The QIIME tutorial contains two shell scripts that a user can run. The included custom_parameters.txt is pre-configured for the QIIME Virtual Box -- if you're running these scripts in a different environment, you'll need to modify two filepath parameters in custom_parameters.txt:

align_seqs:template_fp	/home/qiime/core_set_aligned.fasta.imputed
filter_alignment:lane_mask_fp	/home/qiime/lanemask_in_1s_and_0s

The paths should be changed to point to the greengenes core set alignment and lanemask on your system. As of April 2010, you can grab these files from these two links, respectively:

http://greengenes.lbl.gov/Download/Sequence_Data/Fasta_data_files/core_set_aligned.fasta.imputed
http://greengenes.lbl.gov/Download/Sequence_Data/lanemask_in_1s_and_0s


To use the shell scripts the user may need to make them executable by running one of the following commands:

chmod g+x ./qiime_tutorial_commands_serial.sh

or

chmod g+x ./qiime_tutorial_commands_parallel.sh


To run the shell scripts the user can use the following commands:

./qiime_tutorial_commands_serial.sh

or

./qiime_tutorial_commands_parallel.sh



