[Bio-linux-dev] Qiime update

[Tony Travis]

On 03/11/11 18:08, Tim Booth wrote:
> Hi All,
>
> Following on from the previous discussion, I have uploaded a new qiime
> and bio-linux-qiime package, along with a fix to chimeraslayer.  This
> should address the issues that Mike reported and also clear up some but
> not all of the problems reported by "qiime print_qiime_config -t".

Hi, Tim.

I've decided to uninstall your qiime package and install QIIME from 
source. I'm using this wrapper to create a custom QIIME environment 
under Bio-Linux 6, without breaking anything else:

--- cut here ---
# @(#)qiime.sh  2011-10-05  A.J.Travis

#
# Qiime environment
#

# Python
export QIIME=/usr/local/qiime
export QIIME_CONFIG_FP=$QIIME/etc/qiime_config
export PATH=$QIIME/bin:$PATH
export PYTHONPATH=$QIIME/lib/python2.6/site-packages:$PYTHONPATH

# NCBI BLAST 2.2.22
export BLAST_HOME=/usr/local/blast-2.2.22
export BLASTMAT=$BLAST_HOME/data
export PATH=$BLAST_HOME/bin:$PATH

# AmpliconNoise
export AMPLICON_NOISE=$QIIME/AmpliconNoiseV1.24
export PATH=$AMPLICON_NOISE/Scripts:$AMPLICON_NOISE/bin:$PATH
export PYRO_LOOKUP_FILE=$AMPLICON_NOISE/Data/LookUp_E123.dat
export SEQ_LOOKUP_FILE=$AMPLICON_NOISE/Data/Tran.dat

# ChimeraSlayer
export PATH=/usr/share/ChimeraSlayer:$PATH

# QIIME shell
export debian_chroot=QIIME
exec /bin/bash
--- cut here ---

> rwt017 at topcat:~$ qiime
> (QIIME)rwt017 at topcat:~$ print_qiime_config.py -t
>
> System information
> ==================
>          Platform:	linux2
>    Python version:	2.6.5 (r265:79063, Apr 16 2010, 13:57:41)  [GCC 4.4.3]
> Python executable:	/usr/bin/python
>
> Dependency versions
> ===================
>                      PyCogent version:	1.5.1
>                         NumPy version:	1.3.0
>                    matplotlib version:	0.98.5.3
>                 QIIME library version:	1.3.0
>                  QIIME script version:	1.3.0
>         PyNAST version (if installed):	1.1
> RDP Classifier version (if installed):	rdp_classifier-2.0.jar
>
> QIIME config values
> ===================
>                      blastmat_dir:	None
>       topiaryexplorer_project_dir:	None
>      pynast_template_alignment_fp:	None
>                   cluster_jobs_fp:	/usr/local/qiime/bin/start_parallel_jobs.py
> pynast_template_alignment_blastdb:	None
>                      torque_queue:	friendlyq
>    template_alignment_lanemask_fp:	None
>                     jobs_to_start:	1
>                 cloud_environment:	False
>                 qiime_scripts_dir:	/usr/local/qiime/bin
>             denoiser_min_per_core:	50
>                       working_dir:	None
>                     python_exe_fp:	python
>                          temp_dir:	None
>                       blastall_fp:	blastall
>                  seconds_to_sleep:	60
>
>
> running checks:
>
> FastTree is in path and version is supported ... ok
> INFERNAL is in path and version is supported ... ok
> AmpliconNoise install looks sane. ... ok
> blast is in path and version is supported ... ok
> blastall_fp is set to a valid path ... ok
> blastmat_dir is set to a valid path. ... ok
> cdbtools is in path and version is supported ... ok
> cd-hit is in path and version is supported ... ok
> no obvious problems with ChimeraSlayer install ... ok
> clearcut is in path and version is supported ... ok
> cluster_jobs_fp is set to a valid path and is executable ... ok
> denoiser aligner is ready to use ... ok
> local qiime_config has no extra params ... ok
> maptplotlib version is supported ... ok
> mothur is in path and version is supported ... ok
> muscle is in path and version is supported ... ok
> numpy version is supported ... ok
> pynast version is supported ... ok
> pynast_template_alignment_blastdb, if set, is set to a valid path ... ok
> pynast_template_alignment, if set, is set to a valid path ... ok
> python_exe_fp is set to a working python env ... ok
> python is in path and version is supported ... ok
> qiime_scripts_dir, if set, is set to a valid path ... ok
> raxmlHPC is in path and version is supported ... ok
> temp_dir, if set, is set to a valid path ... ok
> template_alignment_lanemask, if set, is set to a valid path ... ok
> uclust is in path and version is supported ... ok
> working_dir, if set, is set to a valid path ... ok
>
> ----------------------------------------------------------------------
> Ran 28 tests in 0.621s
>
> OK
> (QIIME)rwt017 at topcat:~$

I could adapt your deb package to work like this, but I want to get my 
source version working properly first. In particular, I want all the 
unit tests from the QIIME source distribution tree to run successfully.

Making progress on that objective, but not quite got there yet ;-)

HTH,

   Tony.
-- 
Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition
and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK
tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk
mailto:a.travis at abdn.ac.uk, http://bioinformatics.rri.sari.ac.uk