Overview
opencga.sh is the officially recommended command line tool for users. It implements most of the functionality with many different commands and subcommands. These commands are a one-to-one mapping of Resources from REST web services and subcommands are mapping to end-points. All the operations that can be performed using the command line internally creates one or several REST calls, so access to REST machine/cluster is required.
Correlation Between REST and CLI
In the following URL, "samples" is the resource and "search" is the endpoint:
http://bioinfo.hpc.cam.ac.uk/opencga-demo/webservices/rest/v1/samples/search
the corresponding command in the command line is :
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./opencga.sh samples |
and the corresponding subcommand is :
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./opencga.sh samples search |
Executing ./opencga.sh will return the list of all available commands with a description for each of them as shown below:
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Program: OpenCGA (OpenCB)
Version: 2.0.0-rc1
Git commit: 01cbe42598defa2ef5a192bad1f456166487aee4
Description: Big Data platform for processing and analysing NGS data
Usage: opencga.sh [-h|--help] [--version] <command> [options]
Catalog commands:
users User commands
projects Project commands
studies Study commands
files FilesFile commands
jobs Jobs commands
individuals IndividualsIndividual commands
samplesfamilies SamplesFamily commands
variables Variable set commandspanels cohorts Cohorts Panel commands
samples tools ToolsSamples commands
cohorts panels PanelsCohorts commands
Analysis commands:
alignments Implement several tools for the genomic alignment analysis
variant Variant commands
clinical Clinical analysis commands
Operation commands:
operations Operations commands
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The list of sample subcommands can be retrieved by simply executing the "samples" command without any argument as show below:
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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 a sample
group-by Group samples stats individualsSample stats
Get the individuals of a list of samples. acl Return the acl of the resource
acl-update Update the permissions set for a member
...
annotation-sets-update Update the value of some annotations
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CLI Session Management
Generally, unless we are pointing to a public OpenCGA installation, users will first need to log in using the "users login" command line. Once the user has successfully logged in, a session file will be generated in their home folder:
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~/.opencga/session.json |
This session file contains the following information:
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.
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{
"host" : "http://localhost:8080/opencga",
"version" : "v2",
"user" : "user1",
"token" : "eyJhbGciOiJIUzI1NiJ9.eyJzdWIiOiJ1c2VyMSIsImF1ZCI6Ik9wZW5DR0EgdXNlcnMiLCJpYXQiOjE1NzQxNTcyODIsImV4cCI6MTU3NDE2MDg4Mn0.aMvD28oR_W5ZjWXuVpBXBGVHOEby-lAl7pb8oxOSXxE",
"refreshToken" : "eyJhbGciOiJIUzI1NiJ9.eyJzdWIiOiJ1c2VyMSIsImF1ZCI6Ik9wZW5DR0EgdXNlcnMiLCJpYXQiOjE1NzQxNTcyODIsImV4cCI6MTU3NDE2MDg4Mn0.aMvD28oR_W5ZjWXuVpBXBGVHOEby-lAl7pb8oxOSXxE",
"login" : "20191119095437",
"expirationTime" : "20191119105436",
"studies" : [ "user1@default:study1", "user1@default:study2" ]
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where:
- Line 2: OpenCGA host against which the user has been authenticated.
- Line 3: API version of the OpenCGA host
- Line 4: Authenticated user.
- Line 5: Token generated when the user last logged in.
- Line 6: Token generated when the user last logged in to refresh token without the need to provide user credentials again.
- Line 7: Date when the user last logged in.
- Line 78: Date when the token will expire.
- Line 89: Studies that are accessible by the user
Authenticating is only necessary the first time. Users will have time to execute any other command line without the need to provide any more credentials until the stored token expires. Please note down that the token expiration time is set by the main OpenCGA installation. Once this token has expired, users will need to log back in again to keep working with the command line.