Bioconda - Revision history

Dmitri: /* Centrally Installed BioConda */

2024-11-14T21:55:11Z

Centrally Installed BioConda

← Older revision		Revision as of 21:55, 14 November 2024
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	#SBATCH --time=0-01:00:00		#SBATCH --time=0-01:00:00
	# ====================================		# ====================================
	# Activate ~~Conda and then the environment~~.		# Activate BioConda.
	source /global/software/bioconda/init-2024-10		source /global/software/bioconda/init-2024-10

Dmitri: /* Available modules */

2024-11-14T21:54:03Z

Available modules

← Older revision		Revision as of 21:54, 14 November 2024
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	You can load the module		You can load the module
	<pre>		<pre>
	$ module load ~~biconda~~/2024-10		$ module load bioconda/2024-10

	### !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ###		### !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ###

Dmitri: /* Installing your own personal BioConda */

2024-11-14T21:40:59Z

Installing your own personal BioConda

@@ Line 87: / Line 87: @@
 * '''Install the required packages'''
   conda install -c bioconda samtools star salmon kraken
 = Links =
 [[ARC Software pages]]

Dmitri: /* Using Conda in your job scripts */

2024-11-14T21:40:49Z

Using Conda in your job scripts

@@ Line 73: / Line 73: @@
 starfish                  0.2.2              pyhdfd78af_0    bioconda
 </pre>
 == Installing your own personal BioConda ==

Dmitri: /* Available modules */

2024-11-14T21:40:14Z

Available modules

@@ Line 73: / Line 73: @@
 starfish                  0.2.2              pyhdfd78af_0    bioconda
 </pre>
 == Installing your own personal BioConda ==

Dmitri: /* Installing your own personal BioConda */

2024-11-14T21:34:11Z

Installing your own personal BioConda

← Older revision		Revision as of 21:34, 14 November 2024
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	If the preinstalled versions provided by the modules '''do not work for you''', you can		If the preinstalled versions provided by the modules '''do not work for you''', you can
	* '''Install your own Conda''', following [[Conda on ARC \| these instructions]].		* '''Install your own Conda''', following [[Conda on ARC#Installing Conda \| these instructions]].

	* '''Create a new BioConda environment''':		* '''Create a new BioConda environment''':

Dmitri: /* Available modules */

2024-11-14T21:33:10Z

Available modules

@@ Line 61: / Line 61: @@
 ....
 </pre>
 = Links =
 [[ARC Software pages]]

Dmitri: /* Available modules */

2024-11-14T21:26:06Z

Available modules

← Older revision		Revision as of 21:26, 14 November 2024
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	$ module avail bioconda		$ module avail bioconda
	-------------------- /global/software/Modules/4.6.0/modulefiles -----------------		-------------------- /global/software/Modules/4.6.0/modulefiles -----------------
	bioconda/~~2018~~.11 bioconda/~~conda3~~		bioconda/2024-10
			</pre>

			* '''BioConda/2024-10''' is based on the <code>bioconda</code> and <code>conda-forge</code> channels.
			: It does not depend nor use the Anaconda <code>base</code> and <code>anaconda</code> channels to avoid any licensing complications.
			: It was installed in October 2024 and includes a large number of more popular BioConda packages.

			You can load the module
			<pre>
			$ module load biconda/2024-10

			### !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ###
			This is a stub module. It does not activate the central BioConda install.
			If you want to activate BioConda/2024-10 please use the following command in your job script:

			source /global/software/bioconda/init-2024-10

			Module activation does not work propely for this BioConda due to technical limitaions.
			This may change in the future.
			### !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ###

	~~$ module load biconda/2018.11~~		Loading bioconda/2024-10
	Loading bioconda/~~2018.11~~		ERROR: Module evaluation aborted
	~~Loading requirement~~: ~~bioconda/conda3~~
	</pre>		</pre>
			The message indicate that the module cannot activate BioConda correctly, so you have to use the command
			source /global/software/bioconda/init-2024-10

			instead.

	~~Check~~ software		Once you have BioConda activated you can check the software
	<pre>		<pre>
	$ samtools --version		$ samtools --version
	samtools 1.9		samtools 1.21
	Using htslib 1.9		Using htslib 1.21
	Copyright (C) ~~2018~~ Genome Research Ltd.		Copyright (C) 2024 Genome Research Ltd.

	$ salmon --version		$ salmon --version
	~~salmon~~ 0.11.3		version : 0.8.1

	$ kraken --version		$ kraken --version
	Kraken version 0.10.~~6-unreleased~~		Kraken version 1.1.1
	Copyright 2013-~~2015~~, Derrick Wood (~~dwood~~@~~cs.jhu~~.edu)		Copyright 2013-2019, Derrick Wood, Jennifer Lu (jlu26@jhmi.edu)
	</pre>		</pre>

	Get the list of installed packages:		Get the full list of installed packages:
	<pre>		<pre>
	$ conda list		$ conda list
	~~....~~
	....		....
	</pre>		</pre>

Dmitri: /* General */

2024-03-21T16:31:56Z

General

@@ Line 4: / Line 4: @@
 * List of available packages: https://bioconda.github.io/conda-package_index.html
 = Links =
 [[ARC Software pages]]

Dmitri: Created page with "= General = * Home page: https://bioconda.github.io/index.html * List of available packages: https://bioconda.github.io/conda-package_index.html = Links = ARC Software pages"

2024-03-21T16:25:33Z

Created page with "= General = * Home page: https://bioconda.github.io/index.html * List of available packages: https://bioconda.github.io/conda-package_index.html = Links = ARC Software pages"

New page

= General =

* Home page: https://bioconda.github.io/index.html

* List of available packages: https://bioconda.github.io/conda-package_index.html

= Links =
[[ARC Software pages]]