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Overview
opencga.sh is the officially recommended command line tool for normal users and are encouraged to use this. It implements all most of the functionality in more than 100 commandwith many different commands and subcommands. As per OpenCGA design, these These commands are a 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 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://bioinfointbioinfo.hpc.cam.ac.uk/opencga-1.3.0-devdemo/webservices/rest/v1/samples/search
so the corresponding command in commandLine the command line is :
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./opencga.sh samples |
and search is the endpoint so corresponding subCommand subcommand is :
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./opencga.sh samples search |
User can look at all avaiable commands by simply running 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 families samples Family Samples commands variables Variable set commandspanels cohorts Cohorts Panel commands samples tools ToolsSamples commands cohorts panels Cohorts Panels commands Analysis commands: alignments Implement several tools for the genomic alignment analysis variant Variant commands clinical Clinical analysis commands Operation commands: operations Operations commands |
List The list of subCommand sample subcommands can be retrieved by simply executing a the "samples" command without any other argument as show below:
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. | sh users'./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 |
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" ] } |
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 8: Date when the token will expire.
- Line 9: 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.
Table of Contents:
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