Differences between revisions 22 and 45 (spanning 23 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 22 as of 2017-06-09 17:40:32 → 
  Size: 1559
  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.
 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.
+. 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
}}} 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.
-Line 19:
+Line 25:
-. 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'''. {{{
+. 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:
-export MACOSX_DEPLOYMENT_TARGET=10.7  # only for MacOSX (Yosemite, El Capitan)
-Line 28:
+Line 29:
-make -j      # 'make' should pick the number of available processors,
make -j4     # but you may specify the number if you like
+}}}
 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
-Line 32:
+Line 38:
-== Windows ==