Differences between revisions 2 and 3
⇤ ← Revision 2 as of 2019-05-18 10:57:35 →
Size: 1466
Editor: TunayDurmaz
Comment: Add git instructions
← Revision 3 as of 2019-07-03 04:28:13 → ⇥
Size: 3115
Editor: TunayDurmaz
Comment: upgraded cmake, unpinned boost
Deletions are marked like this. Additions are marked like this.
Line 1: Line 1:
== Setup Python 3 Environment == == Setup Python 2 Environment With CMake 3.14 ==
Line 3: Line 3:
=== Existing Miniconda/Anaconda Installations ===

 1. Create a new environment with python 3{{{
conda create -n eman-deps-15 eman-deps=15 -c cryoem/label/py3 -c cryoem -c defaults -c conda-forge
}}}
 1. Use the activation command printed at the end of the previous command's run to activate the new conda environment {{{
conda activate eman-deps-15
or
source activate eman-deps-15
}}}
 1. To switch to another conda environment, first deactivate your current environment{{{
conda deactivate
or
source deactivate
}}}
 [[https://github.com/cryoem/eman2/pull/407|PR: Upgrade CMake to 3.14]]
Line 26: Line 11:
 1. Update conda {{{
conda update conda -c defaults
}}}
 1. Install eman-deps with python 3{{{
conda install eman-deps=15 -c cryoem/label/py3 -c cryoem -c defaults -c conda-forge		  1. Install eman-deps with cmake 3.14.{{{
conda config --set auto_update_conda False
conda install conda=4.6.14
conda install eman-deps=14.2 cmake=3.14 conda=4.6.14 -c cryoem/label/dev -c cryoem -c defaults -c conda-forge
Line 34: Line 18:

=== Existing Miniconda/Anaconda Installations ===

 1. Pin your conda, you need to do this only once. Skip this step, if you have already done it.{{{
conda config --set auto_update_conda False
conda install conda=4.6.14
}}}
 1. Create a new environment.{{{
conda create -n eman-deps-14.2 eman-deps=14.2 cmake=3.14 -c cryoem/label/dev -c cryoem -c defaults -c conda-forge
}}}
 1. Use the activation command printed at the end of the previous command's run to activate the new conda environment.{{{
conda activate eman-deps-14.2
or
source activate eman-deps-14.2
}}}
 1. To switch to another conda environment, first deactivate your current environment.{{{
conda deactivate
or
source deactivate
}}}



== Setup Python 2 Environment with Boost 1.66 ==

[[https://github.com/cryoem/eman2/pull/410|PR: Build with Boost versions 1.65-1.66]]

=== New Miniconda Installations ===

 1. Download and install [[https://repo.continuum.io/miniconda/|Miniconda]].
 1. Add the new installation to PATH.{{{
export PATH=<new miniconda path>/bin:$PATH
}}}
 1. Install eman-deps with cmake 3.14.{{{
conda config --set auto_update_conda False
conda install conda=4.6.14
conda install eman-deps=14.3 cmake=3.14 boost=1.66 conda=4.6.14 -c cryoem/label/boost -c cryoem -c defaults -c conda-forge
}}}



=== Existing Miniconda/Anaconda Installations ===

 1. Pin your conda, you need to do this only once. Skip this step, if you have already done it.{{{
conda config --set auto_update_conda False
conda install conda=4.6.14
}}}
 1. Create a new environment.{{{
conda create -n eman-deps-14.2 eman-deps=14.3 cmake=3.14 -c cryoem/label/boost -c cryoem -c defaults -c conda-forge
}}}
 1. Use the activation command printed at the end of the previous command's run to activate the new conda environment.{{{
conda activate eman-deps-14.3
or
source activate eman-deps-14.3
}}}
 1. To switch to another conda environment, first deactivate your current environment.{{{
conda deactivate
or
source deactivate
}}}
Line 35: Line 82:
 1. Update eman2 source {{{ Checkout a branch and build as usual.
 1. Update eman2 source.{{{
Line 37: Line 85:
git checkout py3-dev git checkout <branch>
Line 40: Line 88:
 1. Activate the python 3 environment, if it is a conda environment{{{
conda activate eman-deps-15		  1. Activate conda environment, if it is a conda environment.{{{
conda activate <env-name>
Line 43: Line 91:
source activate eman-deps-15
}}} or edit PATH to have the miniconda installation with python 3 as the first entry.
 1. Move into your build directory {{{
cd <python 3 build directory>		 source activate <env-name>
}}} or edit PATH to have the miniconda installation as the first entry.
 1. Move into your build directory.{{{
cd <build directory>
Line 48: Line 96:
 1. Build and install {{{  1. Build and install.{{{

Setup Python 2 Environment With CMake 3.14

PR: Upgrade CMake to 3.14

New Miniconda Installations

  1. Download and install Miniconda.

  2. Add the new installation to PATH.

    export PATH=<new miniconda path>/bin:$PATH

  3. Install eman-deps with cmake 3.14.

    conda config --set auto_update_conda False
conda install conda=4.6.14
conda install eman-deps=14.2 cmake=3.14 conda=4.6.14 -c cryoem/label/dev -c cryoem -c defaults -c conda-forge

Existing Miniconda/Anaconda Installations

  1. Pin your conda, you need to do this only once. Skip this step, if you have already done it.

    conda config --set auto_update_conda False
conda install conda=4.6.14

  2. Create a new environment.

    conda create -n eman-deps-14.2 eman-deps=14.2 cmake=3.14 -c cryoem/label/dev -c cryoem -c defaults -c conda-forge

  3. Use the activation command printed at the end of the previous command's run to activate the new conda environment.

    conda activate eman-deps-14.2
or
source activate eman-deps-14.2

  4. To switch to another conda environment, first deactivate your current environment.

    conda deactivate
or
source deactivate

Setup Python 2 Environment with Boost 1.66

PR: Build with Boost versions 1.65-1.66

New Miniconda Installations

  1. Download and install Miniconda.

  2. Add the new installation to PATH.

    export PATH=<new miniconda path>/bin:$PATH

  3. Install eman-deps with cmake 3.14.

    conda config --set auto_update_conda False
conda install conda=4.6.14
conda install eman-deps=14.3 cmake=3.14 boost=1.66 conda=4.6.14 -c cryoem/label/boost -c cryoem -c defaults -c conda-forge

Existing Miniconda/Anaconda Installations

  1. Pin your conda, you need to do this only once. Skip this step, if you have already done it.

    conda config --set auto_update_conda False
conda install conda=4.6.14

  2. Create a new environment.

    conda create -n eman-deps-14.2 eman-deps=14.3 cmake=3.14 -c cryoem/label/boost -c cryoem -c defaults -c conda-forge

  3. Use the activation command printed at the end of the previous command's run to activate the new conda environment.

    conda activate eman-deps-14.3
or
source activate eman-deps-14.3

  4. To switch to another conda environment, first deactivate your current environment.

    conda deactivate
or
source deactivate

Build

Checkout a branch and build as usual.

  1. Update eman2 source.

    cd <source directory>
git checkout <branch>
git pull --rebase

  2. Activate conda environment, if it is a conda environment.

    conda activate <env-name>
or
source activate <env-name>
    or edit PATH to have the miniconda installation as the first entry.

  3. Move into your build directory.

    cd <build directory>

  4. Build and install.

    cmake <eman2 source directory>
make
make install