[Bio-linux-dev] qiime
Tim Booth
tbooth at ceh.ac.uk
Tue Sep 20 12:31:58 EDT 2011
Hi Tony,
For Qiime, my less-than ideal testing consists of running through the
tutorial that we use for our Bio-Linux course. Of course, this only
tests out some of the Qiime features. I've considered working through
the failures that print_qiime_config.py flags up but what I don't want
to do is create quick fixes that makes the feature appear to work but
which are nevertheless untested. Bela, who did the original packaging,
warned me about this.
So for example if you are trying to use "blast" and can send me a fix
that both satisfies print_qiime_config.py and also works on your own
data then I'd be very pleased to incorporate it. Otherwise, I'm only
fixing these problems as people ask for them specifically. Hopefully at
some point I'll have the time to go through and do a proper job...
In other news, we should be doing an introductory BL course up in
Edinburgh on the 4th November, if any Aberdeen people think it is worth
the trip. I'll send a flyer soon.
Cheers,
TIM
On Wed, 2011-09-07 at 23:31 +0100, Tony Travis wrote:
> Hi, Tim.
>
> I spent today helping my colleague Caroline Reiff try to get "Qiime"
> working properly under Bio-Linux, and Ubuntu 10.04 LTS with Bio-Linux
> repositories enabled. There seem to be quite a lot of version conflicts
> with installed dependencies in your packaged version installed on our
> Beowulf login server "topcat", and we encountered similar problems on
> Caroline's workstation, which is Ubuntu 10.04 LTS _ Bio-Linux repo's:
>
> Are you working on this already, or should we attempt to fix it?
>
> Bye,
>
> Tony.
>
> > rwt017 at topcat:~$ qiime 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/python2.6
> >
> > Dependency versions
> > ===================
> > PyCogent version: 1.5.1
> > NumPy version: 1.3.0
> > matplotlib version: 0.99.1.1
> > 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: /usr/share/ncbi/data
> > rdp_classifier_fp: None
> > topiaryexplorer_project_dir: None
> > pynast_template_alignment_fp: None
> > cluster_jobs_fp: None
> > pynast_template_alignment_blastdb: None
> > torque_queue: friendlyq
> > pyronoise_data_fp: /usr/local/bioinf/denoiser/denoiser/Data/LookUp.dat
> > template_alignment_lanemask_fp: None
> > jobs_to_start: 1
> > cloud_environment: False
> > qiime_scripts_dir: /usr/lib/qiime/bin/
> > denoiser_min_per_core: 50
> > working_dir: .
> > python_exe_fp: python
> > temp_dir: /tmp
> > 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. ... FAIL
> > blast is in path and version is supported ... FAIL
> > 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 ... FAIL
> > clearcut is in path and version is supported ... FAIL
> > cluster_jobs_fp is set to a valid path and is executable ... ok
> > denoiser aligner is ready to use ... FAIL
> > local qiime_config has no extra params ... FAIL
> > maptplotlib version is supported ... FAIL
> > mothur is in path and version is supported ... ERROR
> > muscle is in path and version is supported ... FAIL
> > 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 ... FAIL
> > 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
> >
> > ======================================================================
> > ERROR: mothur is in path and version is supported
> > ----------------------------------------------------------------------
> > Traceback (most recent call last):
> > File "/usr/lib/qiime/bin/print_qiime_config.py", line 472, in test_mothur_supported_version
> > version_string = stdout.strip().split(' ')[1].strip('v.')
> > IndexError: list index out of range
> >
> > ======================================================================
> > FAIL: AmpliconNoise install looks sane.
> > ----------------------------------------------------------------------
> > Traceback (most recent call last):
> > File "/usr/lib/qiime/bin/print_qiime_config.py", line 116, in test_ampliconnoise_install
> > "$PYRO_LOOKUP_FILE variable is not set. See %s for help." % url)
> > AssertionError: $PYRO_LOOKUP_FILE variable is not set. See http://www.qiime.org/install/install.html#ampliconnoise-install for help.
> >
> > ======================================================================
> > FAIL: blast is in path and version is supported
> > ----------------------------------------------------------------------
> > Traceback (most recent call last):
> > File "/usr/lib/qiime/bin/print_qiime_config.py", line 374, in test_blast_supported_version
> > % ('.'.join(map(str,acceptable_version)), version_string))
> > AssertionError: Unsupported blast version. 2.2.22 is required, but running 2.2.21.
> >
> > ======================================================================
> > FAIL: no obvious problems with ChimeraSlayer install
> > ----------------------------------------------------------------------
> > Traceback (most recent call last):
> > File "/usr/lib/qiime/bin/print_qiime_config.py", line 251, in test_chimeraSlayer_install
> > "ChimeraSlayer depends on external files in directoryies relative to its "
> > AssertionError: ChimeraSlayer depends on external files in directoryies relative to its install directory. Thesedo not appear to be present.
> >
> > ======================================================================
> > FAIL: clearcut is in path and version is supported
> > ----------------------------------------------------------------------
> > Traceback (most recent call last):
> > File "/usr/lib/qiime/bin/print_qiime_config.py", line 525, in test_clearcut_supported_version
> > "which components of QIIME you plan to use.")
> > AssertionError: clearcut not found. This may or may not be a problem depending on which components of QIIME you plan to use.
> >
> > ======================================================================
> > FAIL: denoiser aligner is ready to use
> > ----------------------------------------------------------------------
> > Traceback (most recent call last):
> > File "/usr/lib/qiime/bin/print_qiime_config.py", line 497, in test_denoiser_supported_version
> > "which components of QIIME you plan to use.")
> > AssertionError: Denoiser flowgram aligner not found or not executable.This may or may not be a problem depending on which components of QIIME you plan to use.
> >
> > ======================================================================
> > FAIL: local qiime_config has no extra params
> > ----------------------------------------------------------------------
> > Traceback (most recent call last):
> > File "/usr/lib/qiime/bin/print_qiime_config.py", line 224, in test_for_obsolete_values
> > ", ".join(extra_vals))
> > AssertionError: The qiime_config file set via QIIME_CONFIG_FPenviroment variable contains obsolete parameters:
> > rdp_classifier_fp, pyronoise_data_fp
> >
> > ======================================================================
> > FAIL: maptplotlib version is supported
> > ----------------------------------------------------------------------
> > Traceback (most recent call last):
> > File "/usr/lib/qiime/bin/print_qiime_config.py", line 332, in test_matplotlib_suported_version
> > version_string))
> > AssertionError: Unsupported matplotlib version. Must be >= 0.98.5.3 and < 0.98.5.4 , but running 0.99.1.1.
> >
> > ======================================================================
> > FAIL: muscle is in path and version is supported
> > ----------------------------------------------------------------------
> > Traceback (most recent call last):
> > File "/usr/lib/qiime/bin/print_qiime_config.py", line 458, in test_muscle_supported_version
> > % ('.'.join(map(str,acceptable_version)), version_string))
> > AssertionError: Unsupported muscle version. 3.6 is required, but running 3.7.
> >
> > ======================================================================
> > FAIL: raxmlHPC is in path and version is supported
> > ----------------------------------------------------------------------
> > Traceback (most recent call last):
> > File "/usr/lib/qiime/bin/print_qiime_config.py", line 504, in test_raxmlHPC_supported_version
> > "which components of QIIME you plan to use.")
> > AssertionError: raxmlHPC not found. This may or may not be a problem depending on which components of QIIME you plan to use.
> >
> > ----------------------------------------------------------------------
> > Ran 28 tests in 0.149s
> >
> > FAILED (failures=9, errors=1)
>
>
--
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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