How to write the configuration file

Configuration file types

There is a configuration file for each of the HCP tools commands.

#	command	location of configuration files	feature
1	hcp	~/.hcp/hcp.conf	copy files on the server
2	hrm	~/.hcp/hrm.conf	delete files on the server
3	hcp-ls	~/.hcp/hcp-ls.conf	list files on the server
4	hmkdir	~/.hcp/hmkdir.conf	create directories on the server
5	hpwd	~/.hcp/hpwd.conf	retrieve the working directory on the server
6	hmv	~/.hcp/hmv.conf	move files on the server
7	hln	~/.hcp/hln.conf	create file's links on the server
8	hchmod	~/.hcp/hchmod.conf	change the file's permission on the server
9	hchown	~/.hcp/hchown.conf	change the file's owner on the server
10	hsync	~/.hcp/hsync.conf	synchronize files on the server

There are many configuration files, so we recommend that you create a new configuration file named ~/.hcp/hcp-common.conf to describe common settings and include (read) from each configuration file. Add the following line at the top line of each of the above 10 configuration files such as ~/.hcp/hcp.conf. (The path must be written in absolute path.)

For Linux

Include /home/username/.hcp/hcp-common.conf

For Windows

Include C:\Users\username\_hcp\hcp-common.conf

An example of the common configuration file (~/.hcp/hcp-common.conf)

Normally write the contents of hcp-common.conf as follows.

PrivateKeyFile /home/username/.ssh/id_rsa    # Specify the private key
AcceptableCryptMethod   PLAIN              　# Encryption: None
AcceptableDigestMethod  SHA256               # Digest format: SHA256
DisableDataIntegrityChecking yes             # Allow no digest format

(For Windows, you must specify C:\Users\username\.ssh\id_rsa for the pricate key.)

Specify the private key

HCP tools authenticates users using the public/private keys.

In this case, you can use the public/private key files used for SSH login to the NIG supercomputer as the public/private keys. If you use them, make sure that the private key file (id_rsa) addresses under the user directory in the client computer (C:\Users\username\.ssh for Windows). (When you follow how to set up the public key for SSH, the private key file should already be here.)

Encryption

It is not necessary to encrypt by HCPtools because the personal genome analysis division is used SSL-VPN connection. Therefore, normally there is no problem when you create the file with the following content and set it up as ~/.hcp/hcp-hcp-common.conf.

Digest format

This is the setting for check that datas are not corrupted or tampered in file transfers. Normally, enable this setting. When you check the integrity of files, add the -y option.

Example

hcp --user username --hpfp -y  \
    gwa.ddbj.nig.ac.jp:/home/your_account-pg/some_directory/your_file.txt \
    C:\Users\username\your_file.txt