Anaconda - Revision history

Leo at 15:55, 22 April 2024

2024-04-22T15:55:23Z

← Older revision		Revision as of 15:55, 22 April 2024
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	\|Removes an environment		\|Removes an environment
	\|-		\|-
	\|conda install package=version		\|<code>conda install package=version</code>
	\|Install a specific version of a package		\|Install a specific version of a package
			\|-
			\|<code>conda clean --all [--dry-run]</code>
			\|Cleanup unused files in the pkgs directory. Pass in <code>--dry-run</code> to see what would have been done.
	\|}		\|}

Leo: Added HPC category

2021-12-30T02:11:57Z

Added HPC category

← Older revision		Revision as of 02:11, 30 December 2021
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	{{Navbox Linux}}		{{Navbox Linux}}
	[[Category:Linux]]		[[Category:Linux]]
			[[Category:HPC]]
	[[Category:LinuxUtilities]]		[[Category:LinuxUtilities]]

Leo at 19:28, 17 December 2021

2021-12-17T19:28:13Z

← Older revision		Revision as of 19:28, 17 December 2021
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	== Installation ==		==Installation==

	{{highlight\|lang=terminal\|code=		{{highlight\|lang=terminal\|code=
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	}}		}}

	== Usage ==		==Usage==

	{\| class="wikitable"		{\| class="wikitable"
	! Command		!Command
	! Description		!Description
	\|-		\|-
	\| conda create -n env_name pip python=version		\|<code>conda create -n env_name pip python=version</code>
	\| env_name is the name of the new environment. Packages follow.		\|env_name is the name of the new environment. Packages follow.
	\|-		\|-
	\| conda env [-n] list		\|<code>conda env [-n] list</code>
	\| Lists environments. -n lists deactivated environments.		\|Lists environments. -n lists deactivated environments.
	\|-		\|-
	\| conda list		\|<code>conda list</code>
	\| Environment currently activated		\|Environment currently activated
	\|-		\|-
	\| conda info –envs		\|<code>conda info –envs</code>
	\| View list of packages installed on certain environment:		\|View list of packages installed on certain environment:
	\|-		\|-
	\| conda list -n env_name package_name		\|<code>conda list -n env_name package_name</code>
	\| See if a certain package is installed.		\|See if a certain package is installed.
	\|-		\|-
	\| conda activate env_name		\|<code>conda activate env_name</code>
	\| Activates an environment		\|Activates an environment
	\|-		\|-
	\| conda deactivate		\|<code>conda deactivate</code>
	\| Exit from an environment		\|Exit from an environment
	\|-		\|-
	\| conda env remove -n env_name		\|<code>conda env remove -n env_name</code>
	\| Removes an environment		\|Removes an environment
			\|-
			\|conda install package=version
			\|Install a specific version of a package
	\|}		\|}

	== Tasks ==		==Tasks==
	=== Setup an R environment ===
			=== Configuration ===
			Some conda configs including channels are set in the ~/.condarc file.

			===Setup an R environment===
	To create and install a particular package in a new environment, such as R:		To create and install a particular package in a new environment, such as R:
	{{highlight\|lang=terminal\|code=		{{highlight\|lang=terminal\|code=
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	}}		}}

	=== Setup R Bioconda ===		===Setup R Bioconda===
	To get Bioconda working, you will need to add the following channels first:		To get Bioconda working, you will need to add the following channels first:

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	This occurred only on the account with an old version of Miniconda and was fixed by installing the latest version of Anaconda and re-running all the commands above to reinstall the package.		This occurred only on the account with an old version of Miniconda and was fixed by installing the latest version of Anaconda and re-running all the commands above to reinstall the package.

	== See Also ==		== Troubleshooting ==
	* https://linuxize.com/post/how-to-install-anaconda-on-centos-7/
			=== Conda is stuck solving environment ===
			Conda being slow or stuck at solving an environment is a common problem. When running conda with the -vvv option, it eventually prints "Invoking SAT with clause count ###" with some ever-changing (never really decreasing) number while consuming an entire CPU core.

			Anaconda has a blog post about some possible mitigations at https://www.anaconda.com/blog/understanding-and-improving-condas-performance.

			Some suggestions for those running into this issue are to:

			# Remove the conda-forge channel if possible. Replace it with conda-metachannel.
			# Specify a specific package rather than using a broad package spec. Eg. <code>conda install conda=4.11.0</code>
			# Set "<code>conda config --set channel_priority strict</code>"
			# Create a fresh environment and start all over.

			There are [https://github.com/conda/conda/issues/8051#issuecomment-663849490 some other solutions] that other users on GitHub reported to have helped including:

			# Set conda-forge last in the channels list in <code>~/.condarc</code>
			# Set <code>channel_priority to flexible</code>. (which goes against Anaconda's suggestion above)

			==See Also==

			*https://linuxize.com/post/how-to-install-anaconda-on-centos-7/

	{{Navbox Linux}}[[Category:Linux]]		{{Navbox Linux}}
			[[Category:Linux]]
	[[Category:LinuxUtilities]]		[[Category:LinuxUtilities]]

Leo: Added category

2020-06-14T23:29:29Z

Added category

← Older revision		Revision as of 23:29, 14 June 2020
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	== See Also ==		== See Also ==
	* https://linuxize.com/post/how-to-install-anaconda-on-centos-7/		* https://linuxize.com/post/how-to-install-anaconda-on-centos-7/

			{{Navbox Linux}}[[Category:Linux]]
			[[Category:LinuxUtilities]]

Leo: /* Setup R Bioconda */

2020-05-19T19:47:59Z

Setup R Bioconda

← Older revision		Revision as of 19:47, 19 May 2020
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	}}		}}

			After installing a package, it does not load and results in the following error:
			{{highlight\|lang=text\|code=
			‘GenomeInfoDbData’ was installed before R 4.0.0: please re-install it
			}}

			This occurred only on the account with an old version of Miniconda and was fixed by installing the latest version of Anaconda and re-running all the commands above to reinstall the package.

	== See Also ==		== See Also ==
	* https://linuxize.com/post/how-to-install-anaconda-on-centos-7/		* https://linuxize.com/post/how-to-install-anaconda-on-centos-7/

Leo at 17:30, 19 May 2020

2020-05-19T17:30:05Z

@@ Line 55: / Line 55: @@
 |}
-== Other ==
+== Tasks ==
 To create and install a particular package in a new environment, such as R:
 {{highlight|lang=terminal|code=
@@ Line 66: / Line 67: @@
 (base) $ conda deactivate
 }}
 == See Also ==
 * https://linuxize.com/post/how-to-install-anaconda-on-centos-7/

Leo: /* Usage */

2020-03-18T17:34:14Z

Usage

← Older revision		Revision as of 17:34, 18 March 2020
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	== Usage ==		== Usage ==

	{\|		{\| class="wikitable"
	! Command		! Command
	! Description		! Description

Leo at 17:33, 18 March 2020

2020-03-18T17:33:33Z

@@ Line 24: / Line 24: @@
 }}
 To create and install a particular package in a new environment, such as R:
 {{highlight|lang=terminal|code=

Leo at 23:36, 20 January 2020

2020-01-20T23:36:48Z

@@ Line 10: / Line 10: @@
 [no] >>> yes
 }}
 == See Also ==
 * https://linuxize.com/post/how-to-install-anaconda-on-centos-7/

Leo: /* Installation */

2020-01-20T19:51:11Z

Installation

← Older revision		Revision as of 19:51, 20 January 2020
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	Do you wish the installer to initialize Anaconda3		Do you wish the installer to initialize Anaconda3
	in your /gpfs/home/lleung/.bashrc ? [yes\|no]		in your /gpfs/home/lleung/.bashrc ? [yes{{!}}no]
	[no] >>> yes		[no] >>> yes

	}}		}}




	== See Also ==		== See Also ==
	* https://linuxize.com/post/how-to-install-anaconda-on-centos-7/		* https://linuxize.com/post/how-to-install-anaconda-on-centos-7/