Notes on installing Qiime


When running 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 file in pysparce:

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

$python install

Fasttree installation


Build and install:

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

Greengenes installation


Place in /share/apps/qiime/support_files/ 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 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.

python_exe_fp       python
blastall_fp blastall
pynast_template_alignment_fp        /share/apps/qiime/support_files/core_set_aligned.fasta.imputed
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
torque_queue        friendlyq

Biom Format

In /share/apps:

$ svn checkout svn:// biom-format

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