FreeBayes 0.9.9.2.20131031 has been added to the cluster (31/10/2013)
This is a Bayesian genetic variant detector designed to find small polymorphisms.
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$ module load apps/freebayes
apps/freebayes/0.9.9.2.20131031/gcc-4.4.6+bamtools-2.3.0
| -- libs/gcc/system ... SKIPPED (already loaded)
|
OK
ls $FREEBAYESDIR
bin doc share
$ ls $FREEBAYESDIR/*
/opt/gridware/pkg/apps/freebayes/0.9.9.2.20131031/gcc-4.4.6+bamtools-2.3.0/bin:
bamleftalign freebayes
/opt/gridware/pkg/apps/freebayes/0.9.9.2.20131031/gcc-4.4.6+bamtools-2.3.0/doc:
LICENSE README
/opt/gridware/pkg/apps/freebayes/0.9.9.2.20131031/gcc-4.4.6+bamtools-2.3.0/share:
examples python scripts
$ freebayes
usage: freebayes -f [REFERENCE] [OPTIONS] [BAM FILES] >[OUTPUT]
[snip]
parameters:
-h --help Complete description of options.
author: Erik Garrison , Marth Lab, Boston College, 2010-2012
version: v0.9.9.2
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$ module whatis apps/freebayes
apps/freebayes :
Title: FreeBayes
Summary: Bayesian genetic variant detector designed to find small polymorphisms
License: MIT
Group: Bioinformatics
URL: https://github.com/ekg/freebayes
Name: freebayes
Version: 0.9.9.2.20131031
Module: apps/freebayes/0.9.9.2.20131031/gcc-4.4.6+bamtools-2.3.0
Module path: /opt/gridware/etc/modules/apps/freebayes/0.9.9.2.20131031/gcc-4.4.6+bamtools-2.3.0
Package path: /opt/gridware/pkg/apps/freebayes/0.9.9.2.20131031/gcc-4.4.6+bamtools-2.3.0
Repository: git+http://download.alces-software.com/git/packager-base@8cca844
Package: apps/freebayes/0.9.9.2.20131031@7e80c4a4
Last update: 2013-10-31
Builder: root@headnode1.lampredi.cluster.local
Build date: 2013-10-31T12:41:20
Build modules: apps/bamtools/2.3.0/gcc-4.4.6
Compiler: compilers/gcc/system
System: Linux 2.6.32-279.2.1.el6_lustre.gc46c389.x86_64 x86_64
Arch: Intel(R) Xeon(R) CPU E5620 @ 2.40GHz, 2x4 (b6b89932)
Dependencies: libs/gcc/system (using: libs/gcc/system)
For further information, execute:
module help apps/freebayes/0.9.9.2.20131031/gcc-4.4.6+bamtools-2.3.0
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$ module help apps/freebayes/0.9.9.2.20131031/gcc-4.4.6+bamtools-2.3.0
----------- Module Specific Help for 'apps/freebayes/0.9.9.2.20131031/gcc-4.4.6+bamtools-2.3.0' ---------------------------
======== FreeBayes ========
Bayesian genetic variant detector designed to find small
polymorphisms
==========================
This module sets up your environment for the use of the 'freebayes'
application. This module sets up version '0.9.9.2.20131031' of the
application.
>> SYNOPSIS <> LICENSING <> FURTHER INFORMATION <> GET STARTED <<
Please refer to the website for further details on usage of this
package.
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$ module show apps/freebayes/0.9.9.2.20131031/gcc-4.4.6+bamtools-2.3.0
-------------------------------------------------------------------
/opt/gridware/etc/modules/apps/freebayes/0.9.9.2.20131031/gcc-4.4.6+bamtools-2.3.0:
module-whatis
Title: FreeBayes
Summary: Bayesian genetic variant detector designed to find small polymorphisms
License: MIT
Group: Bioinformatics
URL: https://github.com/ekg/freebayes
Name: freebayes
Version: 0.9.9.2.20131031
Module: apps/freebayes/0.9.9.2.20131031/gcc-4.4.6+bamtools-2.3.0
Module path: /opt/gridware/etc/modules/apps/freebayes/0.9.9.2.20131031/gcc-4.4.6+bamtools-2.3.0
Package path: /opt/gridware/pkg/apps/freebayes/0.9.9.2.20131031/gcc-4.4.6+bamtools-2.3.0
Repository: git+http://download.alces-software.com/git/packager-base@8cca844
Package: apps/freebayes/0.9.9.2.20131031@7e80c4a4
Last update: 2013-10-31
Builder: root@headnode1.lampredi.cluster.local
Build date: 2013-10-31T12:41:20
Build modules: apps/bamtools/2.3.0/gcc-4.4.6
Compiler: compilers/gcc/system
System: Linux 2.6.32-279.2.1.el6_lustre.gc46c389.x86_64 x86_64
Arch: Intel(R) Xeon(R) CPU E5620 @ 2.40GHz, 2x4 (b6b89932)
Dependencies: libs/gcc/system (using: libs/gcc/system)
For further information, execute:
module help apps/freebayes/0.9.9.2.20131031/gcc-4.4.6+bamtools-2.3.0
module-prereq libs/gcc/system
module-conflict apps/freebayes
setenv FREEBAYESDIR /opt/gridware/pkg/apps/freebayes/0.9.9.2.20131031/gcc-4.4.6+bamtools-2.3.0
setenv FREEBAYESBIN /opt/gridware/pkg/apps/freebayes/0.9.9.2.20131031/gcc-4.4.6+bamtools-2.3.0/bin
setenv FREEBAYESDOC /opt/gridware/pkg/apps/freebayes/0.9.9.2.20131031/gcc-4.4.6+bamtools-2.3.0/doc
prepend-path PATH /opt/gridware/pkg/apps/freebayes/0.9.9.2.20131031/gcc-4.4.6+bamtools-2.3.0/bin
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Lampredi HPC
igm-lampredi-users@ncl.ac.uk
IGM IT
igmithelp@ncl.ac.uk
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