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The following instructions will work with cmake changes introduced in https://github.com/cryoem/eman2/pull/65.
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1. Download and install Anaconda/Miniconda (:TODO: links).  1. Download and install [[https://www.continuum.io/downloads | Anaconda2]] or [[https://conda.io/miniconda.html | Miniconda2]].
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2. Optionally, activate an existing conda environment, i.e. `source activate eman-env`.

3. Checkout EMAN2 code from GitHub, (link here). {{{		  1. Checkout EMAN2 code from [[https://github.com/cryoem/eman2 | GitHub:cryoem/eman2]]. {{{
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4. Out-of-source builds are recommended, so work in a directory outside of eman2 source. {{{  1. Install dependencies. Follow only one of the steps below:
   a. {{{
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.

   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
}}}

 1. 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'''. {{{
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cmake <some-path-to-keep-eman2-source>
make -j		 rm -f CMakeCache.txt # This is needed to ensure cmake doesn't have any leftovers from previous runs
cmake <some-path-to-keep-eman2-source> -DENABLE_CONDA=ON
make -j # "make" should pick up the number of available processors,
make -j4 # but you may specify the number if you like
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# == Linux == == Instructions valid for code on branch "cmake-refactor-main". ==
Replaces last bullet from the previous section.
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== Windows ==		  1. {{{
cmake <some-path-to-keep-eman2-source>
}}}
 1. If conda is not found in PATH, set CONDA_ROOT to your conda environment directory. It could be the main installation or an environment.
 1. 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.
 1. 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
}}}

!!! 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. 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.

    2. 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

  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>
rm -f CMakeCache.txt  # This is needed to ensure cmake doesn't have any leftovers from previous runs
cmake <some-path-to-keep-eman2-source> -DENABLE_CONDA=ON
make -j           # "make" should pick up the number of available processors,
make -j4          # but you may specify the number if you like
make install

Instructions valid for code on branch "cmake-refactor-main".

Replaces last bullet from the previous section. 

  1. cmake <some-path-to-keep-eman2-source>
  2. If conda is not found in PATH, set CONDA_ROOT to your conda environment directory. It could be the main installation or an environment.
  3. 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.

  4. 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)