Differences between revisions 15 and 49 (spanning 34 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 Miniconda2 or Anaconda2.
1. Miniconda2 (<30MB): Minimal installer that contains conda and Python. Ideal for cluster installations and if you need conda only for EMAN2.
2. 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:
1. 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
```
2. 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.
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.
2. 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

EMAN2/COMPILE_EMAN2_ANACONDA-PRE-CONDA-ENVIRONMENTS (last edited 2019-11-01 14:27:54 by TunayDurmaz)

-  ⇤ ← Revision 15 as of 2017-06-09 03:56:55 → 
  Size: 1015
  Editor: TunayDurmaz
  Comment:
+   ← Revision 49 as of 2017-07-27 03:52:39 → ⇥
  Size: 3024
  Editor: TunayDurmaz
  Comment: add test commands
-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]] or [[https://conda.io/miniconda.html | Miniconda2]].
+. 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.
 Line 17:
-. Optionally, activate an existing conda environment, e.g. `source activate eman-env`.
+. Install dependencies. Follow only one of the steps below:
   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. {{{
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. 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.
-Line 19:
+Line 27:
-. Install dependencies {{{
export MACOSX_DEPLOYMENT_TARGET=10.7  # Yosemite, El Capitan
conda install eman-deps -c cryoem -c defaults -c conda-forge
}}}

 1. Out-of-source builds are recommended, so work in a directory outside of eman2 source. Note '''cmake''', not '''--( 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 28:
+Line 31:
-make -j
make install
-Line 31:
+Line 32:
-== Windows ==
+. 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
}}}