Differences between revisions 29 and 43 (spanning 14 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. ```
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
```

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.

```
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 29 as of 2017-06-09 20:16:23 → 
  Size: 1510
  Editor: TunayDurmaz
  Comment: no export needed, eman-deps 2.0 handles it
+   ← Revision 43 as of 2017-07-21 01:44:55 → ⇥
  Size: 2617
  Editor: TunayDurmaz
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 4:
-The following instructions will work with cmake changes introduced in https://github.com/cryoem/eman2/pull/65.
-Line 17:
+Line 15:
-. Optionally, activate an existing conda environment, e.g. `source activate eman-env`. Skip this step, if you don't understand this statement.

 1. Install dependencies {{{
conda install eman-deps -c cryoem -c defaults -c conda-forge
+. 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
-Line 23:
+Line 21:
-. 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'''. {{{
+   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'''. {{{
-Line 26:
+Line 29:
+rm -f CMakeCache.txt  # This is needed to ensure cmake doesn't have any leftovers from previous runs
-Line 32:
+Line 36:
+== Instructions valid for code on branch "cmake-refactor-main". ==
Replaces last bullet from the previous section.
-Line 33:
+Line 39:
-== Windows ==
+. {{{
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
}}}