The latest version can be downloaded from the download page.
Or clone repository
[user@hostname:~] git clone email@example.com:genotoul-bioinfo/jflow.git
[user@hostname:~] tar xzvf jflow_vx.x.tar.gz [user@hostname:~] cd jflow_vx.x
You must edit the
application.properties file to configure the application.
Here under the required parameters, for advanced configuration please see
[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
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.