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

To build the denoiser you need ghc version 6 because vers. 7 requires glibc7. Beforehand, you need to install gmp and gmp-devel installed from CentOS5base (FAQ)

PyNast needs clustalw old version (1.8)

PySparse installation:

There appears to be an undocumented requirement for PySparse 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) Following these instructions with a change. Download BLAS from here, 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

Build and install:

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

Greengenes installation

Download:

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