How to Use Archaea Tools

If uploading or downloading large datasets to JGA via sftp takes too long, you can request setup of the high-speed transfer tool Archaea tools (formerly HCPtools). The tool will be setup for each account.

Unlike the NIG supercomputer, VPN connection is not required.

Installing the client software

Follow the instructions below to install the client software.

Linux

Configuration files

Place the configuration files in your home directory. You can obtain the files from GitHub.

Linux

cd $HOME
git clone https://github.com/nig-sc/Bytix_Archaea/ .hcp

After git clone, the following files will be created:

$ tree .hcp
.hcp
├── README.md
├── hchmod.conf
├── hchown.conf
├── hcp-common.conf
├── hcp-ls.conf
├── hcp.conf
├── hln.conf
├── hmkdir.conf
├── hmv.conf
├── hpwd.conf
├── hrm.conf
└── hsync.conf

Next, set the absolute path of your private key in the configuration file hcp-common.conf: hcp-common.conf

PrivateKeyFile /home/youraccount/.ssh/id_rsa # Absolute path to your private key
AcceptableCryptMethod   PLAIN                # Encryption: none
AcceptableDigestMethod  SHA256               # Digest method: SHA256
DisableDataIntegrityChecking yes             # Allow no digest

Connection test

After completing the configuration, perform a connection test using the command below. In this example, the account test07 is used. Make sure you have registered your public key with your DDBJ account in advance.

Run the following test command:

$ hcp-ls --user=test07 133.39.233.39

hcp-ls starts :
agd
jga

ExitCode : 0

If ExitCode : 0 appears, the connection is successful.

Downloading

Data you have applied for is located under the directory of the application ID:

133.39.233.39:jga/download/J-DU000024

Decryption tools are available in the following directory:

133.39.233.39:jga/download/J-DU000024/tools

Run the download command. Make sure there is enough free space on your local disk.

$ hcp --user=test07 <remote-directory-path> <local-directory-path>

Example:

$ hcp --user=test07 133.39.233.39:jga/download/J-DU000024 .

Uploading

Run the upload command:

$ hcp --user=test07 <local-directory-path> <remote-directory-path>

Example:

$ hcp --user=test07 files-to-be-uploaded 133.39.233.39:jga/upload/J-DS000014