Differences between revisions 38 and 44 (spanning 6 versions)
⇤ ← Revision 38 as of 2017-06-14 22:04:21 →
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Editor: TunayDurmaz
Comment:
← Revision 44 as of 2017-07-26 19:13:40 → ⇥
Size: 2165
Editor: TunayDurmaz
Comment: after 'cmake-refactor-main' merged
Deletions are marked like this. Additions are marked like this.
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 1. Optionally, activate an existing conda environment, e.g. `source activate eman-env`. Skip this step, if you don't understand this statement. However, if you already use anaconda, you may get package conflicts when you install eman dependencies in the next step. In that case, you need to install eman and its dependencies in its own conda environment and skip the next step, "Install dependencies".{{{  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.{{{
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 1. Install dependencies {{{
conda install eman-deps -c cryoem -c defaults -c conda-forge
}}} 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.

 1. Out-of-source builds are recommended, so work in a directory outside of eman2 source (this is generally true, 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'''. {{{		  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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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 \
                                       -DEMAN_CXX_FLAGS="-D_GLIBCXX_USE_CXX11_ABI=0" # This flag will be set in cmake with https://github.com/cryoem/eman2/pull/80		 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>

!!! 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>
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)