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This is the officially recommended command line tool for normal users and are encouraged to use this. It implements all the functionality in more than 100 command and subcommands. As per OpenCGA design, these commands are one-to-one mapping of Resources from REST web services and subcommands are mapping to end-points. These commands underneath makes REST calls to carry out operations, thus any user who has access to REST cluster can execute these commands.
For example, in the following URL, samples is the resource and search is the endpoint:
http://bioinfoint.hpc.cam.ac.uk/opencga-1.3.0-dev/webservices/rest/v1/samples/search
so the corresponding command in commandLine is :
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./opencga.sh samples |
and search is the endpoint so corresponding subCommand is :
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./opencga.sh samples search |
User can look at all avaiable commands by simply running ./opencga.sh
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Catalog commands: users User commands projects Project commands studies Study commands files Files commands jobs Jobs commands individuals Individuals commands samples Samples commands variables Variable set commands cohorts Cohorts commands tools Tools commands panels Panels commands Analysis commands: alignments Implement several tools for the genomic alignment analysis variant Variant commands |
List of subCommand can be retrieved by simply executing a command without any other argument
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./opencga.sh samples
Usage: opencga.sh samples <subcommand> [options]
Subcommands:
create Create a sample
load Load samples from a pedigree file
info Get samples information
search Search samples
update Update sample
delete Delete the selected sample
group-by Group samples
individuals Get the individuals of a list of samples.
acl Return the acl of the resource
acl-update Update the permissions set for a member
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Table of Contents:
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