Gocommands

iRODS Command-line Tools written in Go

Download pre-built binary

Please download binary file (bundled with tar or zip) at https://github.com/cyverse/gocommands/releases. Be sure to download a binary for your target system architecture.

For Darwin-amd64 (Mac OS):

curl -L -o gocmd.tar.gz https://github.com/cyverse/gocommands/releases/download/v0.6.4/gocmd-v0.6.4-darwin-amd64.tar.gz && \
tar zxvf gocmd.tar.gz && rm gocmd.tar.gz

For Linux-amd64:

curl -L -o gocmd.tar.gz https://github.com/cyverse/gocommands/releases/download/v0.6.4/gocmd-v0.6.4-linux-amd64.tar.gz && \
tar zxvf gocmd.tar.gz && rm gocmd.tar.gz

For Linux-arm64:

curl -L -o gocmd.tar.gz https://github.com/cyverse/gocommands/releases/download/v0.6.4/gocmd-v0.6.4-linux-arm64.tar.gz && \
tar zxvf gocmd.tar.gz && rm gocmd.tar.gz

How to use

Using the iCommands configuration

Gocommands understands the iCommands' configuration files, ~/.irods/irods_environment.json. To create iCommands' configuration file, run gocmd init to create the configuration file under ~/.irods.

gocmd init

If you already have iCommands' configuration files, you don't need any steps to do.

To check what configuration files you are loading

gocmd env

Run ls.

gocmd ls

Using an external configuration file

Gocommands can read configuration from an YAML file.

Create config.yaml file using an editor and type in followings.

irods_host: "data.cyverse.org"
irods_port: 1247
irods_user_name: "your username"
irods_zone_name: "iplant"
irods_user_password: "your password"

When you run Gocommands, provide the configuration file's path with -c flag.

gocmd -c config.yaml ls

Some of field values, such as irods_user_password can be omitted if you don't want to put it in clear text. Gocommands will ask you to type the missing field values in runtime.

Using environmental variables

Gocommands can read configuration from environmental variables.

Set environmental variables

export IRODS_HOST="data.cyverse.org"
export IRODS_PORT=1247
export IRODS_USER_NAME="your username"
export IRODS_ZONE_NAME="iplant"
export IRODS_USER_PASSWORD="your password"

Then run Gocommands with -e flag.

gocmd -e ls

Some of field values, such as IRODS_USER_PASSWORD can be omitted if you don't want to put it in clear text. Gocommands will ask you to type the missing field values in runtime.

Troubleshooting

Getting SYS_NOT_ALLOWED error

put, bput, or sync subcommands throw SYS_NOT_ALLOWED error if iRODS server does not support data replication. To disable data replication, use --no_replication flag.

License

Copyright (c) 2010-2023, The Arizona Board of Regents on behalf of The University of Arizona

All rights reserved.

Developed by: CyVerse as a collaboration between participants at BIO5 at The University of Arizona (the primary hosting institution), Cold Spring Harbor Laboratory, The University of Texas at Austin, and individual contributors. Find out more at http://www.cyverse.org/.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

• Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
• Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
• Neither the name of CyVerse, BIO5, The University of Arizona, Cold Spring Harbor Laboratory, The University of Texas at Austin, nor the names of other contributors may be used to endorse or promote products derived from this software without specific prior written permission.

Please check LICENSE file.