act

act

TLDR

List the available actions

$ act -l
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Run the default event
$ act
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Run a specific event
$ act [event_type]
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Run a specific action
$ act -a [action_id]
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Do not actually run the actions (i.e. a dry run)
$ act -n
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Show verbose logs
$ act -v
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SYNOPSIS

act [options] SEQUENCE_1 COMPARISON_1_2 SEQUENCE_2 ...

OPTIONS

SEQUENCE An EMBL, GenBank, FASTA, or GFF3 file FEATURE An Artemis TAB file, or GFF file COMPARISON A BLAST comparison file in tabular format

-options FILE Read a text file of options from FILE -chado Connect to a Chado database (using PGHOST, PGPORT, PGDATABASE, PGUSER environment variables)

-Dblack_belt_mode=? Keep warning messages to a minimum [true,false] -DuserplotX=FILE[,FILE2] For sequence 'X' open one or more userplots -DloguserplotX=FILE[,FILE2] For sequence 'X' open one or more userplots, take log(data) -DbamX=FILE[,FILE2,...] For sequence 'X' open one or more BAM, CRAM, VCF, or BCF files -Dchado="h:p/d?u" Get ACT to open this CHADO database -Dread_only Open CHADO database read-only

EXAMPLES

% act % act af063097.embl af063097_v_b132222.crunch b132222.embl % act -Dblack_belt_mode=true -Dbam1=MAL_0h.bam -Dbam2=MAL_7h.bam,var.raw.new.bcf % act -Duserplot2=/pathToFile/userPlot

SEE ALSO

https://sanger-pathogens.github.io/Artemis/ACT/ art(1), dnaplotter(1)

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