bin scripts should call python instead of pytom - requires GPU environment fix

[McHaillet]

All bin scripts now start with: #!/usr/bin/env pytom

After the latest updates this can be changed to: #!/usr/bin/env python

[sroet]

reopened as the PR got reverted in SBC-Utrecht/PyTomPrivate#144 , We need to also set the GPU env variables properly to be able to change these defaults