complicated_example – A more ambitious real-world example

See here for an overview and explanations for this code.

The code for this example is in the test subdirectory of the ruffus module:

ruffus/test/complicated_example.py

The data is at:

ruffus/test/data_for_complicated_example

Programme options:

--help, -h

show help message

To specify tasks:

--target_tasks TARGET_TASK, -t TARGET_TASK

Target task(s) of pipeline. TARGET_TASK can be

• split_unknown_gene_setdef
• split_per_species_gene_sets
• all_vs_all_comparisons
• combine_into_gene_familes
• split_gene_family_for_evolutionary_analysis
• evolution_analysis
• combine_evolution_analysis
• summarise_evolution_analysis
• summarise_all

For example:

complicated_example.py -t evolution_analysis -t summarise_all

--forced_tasks FORCED_TASK, -f FORCED_TASK

Pipeline task(s) which will be run even if they are up to date.

See above for a list of pipelined tasks

--jobs N, -j N

N specifies number of concurrent process running jobs in parallel

To specify paths:

--data_dir PATH, -d PATH

Directory with input data.

--working_dir PATH, -d PATH

Direction in which ruffus will run.

To print flowchart:

--dependency FILE, -d file

Print a dependency graph of the pipeline that would be executed to FILE, but do not execute it.

--dependency_graph_format FORMAT, -F FORMAT

Format of dependency graph file.

Can be:

* 'ps'
    (PostScript)

* 'svg'

* 'svgz'
    (Structured Vector Graphics),

* 'png'

* 'gif'
     (bitmap  graphics)

--just_print, -n

Print a description of the jobs that would be executed, but do not execute them.

Code: