Key Concepts
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Key Concepts |
Updated March 13, 2026 |
| Table 1. BIRCH
hierarchical directory structure (for simplicity, not all
directories are shown). |
/home/birch
admin |
The BIRCH home directory
BIRCH is organized as described in Table 1. In the example, BIRCH
is located in '/home/birch'. A sample of directories is shown. The
location of the BIRCH home directory is set in the environment
variables $BIRCH and $birch, which will be used throughout this
document. "$BIRCH" is generally used for readability in
documentation, while "$birch" is easier to type.
Local customizations are contained in a
separate directory, allowing easy upgrades.
The high-level organization of BIRCH is borrowed from Unix. All
Unix systems have standard system directories, and a directory
called /usr/local. /usr/local contains directories such as
/usr/local/bin/, usr/local/lib etc. Ideally, the system
administrator would add new programs only to /usr/local, and not
to other directories such as /bin or /lib, which can be thought of
as belonging to the operating system. Consequently, upgrades of
the operating system shouldn't affect anything in /usr/local/, and
changes to installed software shouldn't affect the operating
system.
Similarly, the high-level structure of BIRCH is mirrored in
$BIRCH/local. With very few exceptions, the local BIRCH
administration should never have to make changes in directories
other than $BIRCH/local. More importantly, programs and
documentation added $BIRCH/local are not clobbered when BIRCH is
upgraded to a new version.
| Table
2.
Summary of BIRCH directories |
|
| Directory |
Description |
| admin |
files and scripts related to BIRCH
administration |
| bin-os-hardware |
executable binaries, specific for a
particular operating system and hardware platform |
| dat |
ancillary datafiles used by programs.
BioLegato PCD menus are also found here |
| doc |
documentation |
| install-scripts |
working directory for initial installation
and updates of BIRCH system |
| java |
Java applications |
| lib-os-hardware | libraries, specific for a particular operating system and hardware platform |
| local |
locally-installed software, libraries,
documentation etc. |
| manl |
Unix-style manual pages for BIRCH software |
| pkg |
packages that need to be kept together in a
specific directory structure |
| public_html |
BIRCH Web pages |
| script |
(presumably) platform-independent scripts.
When possible, scripts are installed here, rather than being
duplicated several times in independent platform-specific
bin directories |
| tutorials |
BIRCH tutorials |
The BIRCH system administrator should
never have to make changes on individual user accounts
Note: BIRCH no longer has any code that
requires the C-shell (csh or tcsh). The C-shell is usually not
installed by default on Linux systems.
In order to use the programs and datafiles in BIRCH, environment
variables need to be set when a user logs in. Most importantly,
the directories containing executable files must be added to the
$PATH. As well, enviroment variables governing how different
programs work must also be set. The exact mechanism for how
these settings are made when a user logs in depends on their
default shell, as summarized in the table below:
| Family |
The BOURNE shell family |
The C-shell family |
| shell executable |
/bin/sh, /bin/ash, /bin/ksh, /bin/bash,
/bin/zsh |
/bin/csh, /bin/tcsh |
| files in $HOME directory |
.profile - executed at login and when
starting a new process |
.cshrc - executed at login and when starting
a new process .login -executed at login only |
For example, if a user's default shell is /bin/sh, then $HOME/.profile will be run at login time. Likewise, if a user's default shell is /bin/csh, then $HOME/.cshrc, followed by $HOME/.login, will be run at login.
To avoid the nightmare in which each user has to modify and
update these files themselves, it is imperative that settings be
centrally administered and automatically set for the user. To make
this work, a few changes must be made to each user's account. When
the user runs $BIRCH/admin/newuser, the following line is
copied from $BIRCH/local/admin/add_to_login to the user's
.login file:
source birch_home_dir/admin/login.source
Similarly, the following line is copied from $BIRCH/local/admin/add_to_cshrc to the user's .login file:
source birch_home_dir/admin/cshrc.source
Finally, the following line is copied from $BIRCH/local/admin/add_to_profile to the user's .profile, .bash_profile and .bash_login files:
. birch_home_dir/admin/profile.source
Thus, regardless of the user's default shell, the correct
environment variables will be set.
| Note: If you have root
access, it is possible to eliminate
the need for users to run the newuser script.
Simply add the contents of admin/add_to_cshrc, add_to_login
and add_to_profile, respectively, to the systemwide cshrc,
login and profile scripts. All users on the system will have
the complete set of BIRCH environment variables. This should
probably be done after you have gotten BIRCH installed and
working. |
ORDER OF EVENTS: The C-shell Family
(seldom installed on modern systems)
ORDER OF EVENTS: The Bourne Shell Family