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README.md

BOOSTER-WEB: Web interface to BOOSTER

build

This interface presents informations about BOOSTER program, and allows to run BOOSTER easily.

Installing BOOSTER-WEB

Already compiled

Download a release in the release section. You can directly run the executable for your platform.

From source

To compile BOOSTER-WEB, you must download and install Go (version >=1.9) on your system.

Then you just have to type :

go get github.com/evolbioinfo/booster-web/
go get -u github.com/golang/dep/cmd/dep

This will download BOOSTER-WEB sources from github, and its dependencies.

You can then build BOOSTER-WEB with:

cd $GOPATH/src/github.com/evolbioinfo/booster-web/
dep ensure
make

The booster-web executable should be located in the $GOPATH/bin folder.

From Docker

A docker image running a Galaxy server with all tools used by booster-web (PhyML-SMS, FastTree, Booster) and an already configured booster-web server is avalaible on docker hub.

  • Download and run already configured booster-web + galaxy servers:
docker run --privileged=true \
            -p 8080:80 -p 8000:8888 \
            -p 8 -p 8121:21 -p 8122:22 \
            evolbioinfo/booster-web:v0.1.8

Then visit http://localhost:8000 .

Running BOOSTER-WEB

Default configuration

You can directly run the booster-web executable without any configuration. It will setup a web server with the following default properties:

  • Run on localhost, port 8080
  • Log to stderr
  • In memory database (analyses will not persist after server shutdown)
  • Local processor (booster jobs will run on the local machine)
  • 1 parallel Runner: One job at a time
  • Job Timeout: unlimited
  • 1 thread per job

To access the web interface, just go to http://localhost:8080

Note that the local processor only allows to run booster from already inferred trees (no PhyML-SMS nor FastTree workflow). To also run tree inference workflows, see "Other configurations", or "Install from Docker".

Other configurations

It is possible to configure booster-web to run with specific options. To do so, create a configuration file booster-web.toml with the following sections:

  • general
    • maintenance = [true|false]
  • database
    • type = "[memory|mysql]"
    • user = "[mysql user]"
    • port = [mysql port]
    • host = "[mysql host]"
    • pass = "[mysql pass]"
    • dbname = "[mysql dbname]"
  • runners
    • type="[galaxy|local]"
    • queuesize=[size of job queue]
    • nbrunners=[number of parallel local runners]
    • jobthreads=[number of threads per local job]
    • timeout=[job timeout in seconds: 0=ulimited]
    • memlimit=[Max allowed Memory in Bytes]
    • keepold=[Number of days to keep results of old analyses]
  • galaxy (Only used if runners.type="galaxy")
    • key="[galaxy api key]"
    • url="[url of the galaxy server: http(s)://ip:port]"
  • galaxy.tools
    • booster="[Id of booster tool on the galaxy server]"
    • phyml="[Id of PHYML-SMS tool on the galaxy server]"
    • fasttree="[Id of FastTree tool on the galaxy server]"
  • notification (for notification when jobs are finished)
    • activated=[true|false]
    • smtp="[smtp serveur for sending email]"
    • port=[smtp port]
    • user="[smtp user]"
    • pass="[smtp password]"
    • resultpage = "[url to result pages]"
    • sender="[sender of the notification]"
  • logging
    • logfile= "[stderr|stdout|/path/to/logfile]"
  • http
    • port=[http server listening port]
  • authentication
    • user="[global username]"
    • password="[global password]"

And run booster web: booster-web --config booster-web.toml

Example of configuration file

[general]
# If booster-web is in maintenance mode or not
maintenance = false

[database]
# Type : memory|mysql (default memory)
type = "mysql"
user = "mysql_user"
port = 3306
host = "mysql_server"
pass = "mysql_pass"
dbname = "mysql_db_name"

[runners]
# galaxy|local if galaxy: required galaxykey & galaxyurl
type="galaxy"
# Maximum number of pending jobs (default : 10): for galaxy & local
queuesize = 200
# Number of parallel running jobs (default : 1): for local only
nbrunners  = 1
# Number of cpus per bootstrap job : for local only
jobthreads  = 10
# Timout for each job in seconds (default unlimited): for local only
#timeout  = 1000
# Memory limit in Bytes for each job (uses job memory estimation): for galaxy only
#memlimit  = 8000000000
# Keep old finished analyses for 10 days, default=0 (unlimited)
keepold = 10

#Only used if runners.type="galaxy"
[galaxy]
key="galaxy_api_key"
url="https://galaxy.server.com/"

[galaxy.tools]
# Id of booster tool on the galaxy server
booster="/.../booster/booster/version"
# Id of PhyML-SMS tool on the galaxy server
phyml="/.../phyml-sms/version"
# Id of FastTree tool on the galaxy server
fasttree="/.../fasttree/version"

# For notification when job is finished
[notification]
# true|false
activated=true
# smtp serveur for sending email
smtp="smtp.serveur.com"
# Port
port=587
# Smtp user 
user="smtp_user"
# Smtp password
pass="smtp_pass"
# booster-web server name:port/view page,
# used to give the right url in result email
resultpage = "http://url/view"
# sender of the notification
sender = "sender@server.com"

[logging]
# Log file : stdout|stderr|any file
logfile = "booster.log"

[http]
# HTTP server Listening port
port = 4000

# For running a private server, default: no authentication
#[authentication]
#user     = "user"
#password = "pass"