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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 :
http://bioinfoint.hpc.cam.ac.uk/opencga-1.3.0-dev/webservices/rest/v1/samples/search
so the corresponding command in commandline 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
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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 ............... |
Table of Contents:
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