sanger-pathogens / Artemis

Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation
http://sanger-pathogens.github.io/Artemis
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running act -help returns non-zero exit code #296

Closed Darkless012 closed 4 years ago

Darkless012 commented 4 years ago

running act -help will print the help, but return 1 as a return code.

It should return 0

$ act -help; echo $?
SYNOPSIS
       Artemis Comparison Tool (ACT): Genome Comparison Tool
USAGE
        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

HOMEPAGE
        http://www.sanger.ac.uk/science/tools/artemis-comparison-tool-act

1
tseemann commented 4 years ago

MEMORIES! I wrote that -h output because I kept having to look it up in the manual. But the exit code stuff was already there :)