[Bio-Linux] Qiime

[Tim Booth]

Hi Alec,

The QIIME quick self-test you get with "print_qiime_config.py -t" always
gives some errors and probably always will because of the way it is set
up.  I verify the QIIME installation with the more comprehensive
regression tests rather than trying to match all the exact software
versions they suggest.  So yes, QIIME seems to work fine with the newer
(actually over a year old) FastTree even though it complains about the
version.

On the second question - If I knew a truly easy way to install QIIME I
wouldn't have gone to all the trouble packaging it for APT!  More
seriously, I would use their VirtualBox version if possible, because
gathering all the old versions of tools needed for the old QIIME will be
hard work.

Cheers,

TIM

On Thu, 2014-09-04 at 14:38 +0100, Alec Colebrook-Clark wrote:
> Hi again!
> 
>  
> 
> Also what would be the easiest way to install qiime 1.7? Im trying
> qiime-deploy but having some difficulty.
> 
>  
> 
> Thanks
> 
> Alec
> 
>  
> 
> From: Alec Colebrook-Clark [mailto:aleleb at sahfos.ac.uk] 
> Sent: 04 September 2014 10:08
> To: bio-linux at nebclists.nerc.ac.uk
> Subject: [Bio-Linux] Qiime
> 
> 
>  
> 
> Hi Tim,
> 
>  
> 
> I’ve just had a person mention that the dependencies for qiime 1.8 are
> throwing out some errors (shown below). 
> 
>  
> 
>  qiime > print_qiime_config.py -t
> 
> System information
> ==================
> Platform:    linux2
> Python version:    2.7.3 (default, Feb 27 2014, 19:58:35) [GCC 4.6.3]
> Python executable:    /usr/bin/python
> 
> Dependency versions
> ===================
> PyCogent version:    1.5.3
> NumPy version:    1.6.1
> matplotlib version:    1.1.1rc
> biom-format version:    1.1.2
> qcli version:    0.1.0
> QIIME library version:    1.8.0
> QIIME script version:    1.8.0-1biolinux1
> PyNAST version (if installed):    1.2.2
> Emperor version:    0.9.3
> RDP Classifier version (if installed):    rdp_classifier.jar
> Java version (if installed):    1.7.0_55
> 
> QIIME config values
> ===================
> blastmat_dir:    /usr/share/ncbi/data
> jobs_to_start:    1
> pynast_template_alignment_blastdb:    None
> qiime_scripts_dir:    /usr/lib/qiime/bin/
> template_alignment_lanemask_fp:    /usr/share/qiime/data/lanemask_in_1s_and_0s
> working_dir:    .
> pynast_template_alignment_fp:    /usr/share/qiime/data/core_set_aligned.fasta.imputed
> python_exe_fp:    python
> temp_dir:    /tmp
> blastall_fp:    blastall
> seconds_to_sleep:    60
> cluster_jobs_fp:    None
> F..............F....F.......FF...F.
> ======================================================================
> FAIL: test_FastTree_supported_version (__main__.QIIMEDependencyFull)
> FastTree is in path and version is supported
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/qiime/bin/print_qiime_config.py", line 364, in
> test_FastTree_supported_version
> % ('.'.join(map(str,acceptable_version)), version_string))
> AssertionError: Unsupported FastTree version. 2.1.3 is required, but
> running 2.1.7.
> 
> ======================================================================
> FAIL: test_gdata_install (__main__.QIIMEDependencyFull)
> gdata is installed
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/qiime/bin/print_qiime_config.py", line 754, in
> test_gdata_install
> self.assertTrue(pass_test, "gdata is not installed.")
> AssertionError: gdata is not installed.
> 
> ======================================================================
> FAIL: test_pplacer_supported_version (__main__.QIIMEDependencyFull)
> pplacer is in path and version is supported
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/qiime/bin/print_qiime_config.py", line 655, in
> test_pplacer_supported_version
> "which components of QIIME you plan to use.")
> AssertionError: pplacer not found. This may or may not be a problem
> depending on which components of QIIME you plan to use.
> 
> ======================================================================
> FAIL: test_rtax_supported_version (__main__.QIIMEDependencyFull)
> rtax is in path and version is supported
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/qiime/bin/print_qiime_config.py", line 634, in
> test_rtax_supported_version
> "which components of QIIME you plan to use.")
> AssertionError: rtax not found. This may or may not be a problem
> depending on which components of QIIME you plan to use.
> 
> ======================================================================
> FAIL: test_sourcetracker_installed (__main__.QIIMEDependencyFull)
> sourcetracker is installed
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/qiime/bin/print_qiime_config.py", line 421, in
> test_sourcetracker_installed
> ("SOURCETRACKER_PATH is not set. This is "
> AssertionError: SOURCETRACKER_PATH is not set. This is only important
> if you plan to use SourceTracker.
> 
> ======================================================================
> FAIL: test_usearch_supported_version (__main__.QIIMEDependencyFull)
> usearch is in path and version is supported
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/qiime/bin/print_qiime_config.py", line 714, in
> test_usearch_supported_version
> % ('.'.join(map(str,acceptable_version)), version_string))
> AssertionError: Unsupported usearch version. (5, 2, 236).(5, 2, 236)
> is required, but running 
> USEARCH is not freely redistributable and is thus not included in the
> default QIIME package.
> You may obtain a personal copy of the 32-bit program at no charge.
> 
> To use this feature, please go to:
> http://www.drive5.com/usearch/download.html
> 
> Download USEARCH v5.2.236, then:
> sudo mv usearch* /usr/local/bin/usearch
> sudo chmod a+x /usr/local/bin/usearch
> 
> You probably also want to install USEARCH 6.1
> as /usr/local/bin/usearch61
> 
> .
> 
> ----------------------------------------------------------------------
> Ran 35 tests in 0.221s
> 
> FAILED (failures=6)
> 
>  
> 
>  
> 
> As far as I know qiime has always been maintained via the apt-get
> command. Are other users seeing the same errors? I am particularly
> puzzled by fasttree. Will qiime 1.8 work with fast tree 2.1.7 but
> throw the error in the qiimw config test?
> 
>  
> 
> Thanks
> 
> Alec
> 
> 

-- 
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