[BioPython] problem installing mxTextTools
Nick Matzke
matzke at berkeley.edu
Fri Jul 25 07:37:15 UTC 2008
Or, even better, version 2 of mxTextTools should be downloaded and used,
it installs easily, and is supposed to work better anyway, however you
can only find this from this page:
http://biopython.org/wiki/Download#Optional_Software
http://www.egenix.com/www2002/python/eGenix-mx-Extensions-v2.x.html/
...but not the "complete instructions" page:
http://biopython.org/DIST/docs/install/Installation.html#htoc9
(Sorry if this stuff is annoying but probably someone else naive will
have these same problems in the future.)
Cheers,
Nick
Nick Matzke wrote:
> Hi all,
>
> An update -- I found a solution by copying the .pck file the download
> actually gave me to the filename that the install was apparently looking
> for. This was not exactly obvious (!!!!) but apparently it worked:
>
> <snipping output of solution which made the email too long for the
> auto-moderator>
>
> ==============================
> wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt
> nick$ cd build
>
> wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt/build
> nick$ ls
> build-darwin-8.11.0-Power_Macintosh-py2.4_ucs4.pck
> temp.darwin-8.11.1-i386-2.3_ucs2
> lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4 temp.macosx-10.3-fat-2.4_ucs2
>
> wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt/build
> nick$ cp build-darwin-8.11.0-Power_Macintosh-py2.4_ucs4.pck
> build-macosx-10.3-fat-py2.4_ucs2.pck
>
> wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt/build
> nick$ cd ..
>
> wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt
> nick$ sudo python setup.py build --skip installPassword:
> running build
> skipping the build process and reusing the existing build files and data
> restoring build data from a previous build run
> running install
> running install_lib
> running build_ext
> creating
> /Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx
>
> copying build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/__init__.py
> ->
> /Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx
>
> creating
>
> [...]
>
> writing byte-compilation script '/tmp/tmpIfqFr6.py'
> /Library/Frameworks/Python.framework/Versions/2.4/Resources/Python.app/Contents/MacOS/Python
> -O /tmp/tmpIfqFr6.py
> removing /tmp/tmpIfqFr6.py
> running install_data
>
>
> wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt
> nick$ more README
> =============================================================================
>
> eGenix mx Base Distribution for Python
> -----------------------------------------------------------------------------
>
>
> Source Installation
> -------------------
>
> In order to build and install the distribution, run
>
> python setup.py install
>
> Then change to some other directory and try to import the packages:
>
> $ cd ~
> $ python
> Python 2.4.3 (#1, May 9 2007, 00:48:21)
> [GCC 3.3.5 20050117 (prerelease) (SUSE Linux)] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
> >>> from mx.DateTime import now
> >>> print now()
> 2007-05-30 11:00:03.24
> >>>
>
> Note that trying this from the installation directory will cause
> Python to pick up the source tree packages which do not contain the
> compiled binaries. This will likely fail with strange error messages.
>
>
> Prebuilt Installation
> ---------------------
>
> If you have downloaded a prebuilt distribution archive, the
> installation is slightly different. You have to run
>
> python setup.py build --skip install
>
> Then follow the same instructions as for the source installation.
>
>
> Copyrights & Licenses
> ---------------------
>
> The software in this distribution is copyrighted and protected by
> international, EU and German copyright law. Please see the COPYRIGHT
> file for details.
>
> The software is licensed to you under the eGenix.com Public License as
> stated in the LICENSE file of the distribution directory. Some
> subpackages may contain third-party software which is licensed under
> different conditions. Please see the documentation and/or LICENSE
> files of the subpackages for details.
>
> If in doubt, please check the web-site at http://www.egenix.com or
> contact sales at egenix.com for more information on copyright, licensing
> conditions and authorized use.
>
>
> -----------------------------------------------------------------------------
>
> eGenix.com GmbH
> Pastor-Loeh-Str. 48
> D-40764 Langenfeld
> Germany
> info at egenix.com
>
> wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt
> nick$
>
> wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt
> nick$
>
> wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt
> nick$ cd ..
>
> wright:/bioinformatics/pythonstuff nick$ ls
> egenix python_notes.rtf
> egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt
>
> wright:/bioinformatics/pythonstuff nick$ python
> Python 2.4.4 (#1, Oct 18 2006, 10:34:39)
> [GCC 4.0.1 (Apple Computer, Inc. build 5341)] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
>
> >>> from mx.DateTime import now
> >>>
>
> >>> print now()
> 2008-07-24 22:39:17.66
> >>>
> ==============================
>
> Several hours of my life gone, but yay!
>
> Cheers,
> Nick
>
--
====================================================
Nicholas J. Matzke
Ph.D. student, Graduate Student Researcher
Huelsenbeck Lab
4151 VLSB (Valley Life Sciences Building)
Department of Integrative Biology
University of California, Berkeley
Lab website: http://ib.berkeley.edu/people/lab_detail.php?lab=54
Dept. personal page:
http://ib.berkeley.edu/people/students/person_detail.php?person=370
Lab personal page:
http://fisher.berkeley.edu/~edna/lab_test/members/matzke.html
Lab phone: 510-643-6299
Cell phone: 510-301-0179
Email: matzke at berkeley.edu
Office hours for Bio1B: Biology: Plants, Evolution, Ecology
VLSB 2013, Monday 1-1:30 (some TA there for all hours during work week)
Mailing address:
Department of Integrative Biology
3060 VLSB #3140
Berkeley, CA 94720-3140
====================================================
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