booster-web

README

BOOSTER-WEB: Web interface to BOOSTER

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/fredericlemoine/booster-web/

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

If you cloned the repository and want to install dependencies manually:

go get github.com/jteeuwen/go-bindata/...
go get github.com/elazarl/go-bindata-assetfs/...
go get github.com/dgrijalva/jwt-go
go get github.com/fredericlemoine/golaxy
go get github.com/fredericlemoine/gotree
go get github.com/go-sql-driver/mysql

You can then build BOOSTER-WEB with:

cd $GOPATH/src/github.com/fredericlemoine/booster-web/
make

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

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

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:

• 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

[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"