Step #1 prerequists

  • Python: the supported versions are 3.2 or higher.
  • Cherrypy: A Minimalist Python Web Framework (python module).
  • Makeflow: a workflow engine for executing large complex workflows on clusters, clouds, and grids. The supported version are v4.4.3 or higher.

Step #2 download the latest copy

The latest version can be downloaded from the download page.

Or clone repository 

[user@hostname:~] git clone git@forgemia.inra.fr:genotoul-bioinfo/jflow.git
.

Step #3 extract the archive

[user@hostname:~] tar xzvf jflow_vx.x.tar.gz
[user@hostname:~] cd jflow_vx.x

Step #4 configure the application

You must edit the application.properties file to configure the application. Here under the required parameters, for advanced configuration please see this page...

[global]
# uncomment and set if not in the PATH, should be version >= 4.4.3
#makeflow = /usr/bin/makeflow
# batch system type: local, condor, sge, moab, cluster, wq, hadoop, mpi-queue
batch_system_type = local
# add these options to all batch submit files
batch_options = 
# add these options to limit the number of jobs sumitted in parallel
limit_submission = 100
# on which socket host should run the web server
server_socket_host = 127.0.0.1
# on which socket port should run the web server
server_socket_port = 8080

[storage]
# where should be written the log file
log_file = /path/to/jflow.log
# Where should the pipelines write results, should be accessible 
# by all cluster nodes
work_directory = /path/to/work
# Where should the pipelines write temporary files, should be 
# accessible by all cluster nodes
tmp_directory = /path/to/tmp

[softwares]
# uncomment and set if not in the PATH
#blastall = /usr/bin/blastall
#formatdb = /usr/bin/formatdb
#sfffile = /usr/bin/sfffile
#fastqc = /usr/bin/fastqc
#runAssembly = /usr/bin/runAssembly
#bwa = /usr/bin/bwa
#samtools = /usr/bin/samtools

Step #5 test your installation

The application embed one website example, enter the following command lines to run the web server:

[user@hostname:~] python bin/jflow_server.py --daemon

And go on the example web page. You should have the following display with the alignment workflow available and no actives workflows.