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# `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:

### Navigation

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Ruffus v. 1.0.8
- Home |
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