Differences between revisions 32 and 45 (spanning 13 versions)

!!! UNDER CONSTRUCTION !!!

All platforms

Mac OS X, Linux

Download and install Anaconda2 or Miniconda2.

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:
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.
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.
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 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)

-  ⇤ ← Revision 32 as of 2017-06-11 21:29:05 → 
  Size: 1702
  Editor: TunayDurmaz
  Comment:
+   ← Revision 45 as of 2017-07-26 22:18:39 → ⇥
  Size: 2229
  Editor: SteveLudtke
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
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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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-. 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.

 1. Install dependencies {{{
conda install eman-deps -c cryoem -c defaults -c conda-forge
+. Install dependencies. Follow only one of the steps below:
   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 {{{
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
-Line 23:
+Line 25:
-. 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'''. {{{
+. 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'''. {{{
-Line 26:
+Line 28:
-cmake <some-path-to-keep-eman2-source> -DENABLE_CONDA=ON
+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>