<div dir="ltr">Hi Matthew,<div><br><div>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.</div></div><div><br></div><div>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,</div><div><br></div><div>1) Type "cd <phenix-installer-1.13-2998 directory>"</div><div>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</div><div>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.</div><div><br></div><div>Let me know if that does not work. Thanks!</div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><div>--</div><div><span style="font-size:12.8000001907349px">Billy K. Poon</span><br></div></div><div>Research Scientist, Molecular Biophysics and Integrated Bioimaging</div><div>Lawrence Berkeley National Laboratory</div><div>1 Cyclotron Road, M/S 33R0345</div><div>Berkeley, CA 94720</div><div>Tel: (510) 486-5709</div><div>Fax: (510) 486-5909</div><div>Web: <a href="https://phenix-online.org" target="_blank">https://phenix-online.org</a></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On Wed, Jan 3, 2018 at 11:00 AM, Whitley, Matthew J <span dir="ltr"><<a href="mailto:mjw100@pitt.edu" target="_blank">mjw100@pitt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<p style="margin-top:0;margin-bottom:0">Hello all,</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">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:</p>
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</p>
<p style="margin-right:0px;margin-left:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">root@linux7 phenix-installer-1.13-2998-<wbr>intel-linux-2.6-x86_64-<wbr>centos5]# ./install</span></p>
<p style="margin-right:0px;margin-left:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">Traceback (most recent call last):</span></p>
<p style="margin-right:0px;margin-left:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures"> File "./bin/install.py", line 20, in ?</span></p>
<p style="margin-right:0px;margin-left:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures"> from libtbx.auto_build import install_distribution</span></p>
<p style="margin-right:0px;margin-left:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures"> File "/usr/local/phenix-installer-<wbr>1.13-2998-intel-linux-2.6-x86_<wbr>64-centos5/lib/libtbx/auto_<wbr>build/install_distribution.py"<wbr>, line 75, in ?</span></p>
<p style="margin-right:0px;margin-left:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures"> from libtbx.auto_build import install_base_packages</span></p>
<p style="margin-right:0px;margin-left:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures"> File "/usr/local/phenix-installer-<wbr>1.13-2998-intel-linux-2.6-x86_<wbr>64-centos5/lib/libtbx/auto_<wbr>build/install_base_packages.<wbr>py", line 864</span></p>
<p style="margin-right:0px;margin-left:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures"> os.chmod(filename, 0o755) # set permissions to -rwxr-xr-x</span></p>
<p style="margin-right:0px;margin-left:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures"> ^</span></p>
<p style="margin-right:0px;margin-left:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">SyntaxError: invalid syntax</span></p>
<p></p>
<p style="margin-right:0px;margin-left:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">[root@linux7 phenix-installer-1.13-2998-<wbr>intel-linux-2.6-x86_64-<wbr>centos5]#</span></p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">Any idea as to what the source of the problem is and how to get around it?</p>
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</p>
<p style="margin-top:0;margin-bottom:0">Thanks for your help.</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">Matthew Whitley</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
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<div>Matthew J. Whitley, Ph.D.</div>
<div>Research Instructor</div>
<div>Department of Pharmacology & Chemical Biology</div>
<div>University of Pittsburgh School of Medicine</div>
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