This is mercury's .bashrc, which is universal in the sense that it sources and adds to the PATH scripts that are farm, host or user specific (in increasing order of precedence):

• Farm-based scripts go in farm/${FARM};
• Host-based scripts go in host/${HOSTNAME};
• User-based scripts go in user/${USERNAME}.

Within these directories there should be an rc directory and a bin directory. The latter will be prepended to the PATH, the former will be iterated through and each script therein will be sourced in numerical order. A profile file may also be placed in these directories, which will be sourced in interactive environments.

The bashrc and profile files in the root of this repository must be symlinked to ~/.bashrc and ~/.profile (or ~/.bash_profile), respectively. Be wary of any process that magically updates the .bashrc on your behalf (e.g., Conda); such changes should not be committed.

Note If you sudo as mercury, then your user scripts will be sourced automatically. However, if you log in directly as mercury (i.e., without sudo'ing), then your user scripts won't be sourced. This can be done manually by running hgi-user ${USERNAME}, or by sending the LC_HGI_USER environment variable in your SSH session:

ssh -o SendEnv=LC_HGI_USER mercury@some_host

The following environment variables will be available upon completion:

• HGI_RC is the directory in which the Universal .bashrc resides;
• HGI_USER is the user from which you sudo'd or set via LC_HGI_USER, if applicable (NONE, otherwise);
• HGI_FARM is the LSF farm you are currently using, if applicable (NONE, otherwise).

In the normal mercury Bash environment, on farm5 machines, the following restrictions are made:

• set -o noclobber will prevent redirecting output into a file that already exists.
• rm will be completely disabled and instead show an error message.
• The --remove-files option to tar will be stripped out and a warning message will be shown.
• The -delete and -exec rm options to find will be forbidden and instead show an error message.
• An rm argument to xargs will be forbidden and instead show an error message.

An "armed environment" is available using the arm command. This environment is intended only for performing data management tasks and should not be for general use; upon entering, the user will be told as such in no uncertain terms. The entire session will be logged to disk.

The armed environment will lift the following restrictions from above:

• rm will now be active and will automatically set the -I and -v flags, for interactive deletion (when deleting more than 3 files) and verbosity, respectively.

The armed environment will impose additional restrictions and safeguards:

• The environment will refuse to work if the user who logged in as mercury cannot be established.
• The environment will refuse to work outside the hours of 9am to 4pm (this can be overridden with the --yes-i-know-its-late option).
• The prompt will show the full path of the current working directory.
• set -f will prevent glob expansion.
• set -u will raise an error on undeclared variables.
• set -B will prevent brace expansion.

Note While the above safety measures can be circumvented relatively easily, this setup is designed to be seamless enough that doing so would be more trouble than it's worth. The armed environment is imposed on mercury users as a matter of policy.