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JABAWS MANUAL
JABAWS Command Line Client Usage
-The command line client comes as a part of client package which you are welcome to download. The command line client can be used to align sequences using any of JABAWS supported web services. The client is OS independent and supports most of the functions which can be accessed programmatically via JABAWS API. Using this client you could align sequences using presets or custom parameters, please see examples of this below. Here is the list of options supported by the command line client.
-Usage: java -jar <path_to_jar_file> -h=host_and_context -s=serviceName ACTION [OPTIONS]+
+The command line client comes as a part of client package which you are welcome to download. +The command line client can be used to align sequences using any of JABAWS supported web services. The client is OS independent and supports most of +the functions which can be accessed programmatically via JABAWS API. Using this client you could align sequences +using presets or custom parameters, please see examples of this below. Here is the list of options supported by the command line client. +
+Usage:java -jar <path_to_jar_file> -h=host_and_context -s=serviceName ACTION [OPTIONS]
-h=<host_and_context> - a full URL to the JABAWS web server including context path e.g. http://10.31.10.159:8080/ws
-s=<ServiceName> - one of [MafftWS, MuscleWS, ClustalWS, ClustalOWS, TcoffeeWS, ProbconsWS, AAConWS, JronnWS, DisemblWS, GlobPlotWS, IUPredWS] - -
-ACTIONS:
+
+ACTIONS:
-i=<inputFile> - full path to fasta formatted sequence file, from which to align sequences
-parameters - lists parameters supported by web service
-presets - lists presets supported by web service
-limits - lists web services limits
Please note that if input file is specified other actions are ignored - -
- OPTIONS: (only for use with -i action):
+
+ OPTIONS: (only for use with -i action):
-r=<presetName> - name of the preset to use
-o=<outputFile> - full path to the file where to write an alignment
-f=<parameterInputFile> - the name of the file with the list of parameters to use.
@@ -92,7 +94,7 @@ Please note that -r and -f options cannot be used together. Alignment is done wi java -jar jabaws-min-client.jar -h=http://myhost.compbio.ac.uk:8080/jabaws -s=MafftWS -parameters
The same client can be used to access JABAWS on different hosts. Just point the client to the host you want to use by changing the value of -h key. For example you used -h=http://myhost.compbio.ac.uk:8080/jabaws server, now you want to use another server to -h=http://mylabserver.myuni.edu. This comes handy if your favorite server is off and you need to do the job yesterday.
Sasha Sherstnev, Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK
Sasha Sherstnev, Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK