As well as the listing file names on the command line, the following switches are available to UNIX users:
This option tells Artemis to suppress normal informational messages while running.
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.
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.
If this is set to false then warning messages are kept to a minimum.
This sets the base position that Artemis opens at, e.g. 10000.
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').
This is the same as the above userplot option except that the log transform of the data is plotted.
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.
The following will open BAM files in separate panels (using -Dbam[1,2,3...]):
art -Dbam1=fileA.bam -Dbam2=fileB.bam
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.
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.
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).
Hide/show forward frame lines.
Hide/show reverse frame lines.