Install EM Hole Finder on CentOS 7

I spoke about the leginon/appion pair. You have leginon for automatic EM data acquisition, and appion for processing. They are super-big complicated software packages, designed to work under CentOS.6. Unfortunately, we are very modern, and we use CentOS.7, so, it’s time to have fun upgrading something that is not mine!

I will follow the original installation guide as described on the Appion page. Even I will use the same paths.  I will quote the steps, and comment them as they fail.

yum install git python-virtualenv libjpeg-devel -y  --> OK
 easy_install pip  --> OK
 cd /opt  --> OK, of course
 git clone https://github.com/hbradlow/em_hole_finder  --> OK
 ls --> OK, of course
 cd em_hole_finder --> OK, of course
 virtualenv env 
New python executable in env/bin/python
Installing Setuptools....................done
Installing Pip............................done.

–> OK, now we have (env) on the prompt. I continue.

source env/bin/activate  --> OK
 pip install numpy  

Downloading/unpacking numpy
 Downloading numpy-1.11.2.tar.gz (4.2MB): 4.2MB downloaded
 Running setup.py egg_info for package numpy
 Running from numpy source directory.

 blas_opt_info:
 blas_mkl_info:
 libraries mkl_rt not found in

.. it goes no for a while, but at the end
Successfully installed numpy
Cleaning up...

–> OK, then , despite of the NOT AVAILABLE messages. I will ignore them later on also.

 pip install Cython
Downloading/unpacking Cython
 Downloading Cython-0.25.1.tar.gz (1.7MB): 1.7MB downloaded
 Running setup.py egg_info for package Cython
 Unable to find pgen, not compiling formal grammar. 
 warning: no files found matching '*.pyx' 
under directory 'Cython/Debugger/Tests'
 warning: no files found matching '*.pxd' 
under directory 'Cython/Debugger/Tests'
 warning: no files found matching '*.h' 
under directory 'Cython/Debugger/Tests'
 warning: no files found matching '*.pxd' 
under directory 'Cython/Utility'
Installing collected packages: Cython
 Running setup.py install for Cython
 Unable to find pgen, not compiling formal grammar.

.. it goes on for a while, but at the end

Successfully installed Cython
Cleaning up...

–> OK. Next one

pip install PIL
Downloading/unpacking PIL
 Could not find any downloads that satisfy the requirement PIL
Cleaning up...
No distributions at all found for PIL
Storing complete log in /root/.pip/pip.log

Similar trials fail to find the package also.

pip install PIL --allow-external PIL --allow-unverified PIL

So it looks like there is no PIL for us. Google is recommending to install  pillow instead.

pip install pillow
Downloading/unpacking pillow
 Downloading Pillow-3.4.2.tar.gz (10.8MB): 10.8MB downloaded
 Running setup.py egg_info for package pillow
.. compilation goes here for a while ...
----------------------
 PIL SETUP SUMMARY
 --------------------
 version Pillow 3.4.2
 platform linux2 2.7.5 (default, Sep 15 2016, 22:37:39)
 [GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
 ------------------
 --- JPEG support available
 *** OPENJPEG (JPEG2000) support not available
 --- ZLIB (PNG/ZIP) support available
 *** LIBIMAGEQUANT support not available
 *** LIBTIFF support not available
 --- FREETYPE2 support available
 *** LITTLECMS2 support not available
 *** WEBP support not available
 *** WEBPMUX support not available
 ---------
 To add a missing option, make sure you have the required
 library and headers.

–> OK, we go ahead

 pip install scipy
Downloading/unpacking scipy
 Downloading scipy-0.18.1.tar.gz (13.1MB): 13.1MB downloaded
 Running setup.py egg_info for package scipy

.. also we get the NOT AVAILABLE message for openblas_lapack_info
Cleaning up...
Command ... 
failed with error code 1 in /opt/em_hole_finder/env/build/scipy

–> maybe NOK, but we go ahead. The error seems to be on installing some headers for the local python. Just in case I try to install scipy with yum

yum install openblas lapack gcc-gfortran python-scipy

–> also NOK, but we go ahead

pip install scikit-image
 Downloading/unpacking scikit-image
 Downloading scikit-image-0.12.3.tar.gz (20.7MB): 20.7MB downloaded

.. a lot of dependent packages are downloaded and installed..
Cleaning up...

Command ... 
failed with error code 1 in /opt/em_hole_finder/env/build/scipy

–> also NOK, but we go ahead, as before

pip install ipython
Successfully installed ipython setuptools 
decorator pickleshare simplegeneric traitlets 
prompt-toolkit pygments pexpect ipython-genutils 
six wcwidth ptyprocess
Cleaning up...

–> OK, we go ahead

pip install wsgiref
Requirement already satisfied (use --upgrade to upgrade): 
wsgiref in /usr/lib64/python2.7
Cleaning up..

–> So OK.

The rest goes smoothly. Once added to the module, the initial tests look fine despite of the errors with the headers. To fix that, we move out of our (env) and try to install them with the “default” python.  Scypy I have already. I can test it opening a pyton prompt and typing “import scipy”.

pip install cython
...
Successfully installed cython-0.25.1
pip install scikit-image
...
Collecting scikit-image
 Using cached scikit-image-0.12.3.tar.gz
...
Successfully installed cycler-0.10.0 dask-0.12.0 matplotlib-1.5.3 
networkx-1.11 pyparsing-2.1.10 python-dateutil-2.6.0 
pytz-2016.7 scikit-image-0.12.3 toolz-0.8.0

–> So OK. Now to wait the output from the users.

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About bitsanddragons

A traveller, an IT professional and a casual writer
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