[Pytom-mail] "Missing lxml in pytom" has been solved, but another problem happened!

[Haixin S. <su...@ho...>]

Hi Tom and all


The missing lxml problem has been solved. It looks like the eman2 and pytom environment interfere with each other. After I disabled eman2, changed PATH setting and reinstalled pytom, the lxml is now available under pytom. However, the UI still does not work.  In fact, I have exactly the same UI issue for the newly installed pytom on my home ubuntu laptop today. The work station in my lab is also an ubuntu 16.04. Has anyone complied a successful Pytem on an Ubuntu system?


UI is not important if command lines work. However, I am not yet able to get the command lines work. I stuck with an IOError when trying the localization.py ("IOError: Reference XML should either have Particles or Filename for ParticleList"). I have attached the job.xml document, and included the screen-output in this email. The job.xml was modified from the example in the directory "pytom-tutorial/RibosFromLysate/localization", and I could find any problem with it.


Please advise what I can do to figure out the cause of the problem.


Thank you!


Haixin



---------
hsui@Thinkpad-HR16395:~/subtomo$ /home/hsui/suilab_apps/pytom/bin/pytom /home/hsui/suilab_apps/pytom/bin/localization.py job.xml 2 2 2
PyTom v0.971

This license affects the software package PyTom and all the herein distributed source / data files.
Authors:
Thomas Hrabe
Yuxiang Chen
Friedrich Foerster

Copyright (c) 2008-2016
Max-Planck-Institute for Biochemistry
Dept. Molecular Structural Biology
82152 Martinsried, Germany
http://www.pytom.org

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

The complete license can be obtained from
http://www.gnu.org/licenses/gpl-3.0.html.

Traceback (most recent call last):
  File "/home/hsui/suilab_apps/pytom/bin/localization.py", line 82, in <module>
    startLocalizationJob(jobName, splitX, splitY, splitZ, doSplitAngles=False)
  File "/home/hsui/suilab_apps/pytom/bin/localization.py", line 10, in startLocalizationJob
    job.fromXMLFile(filename)
  File "/home/hsui/suilab_apps/pytom/basic/structures.py", line 74, in fromXMLFile
    self.fromStr(lines)
  File "/home/hsui/suilab_apps/pytom/basic/structures.py", line 47, in fromStr
    self.fromXML(root)
  File "/home/hsui/suilab_apps/pytom/localization/peak_job.py", line 111, in fromXML
    self.reference.fromXML(ref)
  File "/home/hsui/suilab_apps/pytom/basic/structures.py", line 587, in fromXML
    raise IOError('Reference XML should either have Particles or Filename for ParticleList')
IOError: Reference XML should either have Particles or Filename for ParticleList



________________________________
From: Haixin Sui <su...@ho...>
Sent: Friday, September 29, 2017 5:56 PM
To: pyt...@li...
Subject: [Pytom-mail] Missing lxml in pytom?

Hi ,

I have lxml installed and it works fine in pyton environment. However, lxml can not be found in pytom environment.
My pytom environment seems to be incorrect. Any idea what to do to fix it? I wonder if this is related to why the UI of the pytom did not work here.

The test results are listed in this email.

Thanks!

Haixin

Python 2.7
---------------------------------
hsui@dalian:~/subtomo$ python
Python 2.7.12 (default, Nov 19 2016, 06:48:10)
[GCC 5.4.0 20160609] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from lxml import etree
>>>
-----------------------------------


pytom:
-----------------------------------
hsui@dalian:~/subtomo$ pytom
PyTom v0.971

This license affects the software package PyTom and all the herein distributed source / data files.
......(removed for easy reading)
Python 2.7.13 | packaged by conda-forge | (default, May  2 2017, 12:48:11)
[GCC 4.8.2 20140120 (Red Hat 4.8.2-15)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from lxml import etree
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ImportError: No module named lxml
-------------------------