[Bio-linux-dev] qiime
Mike Cox
mikeyj.cox at gmail.com
Tue Sep 20 12:20:02 EDT 2011
Hi Tony,
I've had some fun with QIIME on Biolinux too. It's dependency city!
I've taken a pragmatic approach as there is a lot of duplication within
QIIME itself, so you might want to decide exactly what you actually need to
get working. For denoising I would recommend AmpliconNoise, rather than
QIIME's denoiser, though it's slower, it's been demonstrated to be the
better at it's job (and to be honest, these things are always going to churn
away for an age anyway). The fail there is fixable with the following in
each users .profile:
PATH=$PATH:/usr/share/ampliconnoise/Data:/usr/share/ampliconnoise/Scripts
export PATH
PYRO_LOOKUP_FILE=/usr/share/ampliconnoise/Data/LookUp_E123.dat
SEQ_LOOKUP_FILE=/usr/share/ampliconnoise/Data/Tran.dat
export PYRO_LOOKUP_FILE
export SEQ_LOOKUP_FILE
If you use AmpliconNoise, you also don't need to worry about ChimeraSlayer,
as Perseus for chimera detection and removal is part of AmpliconNoise.
I'll leave Tim to tackle some of the others...!
Cheers
Mike
Mike Cox
Research Associate
Molecular Genetics & Genomics and Centre for Respiratory Infection
National Heart Lung Institute
Royal Brompton Campus
Guy Scadding Building
London SW3 6LY
02073528121 ext. 3300
http://www1.imperial.ac.uk/medicine/people/michael.cox1/
On Wed, Sep 7, 2011 at 23:31, Tony Travis <a.travis at abdn.ac.uk> wrote:
> Hi, Tim.
>
> I spent today helping my colleague Caroline Reiff try to get "Qiime"
> working properly under Bio-Linux, and Ubuntu 10.04 LTS with Bio-Linux
> repositories enabled. There seem to be quite a lot of version conflicts with
> installed dependencies in your packaged version installed on our Beowulf
> login server "topcat", and we encountered similar problems on Caroline's
> workstation, which is Ubuntu 10.04 LTS _ Bio-Linux repo's:
>
> Are you working on this already, or should we attempt to fix it?
>
> Bye,
>
> Tony.
>
> rwt017 at topcat:~$ 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<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)
>>
>
>
> --
> 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<http://bioinformatics.rri.sari.ac.uk>
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