Differences between revisions 20 and 40 (spanning 20 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
```
  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 \
                                       -DEMAN_CXX_FLAGS="-D_GLIBCXX_USE_CXX11_ABI=0"  # This flag will be set in cmake with https://github.com/cryoem/eman2/pull/80
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 20 as of 2017-06-09 04:38:21 → 
  Size: 1422
  Editor: TunayDurmaz
  Comment:
+   ← Revision 40 as of 2017-06-16 08:06:13 → ⇥
  Size: 1913
  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.
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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.
+. Install dependencies. Follow only one of the steps below:
   a. {{{
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.
-Line 19:
+Line 20:
-. Install dependencies {{{
export MACOSX_DEPLOYMENT_TARGET=10.7  # only for MacOSX (Yosemite, El Capitan)
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.
+   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
}}}
-Line 24:
+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 )--'''. {{{
+. 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 28:
-cmake <some-path-to-keep-eman2-source>
make -j      # 'make' should pick the number of available processors,
make -j4     # but you may specify the number if you like
+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 \
                                       -DEMAN_CXX_FLAGS="-D_GLIBCXX_USE_CXX11_ABI=0"  # This flag will be set in cmake with https://github.com/cryoem/eman2/pull/80
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 35:
-== Windows ==