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⇤ ← Revision 44 as of 2017-07-26 19:13:40 →
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Editor: TunayDurmaz
Comment: after 'cmake-refactor-main' merged
← Revision 45 as of 2017-07-26 22:18:39 → ⇥
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Editor: SteveLudtke
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   a. {{{    a. This option installs Anaconda and sets up a specific environment for EMAN2. It requires running the second command in each shell before trying to run EMAN2/SPARX/SPHIRE commands. {{{
conda create -n eman-env eman-deps -c cryoem -c defaults -c conda-forge
source activate eman-env
}}}
   a. This option is easier, and doesn't use an environment, but may be broken (July 2017) due to recent Qt changes in Anaconda {{{
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   a. If you already use anaconda, you may get package conflicts when you install eman dependencies by following the instructions in the previous step. In that case, you need to install eman and its dependencies in its own conda environment.{{{
conda create -n eman-env eman-deps -c cryoem -c defaults -c conda-forge
source activate eman-env
}}}

!!! UNDER CONSTRUCTION !!!

All platforms

Mac OS X, Linux

  1. Download and install Anaconda2 or Miniconda2.

  2. Checkout EMAN2 code from GitHub:cryoem/eman2. 

    cd <some-path-to-keep-eman2-source>
git clone https://github.com/cryoem/eman2.git
  3. Install dependencies. Follow only one of the steps below:

    1. This option installs Anaconda and sets up a specific environment for EMAN2. It requires running the second command in each shell before trying to run EMAN2/SPARX/SPHIRE commands. 

      conda create -n eman-env eman-deps -c cryoem -c defaults -c conda-forge
source activate eman-env

    2. This option is easier, and doesn't use an environment, but may be broken (July 2017) due to recent Qt changes in Anaconda 

      conda install eman-deps -c cryoem -c defaults -c conda-forge          # Mac OSX
conda install eman-deps=*=np18* -c cryoem -c defaults -c conda-forge  # Linux

      Listing the channels explicitly can be avoided by specifying them in $HOME/.condarc, see conda documentation for more details, https://conda.io/docs/using/index.html.

  4. Out-of-source builds are recommended, so work in a directory outside of eman2 source (this is a recommended practice in general, not EMAN2-specific). Note cmake, not ccmake . CMake will automatically find the dependencies. If you want to change any of the CMake values, then use cmake-gui or ccmake. 

    cd <build-directory>
cmake <some-path-to-keep-eman2-source>
  5. If conda is not found in PATH, set CONDA_ROOT to your conda environment directory. It could be the main installation or an environment.
  6. If you set CONDA_ROOT to an environment, make sure to delete any cmake variables that cmake already found, variables like EMAN_INSTALL_PREFIX, EMAN_PREFIX, *_LIBRARY or similar, *_INCLUDE_PATH or similar.

  7. Rerun cmake and continue with make. 

    cmake <some-path-to-keep-eman2-source>
make -j           # "make" should pick up the number of available processors,
make -j4          # but you may specify the number if you like
make install

EMAN2/COMPILE_EMAN2_ANACONDA-PRE-CONDA-ENVIRONMENTS (last edited 2019-11-01 14:27:54 by TunayDurmaz)