Difference between revisions of "ChlamDB"
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| Line 1: | Line 1: | ||
| + | ==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=== | |
| − | === Setup chlamdb === | ||
[[old setup]] | [[old setup]] | ||
[[new setup]] | [[new setup]] | ||
| + | |||
| + | === Update === | ||
| + | - avril 2019 | ||
| + | {| class="wikitable sortable" | ||
| + | |+ | ||
| + | ! | ||
| + | !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 | ||
| + | |- | ||
| + | |<big>'''Lentisphaerae'''</big> | ||
| + | |62 | ||
| + | |29 | ||
| + | |4 | ||
| + | |1 | ||
| + | |- | ||
| + | |'''Verrucomicrobia''' | ||
| + | |930 | ||
| + | |555 | ||
| + | |158 | ||
| + | |34 | ||
| + | |- | ||
| + | |'''TOTAL''' | ||
| + | |'''2249''' | ||
| + | |'''1443''' | ||
| + | |'''628''' | ||
| + | |'''221''' | ||
| + | |} | ||
| − | === Setup environnement fonctionnel === | + | ===Setup environnement fonctionnel=== |
| − | ==== Conda ==== | + | ====Conda==== |
name: chlamdb | name: chlamdb | ||
| Line 64: | Line 116: | ||
- django-citations | - django-citations | ||
| − | ==== packages R absents de conda à installer à la main ==== | + | ====packages R absents de conda à installer à la main==== |
- genoPlotR | - genoPlotR | ||
- flextable | - flextable | ||
| − | ==== modules python a ajouter à la main ==== | + | ====modules python a ajouter à la main==== |
| − | <syntaxhighlight lang="Bash" line= | + | <syntaxhighlight lang="Bash" line="line"> |
conda develop /home/ubuntu/dev/orthomcl/ | conda develop /home/ubuntu/dev/orthomcl/ | ||
conda develop /home/ubuntu/dev/plots/ | conda develop /home/ubuntu/dev/plots/ | ||
| Line 79: | Line 131: | ||
conda develop /home/ubuntu/dev/network_d3/ | conda develop /home/ubuntu/dev/network_d3/ | ||
</syntaxhighlight> | </syntaxhighlight> | ||
| − | ==== setup X server pour ete3 ==== | + | ====setup X server pour ete3==== |
| − | <syntaxhighlight lang="Bash" line= | + | <syntaxhighlight lang="Bash" line="line"> |
apt-get install xserver-xorg xdm xfonts-base xfonts-100dpi xfonts-75dpi | apt-get install xserver-xorg xdm xfonts-base xfonts-100dpi xfonts-75dpi | ||
</syntaxhighlight> | </syntaxhighlight> | ||
| − | <syntaxhighlight lang="Bash" line= | + | <syntaxhighlight lang="Bash" line="line"> |
In our example, edit the /etc/X11/xdm/xdm-config file and set following values: | In our example, edit the /etc/X11/xdm/xdm-config file and set following values: | ||
| Line 92: | Line 144: | ||
</syntaxhighlight> | </syntaxhighlight> | ||
| − | <syntaxhighlight lang="Bash" line= | + | <syntaxhighlight lang="Bash" line="line"> |
/etc/init.d/xdm restart | /etc/init.d/xdm restart | ||
</syntaxhighlight> | </syntaxhighlight> | ||
| − | <syntaxhighlight lang="Bash" line= | + | <syntaxhighlight lang="Bash" line="line"> |
export DISPLAY=':0' | export DISPLAY=':0' | ||
</syntaxhighlight> | </syntaxhighlight> | ||
| − | == setup https == | + | ==setup https== |
| − | === setup certificate and key with letsencrypt === | + | ===setup certificate and key with letsencrypt=== |
| − | <syntaxhighlight lang="Bash" line= | + | <syntaxhighlight lang="Bash" line="line"> |
systemctl stop nginx | systemctl stop nginx | ||
letsencrypt certonly | letsencrypt certonly | ||
| Line 112: | Line 164: | ||
| − | === | + | ===update config=== |
| − | <syntaxhighlight lang="Bash" line= | + | <syntaxhighlight lang="Bash" line="line"> |
upstream monsite { | upstream monsite { | ||
# Adresse du serveur wsgi, par exemple gunicorn | # Adresse du serveur wsgi, par exemple gunicorn | ||
| Line 155: | Line 207: | ||
</syntaxhighlight> | </syntaxhighlight> | ||
| − | = setup on vital-it = | + | =setup on vital-it= |
| − | == ete3 == | + | ==ete3== |
work with the following variable exported: | work with the following variable exported: | ||
| − | <syntaxhighlight lang="Bash" line= | + | <syntaxhighlight lang="Bash" line="line"> |
export QT_QPA_PLATFORM=offscreen | export QT_QPA_PLATFORM=offscreen | ||
</syntaxhighlight> | </syntaxhighlight> | ||
Revision as of 16:25, 11 April 2019
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'
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