MeV's command line options are relatively simple. To use them, you must edit the MeV launch file (Windows: tmev.bat; *nix: tmev.sh; Mac: ; Webstart: mev.jnlp).
The options are:
-help
Print this help text and exit MeV.
-gaggle
If this flag is present, MeV will automatically try to
connect to the Gaggle boss on startup. It will start the boss if
one is not already started. This option requires an internet
connection.
-fileType TYPE
This flag specifies the type of datafile to be loaded.
Options are:
tdms Tab Delimited, Multiple Sample Files (TDMS) (*.*)
mev MeV Files (*.mev and *.ann)
tav TIGR ArrayViewer Files (*.tav)
affy-gcos Affymetrix GCOS(using MAS5) Files
dchip dChip/DFCI_Core Format Files
gw-affy GW Affymetrix Files
bioconductor-mas5 Bioconductor(using MAS5) Files
rma RMA Files
cgh CGH Tab Delimited, Multiple Sample
affy-gp GEO SOFT Affymetrix Format Files
two-channel-gpl GEO SOFT Two Channel Format Files
genepix GenePix Format Files
agilent Agilent Files
geo-series-matrix GEO Series Matrix Files
geo-gds GEO GDS Format Files
-fileUrl URL
The URL of the data file to be preloaded. This must be a complete
url, including the http:// or ftp:// protocol indicators. Relative
urls are not supported. Local filesystem files are also not
supported at this time.
-firstRow
The index of the first row of expression data (rather than annotation) in a TDMS-like file.
If both this and the firstColumn flag are set, MeV can load TDMS-like datafiles
without interaction from the user. This number is zero-indexed.
-firstColumn
The index of the first column of expression data (rather than annotation) in a TDMS-like file.
If both this and the firstRow flag are set, MeV can load TDMS-like datafiles
without interaction from the user. This number is zero-indexed.
-arrayType
This value specifies the name of the array that the data in -fileUrl came from. The
string must exactly match one of the list of currently-supported arrays, found at
ftp://occams.dfci.harvard.edu/pub/bio/tgi/data/Resourcerer/kingdom_speci....
The species name is not required.