Install QIIME (1.5.0)

apt-get install libssl-dev libzmq-dev libgsl0-dev openjdk-6-jdk libxml2 libxslt1.1 libxslt1-dev ant git subversion build-essential zlib1g-dev libpng12-dev libfreetype6-dev mpich2 libreadline-dev gfortran unzip libmysqlclient18 libmysqlclient-dev ghc
reboot

mkdir /usr/share/qiime_software

cd /root/
git clone git://github.com/qiime/qiime-deploy.git
git clone git://github.com/qiime/qiime-deploy-conf.git
cd qiime-deploy
python qiime-deploy.py /usr/share/qiime_software/ -f /root/qiime-deploy-conf/qiime-1.5.0/qiime.conf --force-remove-failed-dirs

...
DEPLOYMENT SUMMARY

Packages deployed successfully:
data-lanemask, rtax, clearcut, cdbtools, raxml, ampliconnoise, chimeraslayer, vienna, infernal, data-core, fasttree, pplacer, python, parsinsert, blast, muscle, rdpclassifier, drisee, cdhit, uclust, pyzmq, SQLAlchemy, tornado, cytoscape, setuptools, numpy, MySQL-python, mpi4py, biom-format, mothur, pycogent, pynast, pprospector, sphinx, ipython, matplotlib, qiime, r, gg_otus

Packages skipped (assumed successful):

Packages failed to deploy:

user@rachaelx:~$ print_qiime_config.py -t

...
======================================================================
FAIL: test_denoiser_supported_version (__main__.Qiime_config)
denoiser aligner is ready to use
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/share/qiime_software/qiime-1.5.0-release/bin/print_qiime_config.py", line 536, in test_denoiser_supported_version
    "which components of QIIME you plan to use.")
AssertionError: Denoiser flowgram aligner not found or not executable.This may or may not be a problem depending on which components of QIIME you plan to use.

======================================================================
FAIL: test_mothur_supported_version (__main__.Qiime_config)
mothur is in path and version is supported
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/share/qiime_software/qiime-1.5.0-release/bin/print_qiime_config.py", line 523, in test_mothur_supported_version
    % ('.'.join(map(str,acceptable_version)), version_string))
AssertionError: Unsupported mothur version. 1.25.0 is required, but running mothur: error while loading shared libraries: libreadline.so.5: cannot open shared object file: No such file or directory
.

======================================================================
FAIL: test_python_supported_version (__main__.Qiime_config)
python is in path and version is supported
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/share/qiime_software/qiime-1.5.0-release/bin/print_qiime_config.py", line 338, in test_python_supported_version
    version_string))
AssertionError: Unsupported python version. Must be >= 2.7.1 and <= 2.7.2 , but running 2.7.3.

======================================================================
FAIL: test_rtax_supported_version (__main__.Qiime_config)
rtax is in path and version is supported
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/share/qiime_software/qiime-1.5.0-release/bin/print_qiime_config.py", line 620, in test_rtax_supported_version
    % ('.'.join(map(str,acceptable_version)), version_string))
AssertionError: Unsupported rtax version. (0, 981).(0, 981) is required, but running 0.982.

======================================================================
FAIL: test_usearch_supported_version (__main__.Qiime_config)
usearch is in path and version is supported
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/share/qiime_software/qiime-1.5.0-release/bin/print_qiime_config.py", line 668, in test_usearch_supported_version
    "which components of QIIME you plan to use.")
AssertionError: usearch not found. This may or may not be a problem depending on which components of QIIME you plan to use.

----------------------------------------------------------------------
Ran 34 tests in 0.724s

FAILED (failures=5)