[Bio-linux-dev] Qiime update
Tim Booth
tbooth at ceh.ac.uk
Fri Nov 4 08:43:07 EDT 2011
Hi Tony,
Good to hear you are still working on Qiime. Due to some build issues
between Ubuntu LTS and Debian Sid I'm comitting to a fork in SVN just
now, but if you want to do any work on the source package it's all here:
svn://svn.debian.org/svn/debian-med/trunk/packages/qiime/branches/lucid/debian
Or if you just have tested fixes for individual issues just let me know
and I'll fold them in.
For Qiime to really be useful in regular Debian it needs to not use
uClust by default. Other clustering options are available but I don't
know what the implications of using these are and I've not had time to
investigate yet.
Cheers,
TIM
On Thu, 2011-11-03 at 20:03 +0000, Tony Travis wrote:
> 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.
--
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre
Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB
http://nebc.nerc.ac.uk
+44 1491 69 2705
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