I'm using a piece of software (QIIME) that uses its own subshell to run commands:
You no-longer type "macqiime" before QIIME commands! Instead, you just type "macqiime" once when you start a new terminal session. That will start a new subshell with the QIIME environment variables sourced.
Once you've done that, you can run all the qiime commands you want without the "macqiime" command.
I'm developing a bash script which automatically launches jobs and which should automatically run a script through the QIIME environment. I know how to do it manually from the command line (as detailed above); however I don't know how to do it automatically from the bash script.
Can someone help? Thanks!
you can find a solution to what I'm trying to do by reading the section "Advanced MacQIIME hacking"