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| = !!! UNDER CONSTRUCTION !!! = | = Anaconda based Build, All Platforms = |
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| = All platforms = | Note that even with a source build it may be difficult to get this working on systems with very old operating system installs. We normally try to support OS versions 6-7 years old. Please report any problems. |
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| 1. Download and install [[https://www.continuum.io/downloads | Anaconda2]] or [[https://conda.io/miniconda.html | Miniconda2]]. | 1. Download and install [[https://conda.io/miniconda.html | Miniconda2]] or [[https://www.continuum.io/downloads | Anaconda2]]. a. '''Miniconda2 (<30MB)''': Minimal installer that contains conda and Python. Ideal for cluster installations and if you need conda only for EMAN2. a. '''Anaconda2 (270-350 MB)''': Entire Anaconda distribution, open data science platform powered by Python. Includes packages like Jupyter, Spyder, Anaconda Navigator. |
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| a. {{{ 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. 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.{{{ |
a. This option installs EMAN2 dependencies into a conda environment. It requires running the second command in each shell before trying to run EMAN2/SPARX/SPHIRE commands. {{{ |
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| a. This option is easier, and doesn't use an environment. It will work with Miniconda, but will not work with Anaconda versions 4.2.0 (2016-09-28) and newer, because the bundled Qt version was upgraded from version 4 to 5. {{{ 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. |
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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 make -j # "make" should pick up the number of available processors, make -j4 # but you may specify the number if you like make install |
cmake <some-path-to-keep-eman2-source> |
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| 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. This step most likely will be needed only if you use '''cmake-gui'''. a. 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. a. Rerun cmake. 1. Continue with '''make'''. {{{ make -j # "make" should pick up the number of available processors, make -j4 # but you may specify the number if you like make install && make test make test-verbose # this will output more test details and may be helpful to identify failures }}} |
Anaconda based Build, All Platforms
Note that even with a source build it may be difficult to get this working on systems with very old operating system installs. We normally try to support OS versions 6-7 years old. Please report any problems.
Mac OS X, Linux
Download and install Miniconda2 or Anaconda2.
Miniconda2 (<30MB): Minimal installer that contains conda and Python. Ideal for cluster installations and if you need conda only for EMAN2.
Anaconda2 (270-350 MB): Entire Anaconda distribution, open data science platform powered by Python. Includes packages like Jupyter, Spyder, Anaconda Navigator.
Checkout EMAN2 code from GitHub:cryoem/eman2.
cd <some-path-to-keep-eman2-source> git clone https://github.com/cryoem/eman2.git
- Install dependencies. Follow only one of the steps below:
This option installs EMAN2 dependencies into a conda environment. 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
This option is easier, and doesn't use an environment. It will work with Miniconda, but will not work with Anaconda versions 4.2.0 (2016-09-28) and newer, because the bundled Qt version was upgraded from version 4 to 5.
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.
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>
If conda is not found in PATH, set CONDA_ROOT to your conda environment directory. It could be the main installation or an environment. This step most likely will be needed only if you use cmake-gui.
- 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.
- Rerun cmake.
Continue with make.
make -j # "make" should pick up the number of available processors, make -j4 # but you may specify the number if you like make install && make test make test-verbose # this will output more test details and may be helpful to identify failures