how to set up the environment variables on mac os x

Question

I am trying to download myrna tool on mac os x. for one of procedures on installation, "Set the MYRNA_HOME environment variable to point to the extracted directory (containing myrna_emr)"

So i tried this way

echo "export MYRNA_HOME=/.../....directory/.." >> ~/.bashrc

but it seems it does not work.(when i type echo MYRNA_HOME in command line, there is nothing OR when i type printenv MYRNA_HOME does not come out.)

anyone who knows how to set up Env Vars??

thank you,

Pablo Santa Cruz · Accepted Answer · 2011-07-21 19:01:01Z

1

There are several ways to do that. One would be adding your variable to ~/.bash_profile file.

Example:

MYRNA_HOME=/whatever/you/want/
export MYRNA_HOME

Then you can try if it works by logging in again and trying on a terminal:

$ echo $MYRNA_HOME

It should print whatever you set MRYNA_HOME to on ~/.bash_profile.

If you want the environment variable to be available to all users, you can change /etc/bashrc file. But I would prefer just changing one users' environment.

answered Jul 21, 2011 at 19:01

Pablo Santa Cruz

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5 Comments

nana Over a year ago

thanks plabo! it works- btw, Please see this as well. i already have R 2.13 but myrna seems it does not recognize where it is. so i need to set up env var again with MYRNA_RHOME of R directory. so it should be same way. right? but it does not work.

nana Over a year ago

Please see this:To run Myrna on a Hadoop cluster or local computer, R 2.10 and Bioconductor must be installed along with all packages required by Myrna. If you already have R v2.10, Bioconductor and all appropriate packages but Myrna can't find where they're installed, set the MYRNA_RHOME environment variable to point the appropriate R home directory, i.e., the directory containing bin/R and bin/Rscript executables for the proper installation.

nana Over a year ago

echo $MYRNA_RHOME /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/

nana Over a year ago

but, when i run myrna_local --test, an error message with, R: NOT INSTALLED fastq-dump: NOT INSTALLED FAILED install test -MacBook-Pro:~ $ I missed something now???

nana Over a year ago

pablo- it works as well. it was an issue of required packages in R. not for env var. Thank you so much for your help

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