how to uninstall biome and reinstall release version

[metasaur]

Good morning,

I apologize for the incompetency, but I accidentally downloaded and installed the development version of biome and I believe its causing instability when I try to perform the command biom table-summarize...check it out

qiime@qiime-VirtualBox:~/PICRUSt_Dev040814/picrust-master$ biom

usage: biom <command> [<args>]

The currently available commands are:

   add-metadata        Add metadata to a BIOM table

   convert             Convert to/from the BIOM table format

   show-install-info   Provide information about the biom-format installation

   subset-table        Subset a BIOM table

   validate-table      Validate a BIOM-formatted file

The following commands could not be loaded:

   summarize-table     Error: cannot import name write_or_print_list_of_strings

See 'biom help <command>' for more information on a specific command.

If I do print_qiime_config.py here is the output I get:

System information

==================

         Platform: linux2

   Python version: 2.7.3 (default, Dec 19 2013, 03:13:59)  [GCC 4.6.3]

Python executable: /home/qiime/qiime_software/python-2.7.3-release/bin/python

Dependency versions

===================

                     PyCogent version: 1.5.3

                        NumPy version: 1.7.1

                   matplotlib version: 1.3.1

                  biom-format version: 1.3.1-dev

                         qcli version: 0.1.0

                QIIME library version: 1.8.0

                 QIIME script version: 1.8.0

        PyNAST version (if installed): 1.2.2

                      Emperor version: 0.9.3

RDP Classifier version (if installed): rdp_classifier-2.2.jar

          Java version (if installed): 1.6.0_27

So is there a chance the version of biom I have is messing this up? In the case that it is I have tried to download the release version of biom and reinstall but, every method I try still leaves me with this dev version. I'm fairly new to linux, but if I try doing some sort of purge command and type in the biom program it can never find it. Any suggestions?

Thanks!

Blake

[Adam robbins-pianka]

Hi Blake,

The development version of biom depends on another package, pyqi (canonically pronounced "pie-chee").  If you install pyqi, you should be good to go!

Best,

Adam

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[Adam robbins-pianka]

Sorry, that was kind of an incomplete answer; if you want to uninstall your current version of biom, you can just remove the "biom" directory from its location in your PYTHONPATH.  To find out where biom is living, execute this on your command line:

python -c "import biom; print biom"

It should tell you the path to an __init__.py file.  Just remove the directory containing that file (simply called "biom")

You can get the most recent release of biom here: https://pypi.python.org/pypi/biom-format/

Best,

Adam

[metasaur]

-Adam

Thanks for the quick reply! I really appreciate it. Just FYI, I installed pyqi as you suggested and then attempted to use the summarize-table in biom again and it still gave me the error I had before. So I tried reinstalling biom (like I said I'm a fairly new linux user so when it comes to problem solving I use the shotgun approach and guess and check method) thinking that this time when it installed it would have all its dependencies and work. This was not the case however, I was still unable to use the summarize-table function. Not sure what caused this issyue

So from your second post I was able to successfully uninstall biom and then successfully reinstall the release version and everything is working great now! 

Thanks so much,

Blake

[Adam robbins-pianka]

Glad to hear it's working again. Sorry my first suggestion didn't pan out, perhaps it was a PYTHONPATH issue. You can test of python is aware of pyqi in a similar fashion as before:

python -c 'import pyqi; print pyqi'

Best,
Adam