Available Software - Revision history

PeterThorpe: /* module load approach */

2018-10-23T14:38:00Z

‎module load approach

2018-10-23T14:37:49Z

‎Conda. THIS IS THE FUTURE. We highly recommend this

2018-10-23T14:37:31Z

‎Conda. THIS IS THE FUTURE. We highly recommend this

2018-10-23T14:36:07Z

‎Introduction

2016-12-12T15:57:37Z

2016-12-07T13:05:13Z

2016-12-07T13:04:29Z

2016-09-02T12:34:50Z

2016-09-01T14:20:31Z

2016-09-01T14:20:17Z

← Older revision		Revision as of 14:38, 23 October 2018
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	= module load approach =		= module load approach =
		+
		+
		+	The cluster uses the widely used Environment Modules system to manage the wide range of software available for Bioinformatics. It attempts to take care of the necessary environment for running the software, and so minmise (although not erradicate) errors.
		+

	To see all the available software, the command to type is:		To see all the available software, the command to type is:

@@ Line 36: / Line 36: @@
 ''
 installing packages:
   https://bioconda.github.io/recipes.html
 = module load approach =

@@ Line 17: / Line 17: @@
 )	We strongly advise using environments: https://conda.io/docs/user-guide/tasks/manage-environments.html . You can do this in many ways. Please see the link for more details (here you can specifiy eact version etc ..). The easiest usage would be:    e.g.  conda create -n NAME_OF_ENV PACKAGE_TO_INSTALL (pick a package you are interested in from here: installing packages: https://bioconda.github.io/recipes.html ). Roary is a package name as an example.
-''conda create -n roary roary
+ ''conda create -n roary roary
-conda activate roary
+ conda activate roary
-conda update roary
+ conda update roary
-''
+ ''
 You are now ready to use this package.
-''Conda deactivate''        to leave this environment.
+ ''Conda deactivate''        to leave this environment.
@@ Line 33: / Line 33: @@
 To list all the environments you have created:
-''conda info –envs
+ ''conda info –envs
 ''
-installing packages: https://bioconda.github.io/recipes.html
+installing packages:

@@ Line 1: / Line 1: @@
 = Introduction =
 The cluster uses the widely used Environment Modules system to manage the wide range of software available for Bioinformatics. It attempts to take care of the necessary environment for running the software, and so minmise (although not erradicate) errors.
 To see all the available software, the command to type is:

@@ Line 1: / Line 1: @@
 = Introduction =
-The cluster uses the widely used Environment Modules system to manage the wide range of software available for Bioinformatics. It attempts to take care of the necessary environment for running the software, all its dependencies and their versions and some of its documentation.
+The cluster uses the widely used Environment Modules system to manage the wide range of software available for Bioinformatics. It attempts to take care of the necessary environment for running the software, and so minmise (although not erradicate) errors.
-To see all the availabel software, the command to type is:
+To see all the available software, the command to type is:
-  module available
+  moduleav
-A short cut for this is:
+This is a fast wrapper command for the underlying slower:
-  module av
+  module available
 = Categorised Listing =

@@ Line 15: / Line 15: @@
 [[File:sw2.png]]
-= Raw Listing 01 Sep 2016 =
+= Raw Listing 07 Dec 2016 =
   --------------------------------- /usr/local/Modules/versions -----------------------------------------------------
 .2.10

@@ Line 52: / Line 52: @@
   bwa/0.7.7                                general_script_tools/(default)           newick_utils/4.9.3
   CAFE/3.1                                 gsea/2.2.2(default)                      newick_utils/gitv0_614bf6c(default)
-−
   ngs/gitv0_aef5f50                        python/2.7.12                            sra-tools/gitv0_814d6f7(default)
   NGSToolsApp/2.1.5(default)               python/3.4                               srst2/gitv1_e30dd01(default)