view release on metacpan or  search on metacpan

README  view on Meta::CPAN

                    - thing: "other thing"
                process: |
                    cp $INPUT $OUTPUT
            - grep_VARA:
                local:
                    - OUTPUT: "{$self->outdir}/{$sample}.grep_VARA.csv"
                process: |
                    echo "Working on {$self->{indir}}/{$sample.csv}"
                    grep -i "VARA" {$self->indir}/{$sample}.csv >> {$self->outdir}/{$sample}.grep_VARA.csv \
                    || touch {$self->OUTPUT}
            - grep_VARB:
                local:
                    - OUTPUT: "{$self->outdir}/{$sample}.grep_VARA.grep_VARB.csv"
                process: |
                    grep -i "VARB" {$self->indir}/{$sample}.grep_VARA.csv >> {$self->outdir}/{$sample}.grep_VARA.grep_VARB.csv || touch {$self->OUTPUT}

  Notes on the drake.yml

    Drake will stop everything if you're job returns with an exit code of
    anything besides 0. For this reason we have the last command have a
    command1 || command2 syntax, so that even if we don't grep any "VARB"
    from the file the workflow could continue.

  Run it with default setup

        biox-workflow.pl --workflow workflow.yml > workflow.full.drake

  Output with default setup

    I don't want to inlcude the whole file, but you get the idea

        ;
        ; Generated at: 2015-06-21T11:01:24
        ; This file was generated with the following options
        ;   --workflow      drake.yml
        ;   --min   1
        ;
    
        ;
        ; Samples: test1, test2
        ;
        ;
        ; Starting Workflow
        ;
    
        ;
        ; Starting backup
        ;
    
    
        ;
        ; Variables
        ; Indir: /home/guests/jir2004/workflow
        ; Outdir: /home/guests/jir2004/workflow/output/backup
        ; Local Variables:
        ;   INPUT: {$self->indir}/{$sample}.csv
        ;   OUTPUT: {$self->outdir}/{$sample}.csv
        ;   thing: other thing
        ;
    
        /home/guests/jir2004/workflow/output/backup/$[SAMPLE].csv <- /home/guests/jir2004/workflow/$[SAMPLE].csv
            cp $INPUT $OUTPUT
    
    
        ;
        ; Ending backup
        ;
    
    
        ;
        ; Starting grep_VARA
        ;

    Run drake

        drake --workflow workflow.full.drake
    
        The following steps will be run, in order:
          1: /home/user/workflow/output/backup/test1.csv <- /home/user/workflow/test1.csv [timestamped]
          2: /home/user/workflow/output/backup/test2.csv <- /home/user/workflow/test2.csv [timestamped]
          3: /home/user/workflow/output/grep_vara/test1.grep_VARA.csv <- /home/user/workflow/output/backup/test1.csv [projected timestamped]
          4: /home/user/workflow/output/grep_vara/test2.grep_VARA.csv <- /home/user/workflow/output/backup/test2.csv [projected timestamped]
          5: /home/user/workflow/output/grep_varb/test1.grep_VARA.grep_VARB.csv <- /home/user/workflow/output/grep_vara/test1.grep_VARA.csv [projected timestamped]
          6: /home/user/workflow/output/grep_varb/test2.grep_VARA.grep_VARB.csv <- /home/user/workflow/output/grep_vara/test2.grep_VARA.csv [projected timestamped]
        Confirm? [y/n] y
        Running 6 steps with concurrence of 1...
    
        --- 0. Running (timestamped): /home/user/workflow/output/backup/test1.csv <- /home/user/workflow/test1.csv
        --- 0: /home/user/workflow/output/backup/test1.csv <- /home/user/workflow/test1.csv -> done in 0.02s
    
        --- 1. Running (timestamped): /home/user/workflow/output/backup/test2.csv <- /home/user/workflow/test2.csv
        --- 1: /home/user/workflow/output/backup/test2.csv <- /home/user/workflow/test2.csv -> done in 0.01s
    
        --- 2. Running (timestamped): /home/user/workflow/output/grep_vara/test1.grep_VARA.csv <- /home/user/workflow/output/backup/test1.csv
        Working on /home/user/workflow/output/backup/test1csv
        --- 2: /home/user/workflow/output/grep_vara/test1.grep_VARA.csv <- /home/user/workflow/output/backup/test1.csv -> done in 0.01s
    
        --- 3. Running (timestamped): /home/user/workflow/output/grep_vara/test2.grep_VARA.csv <- /home/user/workflow/output/backup/test2.csv
        Working on /home/user/workflow/output/backup/test2csv
        --- 3: /home/user/workflow/output/grep_vara/test2.grep_VARA.csv <- /home/user/workflow/output/backup/test2.csv -> done in 0.01s
    
        --- 4. Running (timestamped): /home/user/workflow/output/grep_varb/test1.grep_VARA.grep_VARB.csv <- /home/user/workflow/output/grep_vara/test1.grep_VARA.csv
        --- 4: /home/user/workflow/output/grep_varb/test1.grep_VARA.grep_VARB.csv <- /home/user/workflow/output/grep_vara/test1.grep_VARA.csv -> done in 0.01s
    
        --- 5. Running (timestamped): /home/user/workflow/output/grep_varb/test2.grep_VARA.grep_VARB.csv <- /home/user/workflow/output/grep_vara/test2.grep_VARA.csv
        --- 5: /home/user/workflow/output/grep_varb/test2.grep_VARA.grep_VARB.csv <- /home/user/workflow/output/grep_vara/test2.grep_VARA.csv -> done in 0.08s
        Done (6 steps run).

  Run in minified mode

    As an alternative you can run this with the --min option, which instead
    of printing out each workflow prints out only one, and creates a
    run-workflow.sh which has all of your environmental variables.

    This option is preferable if running on an HPC cluster with many nodes.

    This WILL break with use of --resample, either local or global. You
    need to split up your workflows as opposed to using the --resample
    option.

        biox-workflow.pl --workflow workflow.yml --min 1 > workflow.drake #This also creates the run-workflow.sh in the same directory