updated seconds_to_sleep to more reasonable value - 60 seconds might as well be a decade.


git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3021 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
fixed bug in testing of usearch version number.


git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3022 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
rolling back a change in start_parallel_jobs.py that introduced a bug.


git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3023 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
modified code to properly cleanup tmp files



git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3024 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
make denoiser haskell files compatible with ghc 7.4.1, which is in the ubuntu for the VB



git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3025 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
updated to point to the new tutorial files on thebeast



git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3026 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
updated documentation



git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3027 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
updated the use of filename concatenation to use join



git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3028 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
fixed issue with how the sort parameters are handled - this revert commit 2905. also added an error message that causes the code to fail if user passes -B/--user_sort alone as this caused some confusion (sf bug#3492189). the -D/-B parameters work as follows:

pick_otus.py default behavior: qiime sorts sequences by abundance before calling uclust so most abundant sequences are most likely to be cluster centroids. uclust's sorting is suppressed.  
-D : suppresses qiime's presort by abundance and enables uclust's built-in sorting
-DB : suppresses uclust's built-in sorting (i.e., uclust --user_sort) and suppresses qiime's presorting by abundance to allow the user to presort data however they see fit
-B : not allowed, and now raises an error. this would mimic the default behavior, so has led to confusion in the past. 



git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3029 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
updated rtax version number.


git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3030 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
updated changelog.


git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3031 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
updates to version numbers, etc.


git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3032 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
updated __version__ and __status__ strings.


git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3033 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
updated documentation



git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3034 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
fixinf $HOME/qiime_software/

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3035 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
updated a python2.6 link to python2.7



git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3036 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
updated rst files to point to a generic filepath instead of my home-dir



git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3038 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
updated AMI id.


git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3039 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
minor edits.


git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3040 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
fixed bad checkin of this code. looks like the previous version commit accidentally included changes to this file.


git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3041 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a