gocommands

Gocommands

iRODS Command-line Tools written in Go

Installation

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 Intel):

GOCMD_VER=$(curl -L -s https://raw.githubusercontent.com/cyverse/gocommands/main/VERSION.txt); \
curl -L -s https://github.com/cyverse/gocommands/releases/download/${GOCMD_VER}/gocmd-${GOCMD_VER}-darwin-amd64.tar.gz | tar zxvf -

For Darwin-arm64 (Mac OS M1/M2):

GOCMD_VER=$(curl -L -s https://raw.githubusercontent.com/cyverse/gocommands/main/VERSION.txt); \
curl -L -s https://github.com/cyverse/gocommands/releases/download/${GOCMD_VER}/gocmd-${GOCMD_VER}-darwin-arm64.tar.gz | tar zxvf -

For Linux-amd64:

GOCMD_VER=$(curl -L -s https://raw.githubusercontent.com/cyverse/gocommands/main/VERSION.txt); \
curl -L -s https://github.com/cyverse/gocommands/releases/download/${GOCMD_VER}/gocmd-${GOCMD_VER}-linux-amd64.tar.gz | tar zxvf -

For Linux-arm64:

GOCMD_VER=$(curl -L -s https://raw.githubusercontent.com/cyverse/gocommands/main/VERSION.txt); \
curl -L -s https://github.com/cyverse/gocommands/releases/download/${GOCMD_VER}/gocmd-${GOCMD_VER}-linux-arm64.tar.gz | tar zxvf -

For Windows-amd64 (using windows Cmd):

curl -L -s -o gocmdv.txt https://raw.githubusercontent.com/cyverse/gocommands/main/VERSION.txt && set /p GOCMD_VER=<gocmdv.txt
curl -L -s -o gocmd.zip https://github.com/cyverse/gocommands/releases/download/%GOCMD_VER%/gocmd-%GOCMD_VER%-windows-amd64.zip && tar zxvf gocmd.zip && del gocmd.zip gocmdv.txt

For Windows-amd64 (using windows PowerShell):

curl -o gocmdv.txt https://raw.githubusercontent.com/cyverse/gocommands/main/VERSION.txt ; $env:GOCMD_VER = (Get-Content gocmdv.txt)
curl -o gocmd.zip https://github.com/cyverse/gocommands/releases/download/$env:GOCMD_VER/gocmd-$env:GOCMD_VER-windows-amd64.zip ; tar zxvf gocmd.zip ; del gocmd.zip ; del gocmdv.txt

Install via Conda (Conda-forge)

Gocommands can be installed via conda if you are using Linux or Mac OS. Unfortunately, Windows system is not yet supported. Please follow instructions below to install.

Add conda-forge channel to conda. This is required because Gocommands is added to conda-forge channel.

conda config --add channels conda-forge
conda config --set channel_priority strict

Install Gocommands with conda.

conda install gocommands

Configuration

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 (YAML)

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. Environmental variables have the highest priority, so configuration values will be overwritten if environmental variables are set.

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.

gocmd 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.

Encryption

Gocommands provides file encryption feature to store cofidential data on iRODS. The encryption encrypts filename and content with a strong encryption algorithm (AES256-CTL) before uploading files to iRODS. Also, it can decrypts filename and content after downloading enrypted files from iRODS. By default, Gocommands uses RSA + AES256-CTL algorithm for encryption with your SSH public key ($HOME/.ssh/id_rsa.pub) and private key ($HOME/.ssh/id_rsa).

put, get, and ls supports file encryption.

Uploading

To upload a file with encryption, use --encrypt flags.

gocmd put --encrypt file1.txt

To specify a SSH public key file, use --encrypt_pub_key flag.

gocmd put --encrypt --encrypt_pub_key id_rsa.pub file1.txt

After uploading the file, you will see that the file will have a new encrypted filename with .rsaaesctr.enc extension.

Downloading

To download an encrypted file, use --decrypt flag.

gocmd get --decrypt XXXXXXXXXXXXXXXXXXXXXXXXX.rsaaesctr.enc

To specify a SSH private key file, use --decrypt_priv_key flag.

gocmd get --decrypt --decrypt_priv_key id_rsa XXXXXXXXXXXXXXXXXXXXXXXXX.rsaaesctr.enc

Directory listing

When listing a directory, use --decrypt flag to display original filenames.

gocmd ls --decrypt dir1

To specify a SSH private key file, use --decrypt_priv_key flag.

gocmd ls --decrypt --decrypt_priv_key id_rsa my_encryption_key dir1

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.