BIRCH - Uninstalling

Deletion using UNINSTALL-birch.sh

This procedure deletes the following directories in the current BIRCH installation:

admin
bin-solaris-sparc, bin-solaris-amd64, bin-linux-intel (optional)
dat
doc
java
manl
ncbi
pkg
public_html
script

Note that you will be prompted with the choice of retaining the bin directories. If you are uninstalling BIRCH prior to installing a new BIRCH framework, you should check the download web site to see if the binaries are also new. If the binaries haven't changed, you can avoid having to download and reinstall the binaries again by choosing not to delete them.

cd $BIRCH/install-birch

We deliberately make it hard to run this script, to prevent unpleasant accidents. So, what we need to do first is to change the permissions to make it executable:

chmod u+x UNINSTALL-birch.sh

Finally, run the script:

./UNINSTALL-birch.sh

The names of directories will be echoed as they are deleted.

To permanently delete BIRCH

If you are uninstalling BIRCH to upgrade to a new version, ignore this section!

If you are permantly deleting BIRCH, and have no plans to make it available to the user community, follow the steps below.

When they ran the 'newuser' script, all BIRCH users caused source lines to be added to their .cshrc, .login, .profile, .bash_login and .bash_profile files, which read commands from files in $BIRCH/admin. These source lines are embedded in an if statement that checks for the presence of the corresponding source files in $BIRCH/admin, and tries to execute them only if they are present. For example, the following lines were added by 'newuser' to the user's .cshrc file:

##################################################     #_BIRCH
# cshrc.source is a file that contains setup commands  #_BIRCH
# for BIRCH users. The source command                  #_BIRCH
# causes it to be read and executed each time a new    #_BIRCH
# c-shell is initiated.                                #_BIRCH
##################################################     #_BIRCH
if (-e /home/psgendb/admin/cshrc.source) then          #_BIRCH
   source /home/psgendb/admin/cshrc.source             #_BIRCH
endif

Therefore, if BIRCH is uninstalled, no error message will be generated at login or when opening a new shell. However, these source lines are now dead code. They have no effect, but clutter up the .cshrc file.

The best compromise is to uninstall BIRCH, but leave in place a script called cshrc.source or profile.source so that, the next time the user logs in, cshrc.source or profile.source will delete these lines. A dummy admin directory already exists in $BIRCH/admin.uninstall. This directory contains cshrc.source and profile.source files that grep through .cshrc, .login etc. and delete any line containing '#_BIRCH'. Simply rename this directory to 'admin' and users' accounts will be changed as they login.

cd $BIRCH
mv admin.uninstall admin

Deletion using UNINSTALL-birch.sh

To permanently delete BIRCH

Please send suggestions of comments regarding this page to psgendb@cc.umanitoba.ca