added a filepath to cleanup



git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2983 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
updated filepath to cleanup



git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2984 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
added a tear down function and added tmp file to teardown procedure



git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2985 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
updated how system call is being made. this may have been leading to some failures, and (as noted in a recent commit) we want all system calls in qiime to happen the same way anyway.


git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2986 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
removed uncessary import.


git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2987 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
Cleaned up some typos in log formatting for split_libraries.py, fixed logging output for median length filtering when no data was present

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2988 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
added required change - need the /tmp dir to be on the shared filesystem in the starcluster instance.


git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2989 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
added removal of 1 filepath from tmp



git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2990 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
added a defined stdout/stderr path, so it can be cleaned up by tests



git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2991 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
updated rst files



git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2992 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
added new script



git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2993 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
Modified example OTU table in 18S tutorial to specify how it can be constructed from the .biom format table and made some other minor changes

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2994 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
Made slight modification to the 'usearch_quality_filtering' tutorial, to show that it was modeled after OTUPipe

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2995 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
update documentation



git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2996 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
updated documentation



git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2997 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
Updated RTAX version to 0.98, which forces global rather than local alignment.  In real circumstances I wouldn't expect much difference in results, but the issue did affect the tests.

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2998 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
fixed version string.


git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@2999 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
fixed mothur tests to not care about order of OTUs. This is in preparation for upgrading the depenency version to get around a failure with 1.6.0 on the StarCluster EC2 instance.


git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3000 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
Don't assert a particular version of RTAX, since doing that is unnecessarily brittle

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3001 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
Clean up RTAX index files, regardless of which extension the local DBM implementation uses

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3002 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a