Notes on installing Qiime
=========================

IMPORTANT
---------

When running ``identify_chimeric_seqs.py`` with ChimeraSlayer at some point it
tries to index a fasta alignment file using cdbfasta. That alignment file could
in in <qiime installation>/support_files. If the user hasnt copied it to their
own directory, the script fails because the user doesnt have permission to write
the index file to that directory. I might be possible to ask each user to copy
that file locally, but probably easier to just change permissions so that all
users can write to the target directory.


`Qiime install documentation <http://qiime.org/install/install.html>`_

To build the *denoiser* you need `ghc <http://www.haskell.org/ghc/download_ghc_6_12_31>`_ version 6 because vers. 7
requires glibc7. Beforehand, you need to install gmp and gmp-devel installed from CentOS5base (`FAQ
<http://www.haskell.org/haskellwiki/GHC:FAQ#Linking_a_program_causes_the_following_error_on_Linux:_.2Fusr.2Fbin.2Fld:_cannot_open_-lgmp:_No_such_file_or_directory>`_)

PyNast needs `clustalw <http://www.clustal.org/download/current/>`_ old version (1.8)

PySparse installation:
======================
There appears to be an undocumented requirement for `PySparse
<http://pysparse.sourceforge.net>`_ which requires a static *libblas.a* library to
be built (NB. the default BLAS library on Centos is crippled and wont work - see
also `Installation with ATLAS and complete LAPACK library <ATLAS_LAPACK_CENTOS5.4.text>`_)
Following these `instructions <http://gcc.gnu.org/wiki/GfortranBuild>`_ *with a
change*.
Download BLAS from `here <http://www.netlib.org/blas/blas.tgz>`_,
unpack, and build::

$ gfortran -O2 -fPIC -c *.f
$ ar cr libblas.a *.o

The **-fPIC** is important.
Copy to /share/apps/lib64, chmod a+x

Edit the setup.py file in pysparce:

    ``library_dirs_list= ['/share/apps/lib64']``

    ``$python setup.py install``

Fasttree installation
=====================

`Download <http://www.microbesonline.org/fasttree/FastTree-2.1.3.c>`_

Build and install:

    ``$ gcc -Wall -O3 -finline-functions -funroll-loops -o FastTree -lm FastTree-2.1.3.c``

Greengenes installation
=======================

Download:

    * `Greengenes core set reference data <http://greengenes.secondgenome.com/downloads>`_
      You need to the file formatted: gg_<year>_<month>_otus.tar.gz

    
    Place in ``/share/apps/qiime/support_files/``

    assign_taxonomy.py needs paths -r and -t, e.g.:
    -r /share/apps/qiime/support_files/gg_13_5_otus/rep_set/97_otus.fasta
    -t /share/apps/qiime/support_files/gg_13_5_otus/taxonomy/97_otu_taxonomy.txt

Build and install Qiime
=======================

    ``python setup.py install --install-scripts=/share/apps/qiime/bin/ --install-purelib=/share/apps/qiime/lib/ --install-data=/share/apps/qiime/lib/``

Default Qiime config in ``/share/apps/qiime``
=============================================

::

    # qiime_config
    # WARNING: DO NOT EDIT OR DELETE Qiime/qiime_config
    # To overwrite defaults, copy this file to $HOME/.qiime_config or a full path
    # specified by $QIIME_CONFIG_FP and edit that copy of the file.
    
    cluster_jobs_fp
    python_exe_fp	python
    working_dir
    blastmat_dir
    blastall_fp	blastall
    pynast_template_alignment_fp	/share/apps/qiime/support_files/core_set_aligned.fasta.imputed
    pynast_template_alignment_blastdb
    template_alignment_lanemask_fp 	/share/apps/qiime/support_files/lanemask_in_1s_and_0s
    jobs_to_start	1
    seconds_to_sleep	60
    qiime_scripts_dir	/share/apps/qiime/bin
    temp_dir	/tmp/
    denoiser_min_per_core	50
    cloud_environment	False
    topiaryexplorer_project_dir
    torque_queue	friendlyq
    assign_taxonomy_reference_seqs_fp
    assign_taxonomy_id_to_taxonomy_fp

Biom Format
===========
In ``/share/apps``::

    $ svn checkout svn://svn.code.sf.net/p/biom-format/code/trunk biom-format

Add ``/share/apps/biom-format/python-code`` to $PYTHONPATH
and ``/share/apps/biom-format/scripts`` to $PATH