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.