Changes between Version 1 and Version 2 of cypress/conda_virtual_environment

Timestamp:

08/08/25 11:45:36 (3 months ago)

Author:

fuji

Comment:

—

cypress/conda_virtual_environment

@@ -3 +3 @@
 The virtual environment is an isolated execution environment that allows software applications to run independently of the host.
 
-[[Image(https://docs.google.com/drawings/d/e/2PACX-1vRT8y0469t50JiKqEbZYCRnDD2hSxdWGqBpWJmRoWRQlksC9-GaXAG0v8KjApAkdCWBVI4Icuv8jS4s/pub?w=960&h=200)]]
+[[Image(https://docs.google.com/drawings/d/e/2PACX-1vRT8y0469t50JiKqEbZYCRnDD2hSxdWGqBpWJmRoWRQlksC9-GaXAG0v8KjApAkdCWBVI4Icuv8jS4s/pub?w=960&h=300)]]
 
 == CONDA virtual environment and package manager ==
@@ -27 +27 @@
 anaconda/2.*.* provides python2. anacoda3/* provides python3. Modules under /share/apps/centos7/modulefiles work on CentOS 7 nodes only.
 
+'''Because software installed via Conda may not be compatible with older operating systems, it's recommended to use the latest Anaconda distribution.'''
+
+===== Using anaconda3/2023.07 =====
+* Start an interactive session on the CentOS7 node.
+{{{
+idev --partition=centos7 -t 8
+}}}
+ This allocates a single CentOS 7 node for a duration of 8 hours.
+* Load module,
+{{{
+module load anaconda3/2023.07
+}}}
+* Display the version of CONDA.
+{{{
+$ conda --version
+conda 23.7.3
+}}}
+
+== Basic Commands ==
+||= Command =||= Description =||
+||{{{ conda init }}}||  Initializing CONDA environment.  ||
+||{{{ conda info  }}}||  Display the CONDA system info.  ||
+||{{{ conda --help }}}||  To learn about available built-in commands.  ||
+||{{{ conda env list }}}||  List all available environments. ||
+||{{{ conda create –n VIRT_ENV }}}||  Create a virtual environment with the CONDA. ||
+||{{{ source activate VIRT_ENV }}}||  Activate the CONDA virtual environment. ||
+||{{{ conda install PACKAGE-NAME  }}}||  Install some packages with the CONDA installation. ||
+||{{{ conda deactivate  }}}||  Deactivates the CONDA virtual environment. ||
+
+== Configuring the CONDA environment on Cypress ==
+By default, Conda environments are stored in your home directory. However, we recommend using your group’s project directory instead. You can set the '''CONDA_ENVS_PATH''' environment variable to specify where Anaconda should create and locate your environments. For example:
+{{{
+export CONDA_ENVS_PATH=/lustre/project/mygroup/myuser/conda-envs
+}}}
+Or {{{ conda config --add envs_dirs /path/to/envs }}} command does the same. For example:
+{{{
+conda config --add envs_dirs /lustre/project/mygroup/myuser/conda-envs
+}}}
+By default, the package cache directory is created in your home directory, which will take up a large space as you use 'conda'. To change the package cache directory,
+{{{
+conda config --add pkgs_dirs /lustre/project/mygroup/myuser/conda-pkgs
+}}}
+The configuration settings are stored in the ~/.condarc file. You can modify this file manually to customize Conda’s behavior.
+
+||= Command =||= Description =||
+||{{{ conda config --add envs_dirs /path/to/envs }}}||  Adding a desired path to the environment directory.  ||
+||{{{ conda config --add pkgs_dirs /path/to/pkgs  }}}||  Adding a desired path to the package directory.  ||
+||{{{ conda config --remove envs_dirs /path/to/envs }}}||  Removing a desired path to the environment directory.  ||
+||{{{ vi ~/.condarc }}}||  Manually add paths to CONDA config file. ||
+
+
+== Installation commands ==
+||= Command =||= Description =||
+||{{{ conda install PACKAGE-NAME }}}||  Install a software package.  ||
+||{{{ conda install PACKAGE-NAME=version   }}}||  Install a software package with a particular version. ||
+||{{{ conda install PACKAGE-NAME=version –c CHANNEL}}}||  Install a software package with a particular version from a specific channel.  ||
+||{{{ conda install PACKAGE-NAME1 PACKAGE-NAME2 … }}}||  Install multiple packages. ||
+
+
+== Some useful commands ==
+||= Command =||= Description =||
+||{{{ conda search PACKAGE-NAME  }}}||  Searching a software package.  ||
+||{{{ conda search PACKAGE-NAME=version --info   }}}||  Search a software package with a particular version and display the information. ||
+||{{{ conda update/upgrade PACKAGE-NAME}}}||  Update a package to the latest version.  ||
+||{{{ conda uninstall/remove PACKAGE-NAME }}}||  Uninstall or remove a package.  ||
+
+== Channels ==
+Conda channels are sources or repositories from which Conda downloads packages.
+- Default Channels: These are pre-configured when you install Conda. They’re hosted by Anaconda, Inc.
+- Community Channels: Popular alternatives maintained by the community, such as: {{{conda-forge}}}, {{{bioconda}}}.
+
+=== Configuring CONDA channels ===
+||= Command =||= Description =||
+||{{{ conda config --show channels  }}}||  List available channels.  ||
+||{{{ conda config --prepend channels   }}}||  Adding a channel with high priority ||
+||{{{ conda config --append channels}}}||  Adding a channel with low priority.  ||
+The configuration settings are stored in the ~/.condarc file. You can modify this file manually to customize Conda’s behavior.
+
+==== Some widely used channels ====
+||= Channel=||= Description =||
+||conda-forge||  Community supported for general purposes. ||
+||bioconda||  Community supported for bioinformatics. ||
+||nvidia / cuda||  NVIDIA official support.  ||
+||pytorch||  Pytorch official support.  ||
+
+
+----
+
+= Example Installation =
+== Installing samtools ==
+[https://www.htslib.org/ Samtools] is a suite of programs designed for working with high-throughput sequencing data. You can download the source code and build it directly on Cypress, or install it in your virtual environment via the '''bioconda''' channel.
+* Create a virtual environment, myenv1:
+{{{
+conda create –n myenv1
+}}}
+* Activate conda virtual environment:
+{{{
+source activate myenv1
+}}}
+* Search for the Samtools version via the '''bioconda''' channel:
+{{{
+conda search samtools -c bioconda
+}}}
+* Install version 1.10:
+{{{
+conda install samtools=1.10 -c bioconda
+}}}
+
+* Check the version of samtools
+{{{
+conda list
+}}}