Running Test Bathches:

1. Download TestReferences and TestFiles from XXX and put in same location as mothur executable
2. Download TestBatches and put in same location as mothur's executable
3. Download mothur's external programs: vsearch, uchime, prefetch and fasterq-dump. Available with mothur's executable versions
4. Run an individual batch test:

    sarahwestcott$ cd mothur_test_batches
    mothur_test_batches sarahwestcott$ ls
    TestBatches    TestReferences    fasterq-dump    prefetch    vsearch
    TestFiles      mothur        uchime
    mothur_test_batches sarahwestcott$ ./mothur "./TestBatches/align.seqs/batch"

    Output to screen will look like:

    mothur > set.dir(input=./TestFiles, output=./TestResults/align.seqs, tempdefault=./TestReferences)
    Mothur's directories:
    outputDir=/Users/sarahwestcott/Desktop/mothur_test_batches/align.seqs/
    inputDir=/Users/sarahwestcott/Desktop/mothur_test_batches/TestFiles/
    tempDefault=/Users/sarahwestcott/Desktop/mothur_test_batches/TestReferences/

    mothur > set.logfile(name=alignseqs.logfile)
    ...

5. Run all test batches:

    
    sarahwestcott$ cd mothur_test_batches
    mothur_test_batches sarahwestcott$ ls
    TestBatches    TestReferences    fasterq-dump    prefetch    vsearch
    TestFiles       mothur        uchime
    mothur_test_batches sarahwestcott$ ./mothur "./TestBatches/master_batch"

    Output to screen will look like:
    
    ...
    Batch Mode

    /*****************************************************************************/

    mothur > set.dir(input=./TestFiles, output=./TestResults/align.seqs, tempdefault=./TestReferences)
    Mothur's directories:
    outputDir=/Users/swestcott/Desktop/batchTest/TestResults/align.seqs/
    inputDir=/Users/swestcott/Desktop/batchTest/TestFiles/
    tempDefault=/Users/swestcott/Desktop/batchTest/TestReferences/

    mothur > set.logfile(name=alignseqs.logfile)

    Setting logfile name to /Users/swestcott/Desktop/batchTest/TestFiles/alignseqs.logfile
    ...
    
    

