ChlamDB

Mise en ligne de la base de donnée Chlamdb

Page d’accueil

• mettre un nouvel onglet avec qq infos
• écrire une page tuto avec fonctions de base
• exporter le fichier avec environnementale conda nécessaire pour faire tourner la base de donnée

Setup chlamdb

old setup

new setup

Update

- avril 2019

	N genomes	N annotated Genbank	N annotated RS	N complete genomes
Planctomycetes	600	423	60	20
Chlamydiae	463	392	401	165
Ca. Omnitrophica	172	137	4	0
Kiritimatiellaeota	13	7	1	1
Lentisphaerae	62	29	4	1
Verrucomicrobia	930	555	158	34
TOTAL	2249	1443	628	221

Setup environnement fonctionnel

Conda

name: chlamdb
channels:
 - r
 - etetoolkit
 - bioconda
 - conda-forge
 - defaults
dependencies:
 - python=3.5.6
 - django=2.1.1
 - django-extensions
 - bibtexparser
 - cairo
 - r-cairo
 - r-vegan
 - r-gplots
 - r-gdtools
 - r-svglite
 - pandas
 - qtconsole
 - ete3
 - ete_toolchain
 - pyqt=4.11.4
 - matplotlib
 - scipy
 - pylibmc
 - simplejson
 - dill
 - gunicorn
 - numpy 
 - pyqt 
 - lxml 
 - conda-build
 - reportlab
 - biopython
 - django-crispy-forms
 - mysqlclient
 - pip:
   - cython
   - django-citations

packages R absents de conda à installer à la main

- genoPlotR - flextable

modules python a ajouter à la main

1conda develop /home/ubuntu/dev/orthomcl/
2conda develop /home/ubuntu/dev/plots/
3conda develop /home/ubuntu/dev/biosqldb/
4conda develop /home/ubuntu/dev/utilitaires/
5conda develop /home/ubuntu/dev/phylo_tree_display/
6conda develop /home/ubuntu/dev/TPutils/
7conda develop /home/ubuntu/dev/network_d3/

setup X server pour ete3

1apt-get install  xserver-xorg xdm  xfonts-base xfonts-100dpi xfonts-75dpi

1In our example, edit the /etc/X11/xdm/xdm-config file and set following values:
2
3DisplayManager*authorize:       false
4DisplayManager*authComplain:    false

1/etc/init.d/xdm restart

1export DISPLAY=':0'

setup https

setup certificate and key with letsencrypt

1systemctl stop nginx
2letsencrypt certonly
3systemctl start nginx

update config

 1upstream monsite {
 2    # Adresse du serveur wsgi, par exemple gunicorn
 3        server localhost:8001;
 4        }
 5
 6# HTTP Request will be Redirected to the HTTPS
 7server {
 8      listen 80;
 9      server_name chlamdb.ch;
10      return 301 https://$server_name$request_uri;
11      }
12
13server {
14    listen 443 ssl;
15    server_name chlamdb.ch;
16    
17    ssl_certificate /etc/letsencrypt/live/chlamdb.ch/fullchain.pem;
18    ssl_certificate_key /etc/letsencrypt/live/chlamdb.ch/privkey.pem;
19    
20    access_log /webapps/logs/GEN.access.log;
21    error_log /webapps/logs/GEN.error.log;
22    
23    location / {
24        #include fastcgi_params;
25        proxy_pass http://monsite;
26        proxy_redirect off;
27        proxy_set_header Host $http_host;
28        proxy_set_header X-Real-IP $remote_addr;
29        proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
30        proxy_set_header X-Forwarded-Proto $scheme;
31    }
32
33    location /assets {
34        autoindex on;
35        alias /home/ubuntu/dev/chlamdb/assets/;
36    }
37}

setup on vital-it

ete3

work with the following variable exported:

1export QT_QPA_PLATFORM=offscreen