[phenixbb] Install Problem Linux CentOs 5

[Billy Poon]

Hi Matthew,

Sorry for the issue! With the latest Phenix release, the minimum required
Python version is 2.5 because there were some changes in the syntax. This
affects the installation step. The default version of Python on CentOS 5 is
2.4.

A workaround would be to use the Python shipped with an older version of
Phenix (e.g. 1.12) to run the installation. To do so,

1) Type "cd <phenix-installer-1.13-2998 directory>"
2) Type "source <phenix-1.12 directory>/phenix_env.sh" or the csh version
if you're using csh. This sets up the newer Python
3) Type "libtbx.python ./bin/install.py". This uses the newer Python for
running the installation script. If you look at ./install, it just calls
./bin/install.py with the system provided Python. You can add the
"--prefix" flag as well to the command if you want to install Phenix
somewhere else.

Let me know if that does not work. Thanks!

--
Billy K. Poon
Research Scientist, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
1 Cyclotron Road, M/S 33R0345
Berkeley, CA 94720
Tel: (510) 486-5709
Fax: (510) 486-5909
Web: https://phenix-online.org

On Wed, Jan 3, 2018 at 11:00 AM, Whitley, Matthew J <mjw100 at pitt.edu> wrote:

> Hello all,
>
>
> We are trying to install the new 1.13-2998 release of Phenix on 64 bit
> Linux CentOs 5 and have run into some problems.  We are logged in as root,
> and we were able to unzip and untar the archive with no problem.  However,
> when we run the install script, we immediately get the following errors:
>
>
> root at linux7 phenix-installer-1.13-2998-intel-linux-2.6-x86_64-centos5]#
> ./install
>
> Traceback (most recent call last):
>
>   File "./bin/install.py", line 20, in ?
>
>     from libtbx.auto_build import install_distribution
>
>   File "/usr/local/phenix-installer-1.13-2998-intel-linux-2.6-x86_
> 64-centos5/lib/libtbx/auto_build/install_distribution.py", line 75, in ?
>
>     from libtbx.auto_build import install_base_packages
>
>   File "/usr/local/phenix-installer-1.13-2998-intel-linux-2.6-x86_
> 64-centos5/lib/libtbx/auto_build/install_base_packages.py", line 864
>
>     os.chmod(filename, 0o755)  # set permissions to -rwxr-xr-x
>
>                            ^
>
> SyntaxError: invalid syntax
>
> [root at linux7 phenix-installer-1.13-2998-intel-linux-2.6-x86_64-centos5]#
>
>
> Any idea as to what the source of the problem is and how to get around it?
>
>
> Thanks for your help.
>
>
> Matthew Whitley
>
>
> ---
> Matthew J. Whitley, Ph.D.
> Research Instructor
> Department of Pharmacology & Chemical Biology
> University of Pittsburgh School of Medicine
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
> Unsubscribe: phenixbb-leave at phenix-online.org
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20180103/bb7d2825/attachment.htm>