Difference between revisions of "ChlamDB"
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[[new setup]] | [[new setup]] | ||
| − | === Update === | + | ===Update=== |
- avril 2019 | - avril 2019 | ||
{| class="wikitable sortable" | {| class="wikitable sortable" | ||
| Line 27: | Line 27: | ||
!N complete genomes | !N complete genomes | ||
|- | |- | ||
| − | + | |'''Planctomycetes''' | |
|600 | |600 | ||
|423 | |423 | ||
| Line 45: | Line 45: | ||
|0 | |0 | ||
|- | |- | ||
| − | |''' | + | |'''Kiritimatiellaeota''' |
|13 | |13 | ||
|7 | |7 | ||
| Line 51: | Line 51: | ||
|1 | |1 | ||
|- | |- | ||
| − | | | + | |'''Lentisphaerae''' |
|62 | |62 | ||
|29 | |29 | ||
| Line 57: | Line 57: | ||
|1 | |1 | ||
|- | |- | ||
| − | |'''Verrucomicrobia''' | + | |'''Verrucomicrobia''' |
|930 | |930 | ||
|555 | |555 | ||
| Line 69: | Line 69: | ||
|'''221''' | |'''221''' | ||
|} | |} | ||
| − | |||
===Setup environnement fonctionnel=== | ===Setup environnement fonctionnel=== | ||
| Line 152: | Line 151: | ||
</syntaxhighlight> | </syntaxhighlight> | ||
| + | Might be necessary to update the Xservers file as well (/etc/X11/xdm/Xservers) | ||
| + | <syntaxhighlight lang="Bash" line="1"> | ||
| + | #:0 local /usr/X11R6/bin/X -dpi 100 -nolisten tcp | ||
| + | :0 local /usr/X11R6/bin/X -dpi 100 | ||
| + | </syntaxhighlight> | ||
==setup https== | ==setup https== | ||
| Line 206: | Line 210: | ||
</syntaxhighlight> | </syntaxhighlight> | ||
| + | |||
| + | =setup celery= | ||
| + | |||
| + | - install celery, django-celery | ||
| + | - install rabbitmq | ||
| + | <syntaxhighlight lang="Bash" line="line"> | ||
| + | sudo apt-get install rabbitmq-server | ||
| + | sudo systemctl enable rabbitmq-server | ||
| + | sudo systemctl start rabbitmq-server | ||
| + | </syntaxhighlight> | ||
| + | |||
| + | - setup user and host | ||
| + | |||
| + | <syntaxhighlight lang="Bash" line="line"> | ||
| + | sudo rabbitmqctl add_vhost my_vhost | ||
| + | sudo rabbitmqctl add_user chlamdb estrella3 | ||
| + | sudo rabbitmqctl set_permissions -p my_vhost chlamdb "." "." ".*" | ||
| + | </syntaxhighlight> | ||
| + | |||
| + | - launch celery workers | ||
| + | |||
| + | <syntaxhighlight lang="Bash" line="line"> | ||
| + | celery -A chlamdb.celeryapp worker -l info | ||
| + | </syntaxhighlight> | ||
| + | |||
=setup on vital-it= | =setup on vital-it= | ||
Latest revision as of 17:48, 10 March 2020
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
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'
Might be necessary to update the Xservers file as well (/etc/X11/xdm/Xservers)
1#:0 local /usr/X11R6/bin/X -dpi 100 -nolisten tcp
2:0 local /usr/X11R6/bin/X -dpi 100
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 celery
- install celery, django-celery - install rabbitmq
1sudo apt-get install rabbitmq-server
2sudo systemctl enable rabbitmq-server
3sudo systemctl start rabbitmq-server
- setup user and host
1sudo rabbitmqctl add_vhost my_vhost
2sudo rabbitmqctl add_user chlamdb estrella3
3sudo rabbitmqctl set_permissions -p my_vhost chlamdb "." "." ".*"
- launch celery workers
1celery -A chlamdb.celeryapp worker -l info
setup on vital-it
ete3
work with the following variable exported:
1export QT_QPA_PLATFORM=offscreen