Fixing errors

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2952 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
updated rst files and change otu_table.txt to otu_table.biom whenever necessary



git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2953 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
updated otu_table.txt to otu_table.biom



git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2954 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
added new scripts to docs



git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2955 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
added new script to docs



git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2956 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
updated example file and file formats reference to biom-format



git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2957 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
update tutorial commands to point to otu_table.biom



git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2958 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
updated the scripts and rst files to resolve sphinx errors building documentation.



git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2959 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
Removed references to QIIME implenetation of OTUPipe per the demands of Robert Edgar.  Now referred to as usearch_qf.  Also changed function names that were called otu_pipe.

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2960 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
added note on using StarCluster and the IPython notebook. This closes ticket #185.


git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2961 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
Made slight modification to split_libraries.py to handle changes from check_id_map.py

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2962 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
Added new code and qiime_config value to support running parallel jobs on StarCluster Sun GridEngine systems.


git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2963 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
updated to allow cluster_jobs_fp to be just a filename (e.g., if it's in $PATH).


git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2964 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
added more information about how to configure parallel jobs in StarCluster instances.


git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2965 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
updated StarCluster documentation. 


git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2966 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
Added missing import statement.

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2967 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
Added section regarding reverse primer removal to the main QIIME tutorial.

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2968 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
Modified qiime install guide to point to Greengenes 4 feb 2011 rather than Oct 2010

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2969 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
Added new tutorial to accompany compare_categories.py. Updated two new scripts to point users to the respective tutorials for more help.

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2970 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a