User:Lindenb/Notebook/UMR915/2012/04/02: Difference between revisions
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(→DJANGO) |
(→DJANGO) |
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$ django-admin startproject gene2pubmed | $ django-admin startproject gene2pubmed | ||
<pre>$ find gene2pubmed/ | <pre>$ find gene2pubmed/ | ||
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gene2pubmed/manage.py | gene2pubmed/manage.py | ||
gene2pubmed/settings.py</pre> | gene2pubmed/settings.py</pre> | ||
Edit gene2pubmed/settings.py | |||
and set the default db to sqlite3: | |||
<pre>DATABASES = { | |||
'default': { | |||
'ENGINE': 'django.db.backends.sqlite3', # Add 'postgresql_psycopg2', 'postgresql', 'mysql', 'sqlite3' or 'oracle'. | |||
'NAME': 'gene2pubmed.sqlite3', # Or path to database file if using sqlite3. | |||
'USER': '', # Not used with sqlite3. | |||
'PASSWORD': '', # Not used with sqlite3. | |||
'HOST': '', # Set to empty string for localhost. Not used with sqlite3. | |||
'PORT': '', # Set to empty string for default. Not used with sqlite3. | |||
} | |||
}</pre> | |||
set the local time in gene2pubmed/settings.py | |||
<pre>TIME_ZONE = 'Europe/Paris'</pre> | |||
synchronize installation for sessions, messages, etc... | |||
<pre>python manage.py syncdb | |||
$ python manage.py syncdb | |||
Creating tables ... | |||
Creating table auth_permission | |||
Creating table auth_group_permissions | |||
Creating table auth_group | |||
Creating table auth_user_user_permissions | |||
Creating table auth_user_groups | |||
Creating table auth_user | |||
Creating table auth_message | |||
Creating table django_content_type | |||
Creating table django_session | |||
Creating table django_site | |||
You just installed Django's auth system, which means you don't have any superusers defined. | |||
Would you like to create one now? (yes/no): y | |||
Please enter either "yes" or "no": yes | |||
Username (Leave blank to use 'lindenb'): | |||
E-mail address: xxxx@xxxx.xxx | |||
Password: | |||
Password (again): | |||
Superuser created successfully. | |||
Installing custom SQL ... | |||
Installing indexes ... | |||
No fixtures found.</pre> | |||
testing the development server: | testing the development server: | ||
Revision as of 06:22, 2 April 2012
 Project name
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<html><img src="/images/9/94/Report.png" border="0" /></html> Main project page <html><img src="/images/c/c3/Resultset_previous.png" border="0" /></html>Previous entry<html> </html>Next entry<html><img src="/images/5/5c/Resultset_next.png" border="0" /></html> |
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
| |
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
Edit gene2pubmed/settings.py and set the default db to sqlite3:
DATABASES = {
'default': {
'ENGINE': 'django.db.backends.sqlite3', # Add 'postgresql_psycopg2', 'postgresql', 'mysql', 'sqlite3' or 'oracle'.
'NAME': 'gene2pubmed.sqlite3', # Or path to database file if using sqlite3.
'USER': '', # Not used with sqlite3.
'PASSWORD': '', # Not used with sqlite3.
'HOST': '', # Set to empty string for localhost. Not used with sqlite3.
'PORT': '', # Set to empty string for default. Not used with sqlite3.
}
}
set the local time in gene2pubmed/settings.py
TIME_ZONE = 'Europe/Paris'
synchronize installation for sessions, messages, etc...
python manage.py syncdb $ python manage.py syncdb Creating tables ... Creating table auth_permission Creating table auth_group_permissions Creating table auth_group Creating table auth_user_user_permissions Creating table auth_user_groups Creating table auth_user Creating table auth_message Creating table django_content_type Creating table django_session Creating table django_site You just installed Django's auth system, which means you don't have any superusers defined. Would you like to create one now? (yes/no): y Please enter either "yes" or "no": yes Username (Leave blank to use 'lindenb'): E-mail address: xxxx@xxxx.xxx Password: Password (again): Superuser created successfully. Installing custom SQL ... Installing indexes ... No fixtures found.
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
DATABASESsetting ingene2pubmed/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!
