https://github.com/evolbioinfo/booster-web
booster-web
https://github.com/evolbioinfo/booster-web
booster bootstrap golang phylogeny transfer webapp
Last synced: 2 months ago
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booster-web
- Host: GitHub
- URL: https://github.com/evolbioinfo/booster-web
- Owner: evolbioinfo
- License: gpl-2.0
- Created: 2017-02-13T16:30:57.000Z (over 9 years ago)
- Default Branch: master
- Last Pushed: 2023-04-19T12:18:24.000Z (about 3 years ago)
- Last Synced: 2026-01-28T17:44:48.007Z (5 months ago)
- Topics: booster, bootstrap, golang, phylogeny, transfer, webapp
- Language: Go
- Homepage: http://booster.c3bi.pasteur.fr
- Size: 4.51 MB
- Stars: 2
- Watchers: 3
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# BOOSTER-WEB: Web interface to [BOOSTER](http://booster.c3bi.pasteur.fr)
This interface presents informations about BOOSTER program, and allows to run BOOSTER easily.
# Installing BOOSTER-WEB
## Already compiled
Download a release in the [release](https://github.com/evolbioinfo/booster-web/releases) section. You can directly run the executable for your platform.
## From source
To compile BOOSTER-WEB, you must [download](https://golang.org/dl/) and [install](https://golang.org/doc/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](https://hub.docker.com/r/evolbioinfo/booster-web/).
* 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](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](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]"
* itol
* key = "[iTOL api key]"
* project = "[itol upload project]"
* 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"
[itol]
key = "xxxxxxxxxx"
project = "booster"
[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"
```