opencga.sh 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 machine/cluster can execute these commands.
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
the corresponding command in commandLine is :
./opencga.sh samples |
and corresponding subCommand is :
./opencga.sh samples search |
Executing ./opencga.sh will return the list of all available commands with description of each as shown below:
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 argument as show below:
./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 ... |
As a first step to execute any command with opencga.sh, user must login. After successfull login, the corresponding JWT sesssion token will be stored on machine under
~/.opencga/session.json |
This makes easier for users to login only once and execute any number of commands till the session token is expired. Please note down, session expiration is set by OpenCGA server independently from client. Once token is expired, user have to login again and can perform desired operations as normal.
{ "userId" : "rjbik", "sessionId" : "eyJhbGciOiJIUzI1NiJ9.eyJzdWIiOiJyamJpayIsImF1ZCI6Ik9wZW5DR0EgdXNlcnMiLCJpYXQiOjE1MDkwMTU0ODgsImV4cCI6MTUwOTAxNzQ4OH0.n2vyq07UL_v7HHl0N-enyBEuy3Wy97b3ZKnA8ksLRIg", "login" : "2017-10-26T11:58:09.146", "logout" : "2017-11-22T14:58:10.097", "timestamp" : 1511362690608, "projectsAndStudies" : null } |
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