ChlamDB - Revision history

Tpillone: /* setup X server pour ete3 */

2020-03-10T17:48:11Z

setup X server pour ete3

Tpillone at 22:50, 26 June 2019

2019-06-26T22:50:30Z

Tpillone: /* Update */

2019-04-11T16:26:49Z

Update

Tpillone at 16:26, 11 April 2019

2019-04-11T16:26:29Z

Tpillone at 16:25, 11 April 2019

2019-04-11T16:25:59Z

Tpillone at 16:25, 11 April 2019

2019-04-11T16:25:19Z

Tpillone at 11:13, 6 March 2019

2019-03-06T11:13:35Z

Tpillone at 09:32, 14 November 2018

2018-11-14T09:32:15Z

Tpillone: /* Conda */

2018-11-06T17:23:59Z

Conda

Show changes

Tpillone at 14:58, 1 November 2018

2018-11-01T14:58:52Z

@@ Line 17: / Line 17: @@
 [[new setup]]
-=== Update ===
+===Update===
 - avril 2019
 {| class="wikitable sortable"
@@ Line 45: / Line 45: @@
 |0
 |-
 |'''Kiritimatiellaeota'''
 |13
 |7
@@ Line 57: / Line 57: @@
 |1
 |-
 |'''Verrucomicrobia'''
 |930
 |555
@@ Line 151: / Line 151: @@
 </syntaxhighlight>
 ==setup https==

← Older revision		Revision as of 22:50, 26 June 2019
Line 205:		Line 205:

	</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=

@@ Line 51: / Line 51: @@
 |1
 |-
-|<big>'''Lentisphaerae'''</big>
+|'''Lentisphaerae'''
 |62
 |29
@@ Line 69: / Line 69: @@
 |'''221'''
 |}
 ===Setup environnement fonctionnel===

@@ Line 27: / Line 27: @@
 !N complete genomes
 |-
-!'''Planctomycetes'''
+|'''Planctomycetes'''
 |600
 |423

@@ Line 45: / Line 45: @@
 |0
 |-
-|'''Kiritimatiellaeota '''
+|'''Kiritimatiellaeota'''
 |13
 |7

@@ Line 1: / Line 1: @@
 ===Setup chlamdb===
 [[old setup]]
 [[new setup]]
-=== Setup environnement fonctionnel ===
+===Setup environnement fonctionnel===
-==== Conda ====
+====Conda====
   name: chlamdb
@@ Line 64: / Line 116: @@
      - django-citations
-==== packages R absents de conda à installer à la main ====
+====packages R absents de conda à installer à la main====
 - genoPlotR
 - flextable
-==== modules python a ajouter à la main ====
+====modules python a ajouter à la main====
-<syntaxhighlight lang="Bash" line='line'>
+<syntaxhighlight lang="Bash" line="line">
 conda develop /home/ubuntu/dev/orthomcl/
 conda develop /home/ubuntu/dev/plots/
@@ Line 79: / Line 131: @@
 conda develop /home/ubuntu/dev/network_d3/
 </syntaxhighlight>
-==== setup X server pour ete3 ====
+====setup X server pour ete3====
-<syntaxhighlight lang="Bash" line='line'>
+<syntaxhighlight lang="Bash" line="line">
 apt-get install  xserver-xorg xdm  xfonts-base xfonts-100dpi xfonts-75dpi
 </syntaxhighlight>
-<syntaxhighlight lang="Bash" line='line'>
+<syntaxhighlight lang="Bash" line="line">
 In our example, edit the /etc/X11/xdm/xdm-config file and set following values:
@@ Line 92: / Line 144: @@
 </syntaxhighlight>
-<syntaxhighlight lang="Bash" line='line'>
+<syntaxhighlight lang="Bash" line="line">
 /etc/init.d/xdm restart
 </syntaxhighlight>
-<syntaxhighlight lang="Bash" line='line'>
+<syntaxhighlight lang="Bash" line="line">
 export DISPLAY=':0'
 </syntaxhighlight>
-== setup https ==
+==setup https==
-=== setup certificate and key with letsencrypt ===
+===setup certificate and key with letsencrypt===
-<syntaxhighlight lang="Bash" line='line'>
+<syntaxhighlight lang="Bash" line="line">
 systemctl stop nginx
 letsencrypt certonly
@@ Line 112: / Line 164: @@
-===  update config ===
+===update config===
-<syntaxhighlight lang="Bash" line='line'>
+<syntaxhighlight lang="Bash" line="line">
 upstream monsite {
      # Adresse du serveur wsgi, par exemple gunicorn
@@ Line 155: / Line 207: @@
 </syntaxhighlight>
-= setup on vital-it =
+=setup on vital-it=
-== ete3 ==
+==ete3==
 work with the following variable exported:
-<syntaxhighlight lang="Bash" line='line'>
+<syntaxhighlight lang="Bash" line="line">
 export QT_QPA_PLATFORM=offscreen
 </syntaxhighlight>

← Older revision		Revision as of 11:13, 6 March 2019
Line 69:		Line 69:
	- flextable		- flextable

		+	==== modules python a ajouter à la main ====
		+	<syntaxhighlight lang="Bash" line='line'>
		+	conda develop /home/ubuntu/dev/orthomcl/
		+	conda develop /home/ubuntu/dev/plots/
		+	conda develop /home/ubuntu/dev/biosqldb/
		+	conda develop /home/ubuntu/dev/utilitaires/
		+	conda develop /home/ubuntu/dev/phylo_tree_display/
		+	conda develop /home/ubuntu/dev/TPutils/
		+	conda develop /home/ubuntu/dev/network_d3/
		+	</syntaxhighlight>
	==== setup X server pour ete3 ====		==== setup X server pour ete3 ====

← Older revision		Revision as of 09:32, 14 November 2018
Line 143:		Line 143:
	}		}

		+	</syntaxhighlight>
		+
		+	= setup on vital-it =
		+
		+	== ete3 ==
		+
		+	work with the following variable exported:
		+
		+
		+	<syntaxhighlight lang="Bash" line='line'>
		+	export QT_QPA_PLATFORM=offscreen
	</syntaxhighlight>		</syntaxhighlight>