Differences between revisions 5 and 46 (spanning 41 versions)

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 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 5 as of 2017-05-15 19:59:21 → 
  Size: 923
  Editor: TunayDurmaz
  Comment: install dependencies with meta-package
+   ← Revision 46 as of 2017-07-26 22:22:20 → ⇥
  Size: 2429
  Editor: SteveLudtke
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
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-= !!! UNDER CONSTRUCTION !!! =
+= Anaconda based Build, All Platforms =
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-= All platforms =

The following instructions will work with cmake changes introduced in https://github.com/cryoem/eman2/pull/65.
+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.
-Line 9:
+Line 7:
-. Download and install [[https://www.continuum.io/downloads | Anaconda2]]/[[https://conda.io/miniconda.html | Miniconda2]].
+. Download and install [[https://www.continuum.io/downloads | Anaconda2]] or [[https://conda.io/miniconda.html | Miniconda2]].
-Line 17:
+Line 15:
-. Install dependencies {{{
conda install eman-meta -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
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+   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 21:
+Line 25:
-. Optionally, activate an existing conda environment, i.e. `source activate eman-env`.

 1. Out-of-source builds are recommended, so work in a directory outside of eman2 source. {{{
+. 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 27:
+Line 29:
-make -j
+}}}
 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 30:
+Line 38:
-# == Linux ==


== Windows ==