>.</li>
 +
    <li>Start your first app by running <code>python gene2pubmed/manage.py startapp [appname]</code>.</li>
 +
  </ul>
 +
  <p>
 +
    You're seeing this message because you have <code>DEBUG = True</code> in your
 +
    Django settings file and you haven't configured any URLs. Get to work!
 +
  </p>
 +
</div>
__NOTOC__
__NOTOC__

Revision as of 09:12, 2 April 2012

Project name Main project page
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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:

$ 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

It worked!

Congratulations on your first Django-powered page.

Of course, you haven't actually done any work yet. Here's what to do next:

  • If you plan to use a database, edit the DATABASES setting in gene2pubmed/settings.py.
  • Start your first app by running python gene2pubmed/manage.py startapp [appname].

You're seeing this message because you have DEBUG = True in your Django settings file and you haven't configured any URLs. Get to work!


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