Conda - Revision history

PeterThorpe at 08:56, 28 July 2020

2020-07-28T08:56:26Z

2019-03-13T14:35:25Z

‎conda

2019-03-13T12:53:23Z

‎conda

2019-02-20T08:37:06Z

‎conda

2019-02-18T12:08:58Z

‎conda

2019-02-18T09:51:02Z

‎conda

2019-02-18T09:49:42Z

‎conda

2019-02-14T09:42:43Z

‎conda installs: This is the future

2019-02-14T09:40:33Z

‎conda installs: This is the future

2019-02-14T09:39:56Z

‎conda installs: This is the future

← Older revision		Revision as of 08:56, 28 July 2020
Line 135:		Line 135:
	if this still doesnt work try:		if this still doesnt work try:
	conda config --set channel_priority strict		conda config --set channel_priority strict
		+
		+
		+	More samtools problems, try:
		+	https://github.com/bioconda/bioconda-recipes/issues/12100
		+	samtools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
		+	conda install -c bioconda samtools openssl=1.0

← Older revision		Revision as of 14:35, 13 March 2019
Line 132:		Line 132:
	conda config --remove channels conda-forge		conda config --remove channels conda-forge
	conda config --add channels conda-forge		conda config --add channels conda-forge
		+
		+	if this still doesnt work try:
		+	conda config --set channel_priority strict

← Older revision		Revision as of 12:53, 13 March 2019
Line 124:		Line 124:

	conda update -n base conda		conda update -n base conda
		+
		+
		+	'''conda hanging on solving environment'''
		+
		+	Can you try this please, then try re installing the beastie package.
		+
		+	conda config --remove channels conda-forge
		+	conda config --add channels conda-forge

← Older revision		Revision as of 08:37, 20 February 2019
Line 119:		Line 119:
	remake this env from the bioconda channel:		remake this env from the bioconda channel:
	conda create -n unicyclerENV -c bioconda unicycler		conda create -n unicyclerENV -c bioconda unicycler
		+
		+
		+	to update the base conda, if required
		+
		+	conda update -n base conda

← Older revision		Revision as of 12:08, 18 February 2019
Line 118:		Line 118:

	remake this env from the bioconda channel:		remake this env from the bioconda channel:
−	conda create -n ~~unicycler~~ -c bioconda unicycler	+	conda create -n unicyclerENV -c bioconda unicycler

← Older revision		Revision as of 09:51, 18 February 2019
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	install from the bioconda channel: -c bioconda		install from the bioconda channel: -c bioconda
	conda install -c bioconda samtools		conda install -c bioconda samtools
		+
		+	or specifically the problem was found with unicycler:
		+	remove the old unicycler failed install:
		+	conda remove --name unicyclerENV --all
		+
		+	remake this env from the bioconda channel:
		+	conda create -n unicycler -c bioconda unicycler

← Older revision		Revision as of 09:49, 18 February 2019
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	installing packages: https://bioconda.github.io/conda-recipe_index.html		installing packages: https://bioconda.github.io/conda-recipe_index.html
		+
		+
		+	'''conda and samtools problems'''
		+
		+	Bascially sometimes this get installed from the wrong channel. This may happen with other tools. We havent come across this yet.
		+
		+	The problem will look like this if you try to use samtools:
		+	samtools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory).
		+
		+	The solution:
		+	install from the bioconda channel: -c bioconda
		+	conda install -c bioconda samtools

← Older revision		Revision as of 09:42, 14 February 2019
Line 1:		Line 1:
−	= conda ~~installs:~~ This is the future=	+	= conda =
		+
		+	'''This is the future'''
		+

	Conda on Marvin on a per user basis, so you have total control over it.		Conda on Marvin on a per user basis, so you have total control over it.

@@ Line 9: / Line 9: @@
   source ~/.bashrc
-This will make a user specific version of conda avible to you.
+This will make a user specific version of conda avaible to you.
 '''To find the package you want, search here:'''
+'''
-  https://bioconda.github.io/conda-recipe_index.html
+  https://bioconda.github.io/conda-recipe_index.html'''
 '''or google search:''' - as there are multiple channels!!

@@ Line 74: / Line 74: @@
-To list all the environments you have created:
+To list all the environments you have created (you will forget the envs after a while, so name them well!!):
   conda info –envs
 installing packages: https://bioconda.github.io/conda-recipe_index.html