Installing Applications on Sapelo2 - Revision history

Chelsea: /* How to install Conda packages */

2025-06-30T17:58:00Z

How to install Conda packages

← Older revision		Revision as of 13:58, 30 June 2025
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	<pre class="gcommand">		<pre class="gcommand">
	module load Miniforge3/24.7.1-0		module load Miniforge3/24.11.3-0
	conda create -p /home/MyID/busco_conda -c bioconda busco=5.7.1		conda create -p /home/MyID/busco_conda -c bioconda busco=5.7.1
	</pre>		</pre>
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	<pre class="gcommand">		<pre class="gcommand">
	module load Miniforge3/24.7.1-0		module load Miniforge3/24.11.3-0
	conda create -p /home/MyID/busco_conda -c bioconda busco		conda create -p /home/MyID/busco_conda -c bioconda busco
	</pre>		</pre>
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	<pre class="gcommand">		<pre class="gcommand">
	module load Miniforge3/24.7.1-0		module load Miniforge3/24.11.3-0
	conda env list		conda env list
	</pre>		</pre>
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	<pre class="gcommand">		<pre class="gcommand">
	module load Miniforge3/24.7.1-0		module load Miniforge3/24.11.3-0
	source activate /home/MyID/busco_conda		source activate /home/MyID/busco_conda
	</pre>		</pre>
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	<pre class="gcommand">		<pre class="gcommand">
	module load Miniforge3/24.7.1-0		module load Miniforge3/24.11.3-0
	source activate /home/MyID/busco_conda		source activate /home/MyID/busco_conda
	conda list		conda list
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	<pre class="gcommand">		<pre class="gcommand">
	module load Miniforge3/24.7.1-0		module load Miniforge3/24.11.3-0
	source activate /home/MyID/busco_conda		source activate /home/MyID/busco_conda
	conda install scipy=1.14.1		conda install scipy=1.14.1
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	<pre class="gcommand">		<pre class="gcommand">
	module load Miniforge3/24.7.1-0		module load Miniforge3/24.11.3-0
	source activate /home/MyID/busco_conda		source activate /home/MyID/busco_conda
	conda remove scipy		conda remove scipy

Chelsea: /* Installing Python packages in your virtual environment from the source code */

2025-03-12T19:49:17Z

Installing Python packages in your virtual environment from the source code

← Older revision		Revision as of 15:49, 12 March 2025
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	module load Python/3.10.4-GCCcore-11.3.0		module load Python/3.10.4-GCCcore-11.3.0
	. ~/env/mypyenv/bin/activate		. ~/env/mypyenv/bin/activate
	</syntaxhighlight>If you would like to use your Python environment in a Jupyter Notebook, please see [[Using a ~~Conda~~ environment in Jupyter]].		</syntaxhighlight>If you would like to use your Python environment in a Jupyter Notebook, please see [[Using a Python environment in Jupyter]].
	----		----
	[[#top\|Back to Top]]		[[#top\|Back to Top]]

Chelsea: /* Installing Python packages in your virtual environment using pip */

2025-03-12T19:48:41Z

Installing Python packages in your virtual environment using pip

← Older revision		Revision as of 15:48, 12 March 2025
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	module load Python/3.10.4-GCCcore-11.3.0		module load Python/3.10.4-GCCcore-11.3.0
	. ~/env/mypyenv/bin/activate		. ~/env/mypyenv/bin/activate
	</syntaxhighlight>		</syntaxhighlight>If you would like to use your Python environment in a Jupyter Notebook, please see [[Using a Conda environment in Jupyter]].
	----		----
	[[#top\|Back to Top]]		[[#top\|Back to Top]]

Shtsai at 16:04, 18 October 2024

2024-10-18T16:04:37Z

← Older revision		Revision as of 12:04, 18 October 2024
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	Once you have created your Python virtual environment and installed the packages you need, you can use it in a job on the cluster by loading the Python module you used to create the environment and then activating the environment:<syntaxhighlight lang="bash">		Once you have created your Python virtual environment and installed the packages you need, you can use it in a job on the cluster by loading the Python module you used to create the environment and then activating the environment:<syntaxhighlight lang="bash">
	module load Python/3.10.4-GCCcore-11.3.0		module load Python/3.10.4-GCCcore-11.3.0
	. ~/env/mypyenv/activate		. ~/env/mypyenv/bin/activate
	</syntaxhighlight>		</syntaxhighlight>
	----		----

Moses: /* Using your Python virtual environment in a job */

2024-10-18T15:59:58Z

Using your Python virtual environment in a job

← Older revision		Revision as of 11:59, 18 October 2024
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	Once you have created your Python virtual environment and installed the packages you need, you can use it in a job on the cluster by loading the Python module you used to create the environment and then activating the environment:<syntaxhighlight lang="bash">		Once you have created your Python virtual environment and installed the packages you need, you can use it in a job on the cluster by loading the Python module you used to create the environment and then activating the environment:<syntaxhighlight lang="bash">
	module load Python/3.10.4-GCCcore-11.3.0		module load Python/3.10.4-GCCcore-11.3.0
	. ~/~~envs~~/mypyenv/activate		. ~/env/mypyenv/activate
	</syntaxhighlight>		</syntaxhighlight>
	----		----

Shtsai at 15:40, 8 October 2024

2024-10-08T15:40:27Z

← Older revision		Revision as of 11:40, 8 October 2024
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	Once a conda environment is deactivated, its conda layer will be removed from your Linux shell environment.		Once a conda environment is deactivated, its conda layer will be removed from your Linux shell environment.

			If you would like to use your conda environment in a Jupyter Notebook, please see [[Using a Conda environment in Jupyter]].

	----		----

Shtsai: /* How to install Conda packages */

2024-10-08T15:28:21Z

How to install Conda packages

← Older revision		Revision as of 11:28, 8 October 2024
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	</pre>		</pre>

	Once a conda environment is activated, you can list packages installed inside, with their names, versions, and downloading channels. For example, to list packages installed in busco v3.0.2 conda environment:		Once a conda environment is activated, you can list packages installed inside, with their names, versions, and downloading channels. For example, to list packages installed in busco v5.7.1 conda environment:

	<pre class="gcommand">		<pre class="gcommand">

Shtsai: /* How to install Conda packages */

2024-10-08T15:27:47Z

How to install Conda packages

← Older revision		Revision as of 11:27, 8 October 2024
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	To install a software package as a conda environment in user's Sapelo2 home directory, please use the option "-p" to define your environment installation path, e.g., /home/MyID/busco_conda.		To install a software package as a conda environment in user's Sapelo2 home directory, please use the option "-p" to define your environment installation path, e.g., /home/MyID/busco_conda.

	For example, to install busco v3.0.2 conda environment at /home/MyID/busco_conda:		For example, to install busco v5.7.1 conda environment at /home/MyID/busco_conda:

	<pre class="gcommand">		<pre class="gcommand">
	module load Miniforge3/24.7.1-0		module load Miniforge3/24.7.1-0
	conda create -p /home/MyID/busco_conda -c bioconda busco=3.0.2		conda create -p /home/MyID/busco_conda -c bioconda busco=5.7.1
	</pre>		</pre>

	where '''bioconda''' is the channel where busco v3.0.2 source is downloaded. Other common conda channels are, for example, '''conda-forge''', '''r''', '''defaults''', and '''qiime2''', etc.. Please refer to [https://docs.conda.io/projects/conda/en/latest/user-guide/concepts/channels.html# Conda channels]		where '''bioconda''' is the channel where busco v5.7.1 source is downloaded. Other common conda channels are, for example, '''conda-forge''', '''r''', '''defaults''', and '''qiime2''', etc.. Please refer to [https://docs.conda.io/projects/conda/en/latest/user-guide/concepts/channels.html# Conda channels]

	If the busco version 3.0.2 is not specified, the most recent version of busco will be downloaded and installed, i.e.,		If the busco version 5.7.1 is not specified, the most recent version of busco will be downloaded and installed, i.e.,

	<pre class="gcommand">		<pre class="gcommand">
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	</pre>		</pre>

	You can add or install new packages to an existing environment. For example, to install scipy v1.14.1 package to busco v3.0.2 conda environment:		You can add or install new packages to an existing environment. For example, to install scipy v1.14.1 package to busco v5.7.1 conda environment:

	<pre class="gcommand">		<pre class="gcommand">

Shtsai at 15:19, 8 October 2024

2024-10-08T15:19:05Z

← Older revision		Revision as of 11:19, 8 October 2024
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	<pre class="gcommand">		<pre class="gcommand">
	module load ~~Miniconda3~~/4.12.0		module load Miniforge3/24.7.1-0
	conda create -p /home/MyID/busco_conda -c bioconda busco=3.0.2		conda create -p /home/MyID/busco_conda -c bioconda busco=3.0.2
	</pre>		</pre>
Line 473:		Line 473:

	<pre class="gcommand">		<pre class="gcommand">
	module load ~~Miniconda3~~/4.12.0		module load Miniforge3/24.7.1-0
	conda create -p /home/MyID/busco_conda -c bioconda busco		conda create -p /home/MyID/busco_conda -c bioconda busco
	</pre>		</pre>
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	<pre class="gcommand">		<pre class="gcommand">
	module load ~~Miniconda3~~/4.12.0		module load Miniforge3/24.7.1-0
	conda env list		conda env list
	</pre>		</pre>
Line 487:		Line 487:

	<pre class="gcommand">		<pre class="gcommand">
	module load ~~Miniconda3~~/4.12.0		module load Miniforge3/24.7.1-0
	source activate /home/MyID/busco_conda/		source activate /home/MyID/busco_conda
	</pre>		</pre>

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	<pre class="gcommand">		<pre class="gcommand">
	module load ~~Miniconda3~~/4.12.0		module load Miniforge3/24.7.1-0
	source activate /home/MyID/busco_conda/		source activate /home/MyID/busco_conda
	conda list		conda list
	</pre>		</pre>

	You can add or install new packages to an existing environment. For example, to install scipy v1.5.0 package to busco v3.0.2 conda environment:		You can add or install new packages to an existing environment. For example, to install scipy v1.14.1 package to busco v3.0.2 conda environment:

	<pre class="gcommand">		<pre class="gcommand">
	module load ~~Miniconda3~~/4.12.0		module load Miniforge3/24.7.1-0
	source activate /home/MyID/busco_conda/		source activate /home/MyID/busco_conda
	conda install scipy=1.5.0		conda install scipy=1.14.1
	</pre>		</pre>

	Likewise, if the scipy version 1.5.0 is not specified, the most recent version of scipy will be downloaded and installed for you.		Likewise, if the scipy version 1.14.1 is not specified, the most recent version of scipy will be downloaded and installed for you.

	To remove an installed package, e.g., the scipy package, from your conda environment:		To remove an installed package, e.g., the scipy package, from your conda environment:

	<pre class="gcommand">		<pre class="gcommand">
	module load ~~Miniconda3~~/4.12.0		module load Miniforge3/24.7.1-0
	source activate /home/MyID/busco_conda/		source activate /home/MyID/busco_conda
	conda remove scipy		conda remove scipy
	</pre>		</pre>

	To deactivate a conda environment:		To deactivate a conda environment that is currently activated:

	<pre class="gcommand">		<pre class="gcommand">
	~~module load Miniconda3/4.12.0~~		conda deactivate
	conda deactivate ~~/home/MyID/busco_conda/~~
	</pre>		</pre>

Moses: /* Installing Python packages in your virtual environment using pip */

2023-10-31T18:57:30Z

Installing Python packages in your virtual environment using pip

← Older revision		Revision as of 14:57, 31 October 2023
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	</syntaxhighlight>Then all you have to do is pip install the package, and it will be installed in your virtual environment:<syntaxhighlight lang="bash">		</syntaxhighlight>Then all you have to do is pip install the package, and it will be installed in your virtual environment:<syntaxhighlight lang="bash">
	pip install <package name>		pip install <package name>
	</syntaxhighlight>		</syntaxhighlight>or using a requirements.txt file:

			<code>pip install -r requirements.txt</code>

	==== Installing Python packages in your virtual environment from the source code ====		==== Installing Python packages in your virtual environment from the source code ====