Merge pull request #1846 from gregcaporaso/quick-fix-party

QIIME 1.9.0-rc2
biocore · Jan 10, 2015 · f1802b7 · f1802b7
2 parents 7c2007b + 897c37d
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diff --git a/ChangeLog.md b/ChangeLog.md
diff --git a/doc/conf.py b/doc/conf.py
@@ -46,9 +46,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '1.9.0-rc1'
+version = '1.9.0-rc2'
 # The full version, including alpha/beta/rc tags.
-release = '1.9.0-rc1'
+release = '1.9.0-rc2'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/doc/install/install.rst b/doc/install/install.rst
@@ -149,6 +149,11 @@ If you plan to use SourceTracker with QIIME:
 
 * SourceTracker 0.9.5 (`src <http://downloads.sourceforge.net/project/sourcetracker/sourcetracker-0.9.5.tar.gz>`_) (license: GPL)
 
+For joining paired end reads, with ``join_paired_ends.py`` and ``multiple_join_paired_ends.py``:
+
+* ea-utils 1.1.2-537 (`web <https://code.google.com/p/ea-utils/>`_) (license: MIT)
+* SeqPrep v1.1 (`src <https://github.com/jstjohn/SeqPrep>`_) (license: MIT)
+
 For improved performance with large BIOM files, or if you're working with BIOM format 2.x files:
 
 * HDF5 (`web_hdf5 <http://www.hdfgroup.org/HDF5/>`_)

diff --git a/doc/tutorials/category_comparison.rst b/doc/tutorials/category_comparison.rst
@@ -12,7 +12,7 @@ This tutorial explains the use of several different mapping file category compar
 
 Input Files
 -----------
-You can obtain the files used in this tutorial `here <https://s3.amazonaws.com/s3-qiime_tutorial_files/keyboard.zip>`_. The files are taken from a study (Fierer et al., 2010) where samples were collected from the fingertips of three individuals and the keys of their keyboards. Researchers found that an individual's fingertip samples clustered very closely with his or her corresponding keyboard samples. These results have potential application in the field of forensic science. Throughout this tutorial, we will explore various ways of determining whether the clustering of fingertip and keyboard samples is statistically significant by analyzing the groups of samples.
+You can obtain the files used in this tutorial `here <ftp://ftp.microbio.me/qiime/tutorial_files/keyboard.zip>`_. The files are taken from a study (Fierer et al., 2010) where samples were collected from the fingertips of three individuals and the keys of their keyboards. Researchers found that an individual's fingertip samples clustered very closely with his or her corresponding keyboard samples. These results have potential application in the field of forensic science. Throughout this tutorial, we will explore various ways of determining whether the clustering of fingertip and keyboard samples is statistically significant by analyzing the groups of samples.
 
 Output Files
 ------------

diff --git a/doc/tutorials/creating_distance_comparison_plots.rst b/doc/tutorials/creating_distance_comparison_plots.rst
@@ -18,7 +18,7 @@ Input Files
 -----------
 The first part of this tutorial that details how to use `make_distance_boxplots.py <../scripts/make_distance_boxplots.html>`_ uses the dataset found in the `QIIME tutorial <./tutorial.html>`_. It assumes that you have already performed the beta diversity step to generate a distance matrix which will be used as input to these scripts. You can use any of the distance matrices that are generated by this step as input to these scripts. You will also use the mapping file for this dataset as input to the scripts. All commands assume you are within the top-level directory of the QIIME tutorial's data directory.
 
-The second part of this tutorial that details how to use `make_distance_comparison_plots.py <../scripts/make_distance_comparison_plots.html>`_ uses the dataset from a study that transplanted samples from one part of the body to another (Costello et al., 2009). The metadata mapping file can be found here: `download mapping file <https://s3.amazonaws.com/s3-qiime_tutorial_files/costello_whole_body/costello_timeseries_map.txt>`_ and the unweighted UniFrac distance matrix can be found here: `download distance matrix <https://s3.amazonaws.com/s3-qiime_tutorial_files/costello_whole_body/forearm_only_unweighted_unifrac_dm.txt>`_.
+The second part of this tutorial that details how to use `make_distance_comparison_plots.py <../scripts/make_distance_comparison_plots.html>`_ uses the dataset from a study that transplanted samples from one part of the body to another (Costello et al., 2009). The metadata mapping file can be found here: `download mapping file <ftp://ftp.microbio.me/qiime/tutorial_files/costello_whole_body/costello_timeseries_map.txt>`_ and the unweighted UniFrac distance matrix can be found here: `download distance matrix <ftp://ftp.microbio.me/qiime/tutorial_files/costello_whole_body/forearm_only_unweighted_unifrac_dm.txt>`_.
 
 Plotting Within and Between Distances
 -------------------------------------

diff --git a/doc/tutorials/distance_matrix_comparison.rst b/doc/tutorials/distance_matrix_comparison.rst
@@ -14,7 +14,7 @@ Please note that this tutorial does not attempt to cover every possible option t
 
 Input Files
 -----------
-You can obtain the files used in this tutorial `here <https://s3.amazonaws.com/s3-qiime_tutorial_files/88_soils.zip>`_. The files are taken from a study (Lauber et al., 2009) where 88 soil samples were collected at various regions around the world. pH was recorded for each of the soil samples. Using `distance_matrix_from_mapping.py <../scripts/distance_matrix_from_mapping.html>`_, we created a distance matrix containing differences in pH between each pair of samples. Throughout this tutorial, we will explore various ways of comparing these matrices for correlation.
+You can obtain the files used in this tutorial `here <ftp://ftp.microbio.me/qiime/tutorial_files/88_soils.zip>`_. The files are taken from a study (Lauber et al., 2009) where 88 soil samples were collected at various regions around the world. pH was recorded for each of the soil samples. Using `distance_matrix_from_mapping.py <../scripts/distance_matrix_from_mapping.html>`_, we created a distance matrix containing differences in pH between each pair of samples. Throughout this tutorial, we will explore various ways of comparing these matrices for correlation.
 
 Output Files
 ------------

diff --git a/doc/tutorials/filtering_contamination_otus.rst b/doc/tutorials/filtering_contamination_otus.rst
@@ -8,7 +8,7 @@ This tutorial explains how to use several QIIME scripts to filter all OTUs that
 
 To accomplish this task several scripts are used to first generate an OTU table of target OTUs to remove, then filter those OTUs from the original OTU table, and finally to perform a clean-up step to remove the control samples that would now have zero sequences associated with them.
 
-The OTU table and mapping file (generated from the QIIME tutorial data set) are available `here <https://s3.amazonaws.com/s3-qiime_tutorial_files/filtering_otus_tutorial_data.zip>`_.
+The OTU table and mapping file (generated from the QIIME tutorial data set) are available `here <ftp://ftp.microbio.me/qiime/tutorial_files/filtering_otus_tutorial_data.zip>`_.
 
 Once these files are downloaded and extracted, open a terminal and change to the directory of the extracted files to begin processing.
 

diff --git a/doc/tutorials/procrustes_analysis.rst b/doc/tutorials/procrustes_analysis.rst
@@ -26,7 +26,7 @@ Do some initial set up for the tutorial. This version of the tutorial is based o
 ::
 
 	cd
-	wget https://s3.amazonaws.com/s3-qiime_tutorial_files/moving_pictures_procrustes_demo.tgz
+	wget ftp://ftp.microbio.me/qiime/tutorial_files/moving_pictures_procrustes_demo.tgz
 	tar -xzf moving_pictures_procrustes_demo.tgz
 	screen
 	cd moving_pictures_procrustes_demo

diff --git a/doc/tutorials/shotgun_analysis.rst b/doc/tutorials/shotgun_analysis.rst
@@ -12,7 +12,7 @@ QIIME can perform translated search to assign nucleic acid sequence reads to a r
 
 This tutorial is based on Guerrero Negro microbial mat metagenome data. This data was generated on Sanger, and contains approximately 120k sequences. You should begin by obtaining that data with the following command::
 	
-	curl -O https://s3.amazonaws.com/s3-qiime_tutorial_files/shotgun_analysis_gn.tgz
+	curl -O ftp://ftp.microbio.me/qiime/tutorial_files/shotgun_analysis_gn.tgz
 
 See below for the relevant references for this data set.
 

diff --git a/doc/tutorials/source_tracking.rst b/doc/tutorials/source_tracking.rst
@@ -12,7 +12,7 @@ This tutorial does not attempt to cover every possible usage of SourceTracker. I
 
 Tutorial data
 -------------
-You can obtain the files used in this tutorial `here <https://s3.amazonaws.com/s3-qiime_tutorial_files/sourcetracker_tutorial_files.tgz>`_. These are derived from `Hewitt et al., 2013 <http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0054703>`_, where samples were collected from various surfaces in two different Neonatal Intensive Care Units (NICUs). The 16S rRNA was sequenced from these samples, and compared against pre-existing data sets using SourceTracker in order to predict the likely origin of the microbial contaminants on each NICU surface.
+You can obtain the files used in this tutorial `here <ftp://ftp.microbio.me/qiime/tutorial_files/sourcetracker_tutorial_files.tgz>`_. These are derived from `Hewitt et al., 2013 <http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0054703>`_, where samples were collected from various surfaces in two different Neonatal Intensive Care Units (NICUs). The 16S rRNA was sequenced from these samples, and compared against pre-existing data sets using SourceTracker in order to predict the likely origin of the microbial contaminants on each NICU surface.
 
 This tutorial begins with an OTU table. For information on various ways to generate OTU tables with QIIME, see :ref:`otu_picking`.
 

diff --git a/doc/tutorials/taxa_summary_comparison.rst b/doc/tutorials/taxa_summary_comparison.rst
@@ -18,7 +18,7 @@ Please note that this tutorial does not attempt to cover every possible option t
 
 Input Files
 -----------
-You can obtain the files used in this tutorial `here <https://s3.amazonaws.com/s3-qiime_tutorial_files/taxa_summary_comparison_tutorial_data.zip>`_. The files are derived from the `overview tutorial <./tutorial.html>`_. The unzipped directory will contain two taxa summary files named :file:`ts_rdp_0.60.txt` and :file:`ts_rdp_0.80.txt`. These taxa summaries were constructed from the overview tutorial representative sequence set by assigning taxonomy to it using the RDP classifier with two different confidence levels (0.60 and 0.80). The gg_otus_4feb2011 97% representative set was used as training input to the RDP classifier.
+You can obtain the files used in this tutorial `here <ftp://ftp.microbio.me/qiime/tutorial_files/taxa_summary_comparison_tutorial_data.zip>`_. The files are derived from the `overview tutorial <./tutorial.html>`_. The unzipped directory will contain two taxa summary files named :file:`ts_rdp_0.60.txt` and :file:`ts_rdp_0.80.txt`. These taxa summaries were constructed from the overview tutorial representative sequence set by assigning taxonomy to it using the RDP classifier with two different confidence levels (0.60 and 0.80). The gg_otus_4feb2011 97% representative set was used as training input to the RDP classifier.
 
 Output Files
 ------------

diff --git a/examples/ipynb/Fungal-ITS-analysis.ipynb b/examples/ipynb/Fungal-ITS-analysis.ipynb
@@ -23,7 +23,7 @@
      "cell_type": "code",
      "collapsed": true,
      "input": [
-      "tutorial_url = \"https://s3.amazonaws.com/s3-qiime_tutorial_files/its-soils-tutorial.tgz\"\n",
+      "tutorial_url = \"ftp://ftp.microbio.me/qiime/tutorial_files/its-soils-tutorial.tgz\"\n",
       "reference_url = \"https://github.com/downloads/qiime/its-reference-otus/its_12_11_otus.tar.gz\"\n",
       "!wget $tutorial_url\n",
       "!wget $reference_url"

diff --git a/examples/ipynb/illumina_overview_tutorial.ipynb b/examples/ipynb/illumina_overview_tutorial.ipynb
@@ -46,7 +46,7 @@
      "cell_type": "code",
      "collapsed": false,
      "input": [
-      "!(wget https://s3.amazonaws.com/s3-qiime_tutorial_files/moving_pictures_tutorial-1.9.0.tgz || curl -O https://s3.amazonaws.com/s3-qiime_tutorial_files/moving_pictures_tutorial-1.9.0.tgz)\n",
+      "!(wget ftp://ftp.microbio.me/qiime/tutorial_files/moving_pictures_tutorial-1.9.0.tgz || curl -O ftp://ftp.microbio.me/qiime/tutorial_files/moving_pictures_tutorial-1.9.0.tgz)\n",
       "!tar -xzf moving_pictures_tutorial-1.9.0.tgz"
      ],
      "language": "python",

diff --git a/examples/ipynb/illumina_overview_tutorial_workshop_template.ipynb b/examples/ipynb/illumina_overview_tutorial_workshop_template.ipynb
@@ -50,7 +50,7 @@
       "makedirs(working_dir)\n",
       "chdir(working_dir)\n",
       "\n",
-      "!wget https://s3.amazonaws.com/s3-qiime_tutorial_files/moving_pictures_tutorial-1.8.0.tgz\n",
+      "!wget ftp://ftp.microbio.me/qiime/tutorial_files/moving_pictures_tutorial-1.8.0.tgz\n",
       "!tar -xzf moving_pictures_tutorial-1.8.0.tgz\n",
       "\n",
       "# To use FileLink(s), but link to files in the user's working directory\n",

diff --git a/qiime/__init__.py b/qiime/__init__.py
@@ -18,7 +18,7 @@
                "Daniel McDonald",
                "Catherine Lozupone"]
 __license__ = "GPL"
-__version__ = "1.9.0-rc1"
+__version__ = "1.9.0-rc2"
 __maintainer__ = "Greg Caporaso"
 __email__ = "[email protected]"
 

diff --git a/qiime/add_alpha_to_mapping_file.py b/qiime/add_alpha_to_mapping_file.py
@@ -6,7 +6,7 @@
 __copyright__ = "Copyright 2011, The QIIME project"
 __credits__ = ["Yoshiki Vazquez-Baeza", "Antonio Gonzalez-Pena"]
 __license__ = "GPL"
-__version__ = "1.9.0-rc1"
+__version__ = "1.9.0-rc2"
 __maintainer__ = "Yoshiki Vazquez-Baeza"
 __email__ = "[email protected]"
 

diff --git a/qiime/add_qiime_labels.py b/qiime/add_qiime_labels.py
@@ -5,7 +5,7 @@
 __copyright__ = "Copyright 2011, The QIIME Project"
 __credits__ = ["William Walters", "Emily TerAvest"]
 __license__ = "GPL"
-__version__ = "1.9.0-rc1"
+__version__ = "1.9.0-rc2"
 __maintainer__ = "William Walters"
 __email__ = "[email protected]"
 

diff --git a/qiime/adjust_seq_orientation.py b/qiime/adjust_seq_orientation.py
@@ -6,7 +6,7 @@
 __copyright__ = "Copyright 2011, The QIIME Project"
 __credits__ = ["Greg Caporaso", "Antonio Gonzalez Pena"]
 __license__ = "GPL"
-__version__ = "1.9.0-rc1"
+__version__ = "1.9.0-rc2"
 __maintainer__ = "Greg Caporaso"
 __email__ = "[email protected]"
 

diff --git a/qiime/align_seqs.py b/qiime/align_seqs.py
@@ -8,7 +8,7 @@
     "Jeremy Widmann",
     "Kyle Bittinger"]
 __license__ = "GPL"
-__version__ = "1.9.0-rc1"
+__version__ = "1.9.0-rc2"
 __maintainer__ = "Greg Caporaso"
 __email__ = "[email protected]"
 

diff --git a/qiime/alpha_diversity.py b/qiime/alpha_diversity.py
@@ -6,7 +6,7 @@
                "William Van Treuren", "Jose Antonio Navas Molina",
                "Jai Ram Rideout"]
 __license__ = "GPL"
-__version__ = "1.9.0-rc1"
+__version__ = "1.9.0-rc2"
 __maintainer__ = "Justin Kuczynski"
 __email__ = "[email protected]"
 

diff --git a/qiime/assign_taxonomy.py b/qiime/assign_taxonomy.py
@@ -7,7 +7,7 @@
 __credits__ = ["Rob Knight", "Greg Caporaso", "Kyle Bittinger",
                "Antonio Gonzalez Pena", "David Soergel", "Jai Ram Rideout"]
 __license__ = "GPL"
-__version__ = "1.9.0-rc1"
+__version__ = "1.9.0-rc2"
 __maintainer__ = "Greg Caporaso"
 __email__ = "[email protected]"
 

diff --git a/qiime/barcode.py b/qiime/barcode.py
@@ -5,7 +5,7 @@
 __copyright__ = "Copyright 2011, The QIIME Project"
 __credits__ = ["Justin Kuczynski"]  # remember to add yourself
 __license__ = "GPL"
-__version__ = "1.9.0-rc1"
+__version__ = "1.9.0-rc2"
 __maintainer__ = "Justin Kuczynski"
 __email__ = "[email protected]"
 

diff --git a/qiime/beta_diversity.py b/qiime/beta_diversity.py
@@ -6,7 +6,7 @@
                "Jose Carlos Clemente Litran", "Jai Ram Rideout",
                "Jose Antonio Navas Molina"]
 __license__ = "GPL"
-__version__ = "1.9.0-rc1"
+__version__ = "1.9.0-rc2"
 __maintainer__ = "Justin Kuczynski"
 __email__ = "[email protected]"
 

diff --git a/qiime/beta_metrics.py b/qiime/beta_metrics.py
@@ -4,7 +4,7 @@
 __copyright__ = "Copyright 2011, The QIIME Project"
 __credits__ = ["Rob Knight", "Justin Kuczynski"]
 __license__ = "GPL"
-__version__ = "1.9.0-rc1"
+__version__ = "1.9.0-rc2"
 __maintainer__ = "Justin Kuczynski"
 __email__ = "[email protected]"
 

diff --git a/qiime/biplots.py b/qiime/biplots.py
@@ -5,7 +5,7 @@
 __copyright__ = "Copyright 2011, The QIIME Project"
 __credits__ = ["Dan Knights", "Justin Kuczynski"]  # remember to add yourself
 __license__ = "GPL"
-__version__ = "1.9.0-rc1"
+__version__ = "1.9.0-rc2"
 __maintainer__ = "Dan Knights"
 __email__ = "[email protected]"
 

diff --git a/qiime/categorized_dist_scatterplot.py b/qiime/categorized_dist_scatterplot.py
@@ -6,7 +6,7 @@
 __copyright__ = "Copyright 2011, The QIIME Project"
 __credits__ = ["Justin Kuczynski"]
 __license__ = "GPL"
-__version__ = "1.9.0-rc1"
+__version__ = "1.9.0-rc2"
 __maintainer__ = "Justin Kuczynski"
 __email__ = "[email protected]"
 

diff --git a/qiime/check_id_map.py b/qiime/check_id_map.py
@@ -43,7 +43,7 @@
 __copyright__ = "Copyright 2011, The QIIME Project"
 __credits__ = ["Rob Knight", "William Walters"]  # remember to add yourself
 __license__ = "GPL"
-__version__ = "1.9.0-rc1"
+__version__ = "1.9.0-rc2"
 __maintainer__ = "William Walters"
 __email__ = "[email protected]"
 

diff --git a/qiime/clean_raxml_parsimony_tree.py b/qiime/clean_raxml_parsimony_tree.py
@@ -6,7 +6,7 @@
 __copyright__ = "Copyright 2011, The QIIME project"
 __credits__ = ["Jesse Stombaugh"]
 __license__ = "GPL"
-__version__ = "1.9.0-rc1"
+__version__ = "1.9.0-rc2"
 __maintainer__ = "Jesse Stombaugh"
 __email__ = "[email protected]"
 

diff --git a/qiime/cluster_quality.py b/qiime/cluster_quality.py
@@ -4,7 +4,7 @@
 __copyright__ = "Copyright 2011, The QIIME Project"
 __credits__ = ["Justin Kuczynski"]
 __license__ = "GPL"
-__version__ = "1.9.0-rc1"
+__version__ = "1.9.0-rc2"
 __maintainer__ = "Justin Kuczynski"
 __email__ = "[email protected]"
 """ computes cluster quality the default way, bet/within"""

diff --git a/qiime/collate_alpha.py b/qiime/collate_alpha.py
@@ -4,7 +4,7 @@
 __copyright__ = "Copyright 2011, The QIIME Project"
 __credits__ = ["Justin Kuczynski"]
 __license__ = "GPL"
-__version__ = "1.9.0-rc1"
+__version__ = "1.9.0-rc2"
 __maintainer__ = "Justin Kuczynski"
 __email__ = "[email protected]"
 

diff --git a/qiime/colors.py b/qiime/colors.py
@@ -6,7 +6,7 @@
 # remember to add yourself
 __credits__ = ["Rob Knight", "Jesse Stombaugh", "Yoshiki Vazquez-Baeza"]
 __license__ = "GPL"
-__version__ = "1.9.0-rc1"
+__version__ = "1.9.0-rc2"
 __maintainer__ = "Jesse Stombaugh"
 __email__ = "[email protected]"
 

diff --git a/qiime/compare_alpha_diversity.py b/qiime/compare_alpha_diversity.py
@@ -6,7 +6,7 @@
 __copyright__ = "Copyright 2011, The QIIME project"
 __credits__ = ["William Van Treuren", "Greg Caporaso", "Jai Ram Rideout"]
 __license__ = "GPL"
-__version__ = "1.9.0-rc1"
+__version__ = "1.9.0-rc2"
 __maintainer__ = "William Van Treuren"
 __email__ = "[email protected]"
 

diff --git a/qiime/compare_categories.py b/qiime/compare_categories.py
@@ -6,7 +6,7 @@
 __credits__ = ["Jai Ram Rideout", "Michael Dwan", "Logan Knecht",
                "Damien Coy", "Levi McCracken"]
 __license__ = "GPL"
-__version__ = "1.9.0-rc1"
+__version__ = "1.9.0-rc2"
 __maintainer__ = "Jai Ram Rideout"
 __email__ = "[email protected]"
 

diff --git a/qiime/compare_distance_matrices.py b/qiime/compare_distance_matrices.py
@@ -6,7 +6,7 @@
 __credits__ = ["Jai Ram Rideout", "Michael Dwan", "Logan Knecht",
                "Damien Coy", "Levi McCracken", "Greg Caporaso"]
 __license__ = "GPL"
-__version__ = "1.9.0-rc1"
+__version__ = "1.9.0-rc2"
 __maintainer__ = "Jai Ram Rideout"
 __email__ = "[email protected]"
 

diff --git a/qiime/compare_taxa_summaries.py b/qiime/compare_taxa_summaries.py
@@ -5,7 +5,7 @@
 __copyright__ = "Copyright 2012, The QIIME project"
 __credits__ = ["Jai Ram Rideout", "Greg Caporaso"]
 __license__ = "GPL"
-__version__ = "1.9.0-rc1"
+__version__ = "1.9.0-rc2"
 __maintainer__ = "Jai Ram Rideout"
 __email__ = "[email protected]"
 

diff --git a/qiime/compare_trajectories.py b/qiime/compare_trajectories.py
@@ -5,7 +5,7 @@
 __credits__ = ["Jose Antonio Navas Molina", "Antonio Gonzalez Pena",
                "Yoshiki Vazquez Baeza"]
 __license__ = "GPL"
-__version__ = "1.9.0-rc1"
+__version__ = "1.9.0-rc2"
 __maintainer__ = "Jose Antonio Navas Molina"
 __email__ = "[email protected]"
 

diff --git a/qiime/compute_taxonomy_ratios.py b/qiime/compute_taxonomy_ratios.py
@@ -11,7 +11,7 @@
 __copyright__ = "Copyright 2014, The QIIME project"
 __credits__ = ["Daniel McDonald"]
 __license__ = "GPL"
-__version__ = "1.9.0-rc1"
+__version__ = "1.9.0-rc2"
 __maintainer__ = "Daniel McDonald"
 __email__ = "[email protected]"
 

diff --git a/qiime/convert_fastaqual_fastq.py b/qiime/convert_fastaqual_fastq.py
@@ -4,7 +4,7 @@
 __copyright__ = "Copyright 2011, The QIIME project"
 __credits__ = ["Adam Robbins-Pianka, Abhisaar Yadav"]
 __license__ = "GPL"
-__version__ = "1.9.0-rc1"
+__version__ = "1.9.0-rc2"
 __maintainer__ = "Adam Robbins-Pianka"
 __email__ = "[email protected]"
 

diff --git a/qiime/core_microbiome.py b/qiime/core_microbiome.py
@@ -6,7 +6,7 @@
 __copyright__ = "Copyright 2011, The QIIME project"
 __credits__ = ["Greg Caporaso", "Jai Ram Rideout"]
 __license__ = "GPL"
-__version__ = "1.9.0-rc1"
+__version__ = "1.9.0-rc2"
 __maintainer__ = "Greg Caporaso"
 __email__ = "[email protected]"
 

diff --git a/qiime/demultiplex_fasta.py b/qiime/demultiplex_fasta.py
@@ -13,7 +13,7 @@
     "Jens Reeder",
     "Emily TerAvest"]  # remember to add yourself
 __license__ = "GPL"
-__version__ = "1.9.0-rc1"
+__version__ = "1.9.0-rc2"
 __maintainer__ = "William Walters"
 __email__ = "[email protected]"
 

diff --git a/qiime/denoise_wrapper.py b/qiime/denoise_wrapper.py
@@ -7,7 +7,7 @@
 __copyright__ = "Copyright 2011, The QIIME Project"
 __credits__ = ["Jens Reeder", "Greg Caporaso"]
 __license__ = "GPL"
-__version__ = "1.9.0-rc1"
+__version__ = "1.9.0-rc2"
 __maintainer__ = "Justin Kuczynski"
 __email__ = "[email protected]"
 

diff --git a/qiime/denoiser/__init__.py b/qiime/denoiser/__init__.py
@@ -5,7 +5,7 @@
 # remember to add yourself if you make changes
 __credits__ = ["Jens Reeder", "Rob Knight"]
 __license__ = "GPL"
-__version__ = "1.9.0-rc1"
+__version__ = "1.9.0-rc2"
 __maintainer__ = "Jens Reeder"
 __email__ = "[email protected]"
 

diff --git a/qiime/denoiser/cluster_utils.py b/qiime/denoiser/cluster_utils.py
@@ -7,7 +7,7 @@
 # remember to add yourself if you make changes
 __credits__ = ["Jens Reeder", "Rob Knight", "Nigel Cook", "Jai Ram Rideout"]
 __license__ = "GPL"
-__version__ = "1.9.0-rc1"
+__version__ = "1.9.0-rc2"
 __maintainer__ = "Jens Reeder"
 __email__ = "[email protected]"
 

diff --git a/qiime/denoiser/denoise_postprocess.py b/qiime/denoiser/denoise_postprocess.py
@@ -5,7 +5,7 @@
 # remember to add yourself if you make changes
 __credits__ = ["Jens Reeder", "Rob Knight"]
 __license__ = "GPL"
-__version__ = "1.9.0-rc1"
+__version__ = "1.9.0-rc2"
 __maintainer__ = "Jens Reeder"
 __email__ = "[email protected]"