biostar-shell.in

#!/bin/sh -e

ucsc_bin=%%PREFIX%%/userapps/bin
emboss_bin=%%PREFIX%%/emboss/bin
cat << EOM

Adding $ucsc_bin and $emboss_bin to \$PATH.

UCSC kent utils and emboss contain commands that conflict with other tools,
including at least "calc", "mktime", and "stringify".

The other commands with these names may serve entirely different functions
and will not be accessible while running this shell unless you refer to them
by their absolute path name (e.g. /usr/local/bin/calc), which is not portable,
BTW, so don't hard-code such paths into your scripts.

Type "exit" or "Ctrl+D" to return to your normal shell.

EOM

export PATH=${ucsc_bin}:${emboss_bin}:$PATH

# FIXME: Update shell prompts to include (ucsc-kent)?

# Invoke the user's chosen shell
if echo $SHELL | egrep -q '/t?csh'; then
    args='-f'
fi
exec $SHELL $args