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Strange .bashrc Problem

I am running Debian Stretch on my 64-bit Linux platform. I have just installed the molecular docking program HEX. The installation program added the line shown below to .bash_profile:

#  Lines added by 'hex_setup.bin' for Hex 8.0.0

export HEX_ROOT=/home/comp/Apps/Hex
export HEX_VERSION=8.0.0
export PATH=${PATH}:${HEX_ROOT}/bin

export HEX_CACHE=/home/comp/Apps/Hex/hex_cache

Whie the additional lines are necessary for the execution of HEX they seem to have wiped oour all of the alias entries I have in .bashrc. Rebooting the system does not eliminate the problem! Bu bumbling about I discovered the it is necessary to source .bashrc inorder to recticate the alias lines in .bashrc (note: commenting out the added lines in .bash_profile did not solve the problem).

What's going on what is the fix?

Thanks in advance.

Stephen P. Molnar, Ph.D.
(614)312-7528 (c)
Skype: smolnar1