Sourcetracker running error

[Michal]

Hi,

I'm trying to run sourcetracker with the following script:

R --slave --vanilla --args -i filtered_otu_table_2OTUs.txt -m USB.map.Day6.txt -o sourcetracker_out < $SOURCETRACKER_PATH/sourcetracker_for_qiime.r


I am getting the following error:

Error: Please add SOURCETRACKER_PATH environment variable pointing to the SourceTracker top-level directory (containing 'sourcetracker_for_qiime.r')
Execution halted


I believe I do have a SOURCETRACKER_PATH environmental variable as indicated.  I checked this by entering the following:

michal@biolinux-01: echo "$SOURCETRACKER_PATH"
/home/michal/Projects/Scripts/sourcetracker-0.9.5/

It is also in my $PATH.

What else could be going wrong?

Thanks very much for your help,

Michal

[Dan Knights]

Hi Michal,

I agree, it does look like you have the right environment variable set. Would you mind opening R (enter "R" and the command line), and then running this command? Then please send the output.

Sys.getenv('SOURCETRACKER_PATH')

Thanks,

Dan

[Michal Ziv-El]

Hi Dan,

Thanks for getting back to me on this.  Here is the output for Sys.getenv('SOURCETRACKER_PATH'):

[1] ""

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[Dan Knights]

For some reason R isn't seeing your environment variables. What happens when you run your command explicitly setting the env variable with this?

env SOURCETRACKER_PATH='/home/michal/Projects/Scripts/sourcetracker-0.9.5/' R --slave --vanilla --args -i filtered_otu_table_2OTUs.txt -m USB.map.Day6.txt -o sourcetracker_out < $SOURCETRACKER_PATH/sourcetracker_for_qiime.r

or for a simpler test, this?

echo "print(Sys.getenv('TESTVAR2')); q()" | env TESTVAR2='Hello world' R --no-save --vanilla

The second command should print "Hello world" (plus maybe some R startup output).

[Michal Ziv-El]

Hi Dan,

The 'Hello World' test worked right away.  For sourcetracker, the script you listed did not initially work.  Then I reset SOURCETRACKER as an environmental variable and reran what you listed, and this time it worked!

Is there some setting I should change so that I don't need to use this work-around?

Thanks,

Michal