UNIX Command Line Arguments for ACT

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

-quiet

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

-options

This option instructs ACT to read an extra file of options after reading the standard options. (See the section called The Options File in Chapter 5 for more about the ACT options file.)

For example -options ./new_options will instruct ACT 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 ACT 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').

-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.

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

This is used to get ACT 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.