UNIX Command Line Arguments for Artemis

As well as the listing file names on the command line, the following switches are available to UNIX users:

-quiet

This option tells Artemis to suppress normal informational messages while running.

-options

This option instructs Artemis to read an extra file of options after reading the standard options. (See the section called The Options File in Chapter 6 for more about the Artemis options file.)

For example -options ./new_options will instruct Artemis to read new_options in the current directory as an options file.

-Xmsn -Xmxn

Use -Xmsn to specify the initial size, in bytes, of the memory allocation pool. This value must be a multiple of 1024 greater than 1MB. Append the letter k or K to indicate kilobytes, or m or M to indicate megabytes.

Use -Xmxn to specify the maximum size, in bytes, of the memory allocation pool. This value must a multiple of 1024 greater than 2MB. Append the letter k or K to indicate kilobytes, or m or M to indicate megabytes.

-Dblack_belt_mode=false

If this is set to false then warning messages are kept to a minimum.

-Doffset=10000

This sets the base position that Artemis opens at, e.g. 10000.

-Duserplot=pathToFile

This can be used to open userplots from the command line. The paths are comma separated to open multiple plots (-Duserplot='/pathToFile/userPlot1,/pathToFile/userPlot2').

-Dloguserplot=pathToFile

This is the same as the above userplot option except that the log transform of the data is plotted.

-Dbam=pathToFile

This can be used to open BAM files and/or VCF/BCF files (see the section called Read BAM / VCF ... in Chapter 3 for more about the using these file types). This can take a path name to a file or an HTTP address.

-Dbam1=pathToFile1 -Dbam2=pathToFile2

The following will open BAM files in separate panels (using -Dbam[1,2,3...]):

art -Dbam1=fileA.bam -Dbam2=fileB.bam

-DbamClone=n

Multiple BAM panels can be opened using the bamClone flag this is used with the -Dbam flag:

art -Dbam='/pathToFile/file1.bam,/pathToFile/file2.bam' -DbamClone=n

(where n is an integer greater than 1). All BAM files are then shown in each panel.

-Dchado="hostname:port/database?username"

This is used to get Artemis to look for the database. The address of the database (hostname, port and name) can be conveniently included (e.g. -Dchado="genedb-db.sanger.ac.uk:5432/snapshot?genedb_ro") and these details are then the default database address in the popup login window.

-Dread_only

For a read only chado connection -Dread_only is specified on the command line (e.g. art -Dchado="genedb-db.sanger.ac.uk:5432/snapshot?genedb_ro" -Dread_only).

-Dshow_forward_lines=false

Hide/show forward frame lines.

-Dshow_reverse_lines=false

Hide/show reverse frame lines.