{"id":291,"date":"2013-10-31T14:31:36","date_gmt":"2013-10-31T14:31:36","guid":{"rendered":"https:\/\/blogs.ncl.ac.uk\/igmit\/?p=291"},"modified":"2013-10-31T14:31:36","modified_gmt":"2013-10-31T14:31:36","slug":"hpc-lampredi-software-update-freebayes-0-9-9-2-20131031","status":"publish","type":"post","link":"https:\/\/blogs.ncl.ac.uk\/igmit\/?p=291","title":{"rendered":"HPC \u2013 Lampredi \u2013 software update \u2013 FreeBayes 0.9.9.2.20131031"},"content":{"rendered":"

FreeBayes 0.9.9.2.20131031 has been added to the cluster (31\/10\/2013)<\/p>\n

This is a Bayesian genetic variant detector designed to find small polymorphisms.<\/p>\n

\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014-<\/p>\n

$ module load apps\/freebayes
\napps\/freebayes\/0.9.9.2.20131031\/gcc-4.4.6+bamtools-2.3.0
\n | -- libs\/gcc\/system ... SKIPPED (already loaded)
\n |
\n OK<\/p>\n

ls $FREEBAYESDIR
\nbin doc share<\/p>\n

$ ls $FREEBAYESDIR\/*
\n\/opt\/gridware\/pkg\/apps\/freebayes\/0.9.9.2.20131031\/gcc-4.4.6+bamtools-2.3.0\/bin:
\nbamleftalign freebayes<\/p>\n

\/opt\/gridware\/pkg\/apps\/freebayes\/0.9.9.2.20131031\/gcc-4.4.6+bamtools-2.3.0\/doc:
\nLICENSE README<\/p>\n

\/opt\/gridware\/pkg\/apps\/freebayes\/0.9.9.2.20131031\/gcc-4.4.6+bamtools-2.3.0\/share:
\nexamples python scripts<\/p>\n

$ freebayes
\nusage: freebayes -f [REFERENCE] [OPTIONS] [BAM FILES] >[OUTPUT]<\/p>\n

[snip]<\/p>\n

parameters:<\/p>\n

-h --help Complete description of options.<\/p>\n

author: Erik Garrison , Marth Lab, Boston College, 2010-2012
\nversion: v0.9.9.2
\n<\/code>
\n\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014-<\/p>\n

$ module whatis apps\/freebayes
\napps\/freebayes : <\/p>\n

Title: FreeBayes
\n Summary: Bayesian genetic variant detector designed to find small polymorphisms
\n License: MIT
\n Group: Bioinformatics
\n URL: https:\/\/github.com\/ekg\/freebayes<\/p>\n

Name: freebayes
\n Version: 0.9.9.2.20131031
\n Module: apps\/freebayes\/0.9.9.2.20131031\/gcc-4.4.6+bamtools-2.3.0
\n Module path: \/opt\/gridware\/etc\/modules\/apps\/freebayes\/0.9.9.2.20131031\/gcc-4.4.6+bamtools-2.3.0
\n Package path: \/opt\/gridware\/pkg\/apps\/freebayes\/0.9.9.2.20131031\/gcc-4.4.6+bamtools-2.3.0<\/p>\n

Repository: git+http:\/\/download.alces-software.com\/git\/packager-base@8cca844
\n Package: apps\/freebayes\/0.9.9.2.20131031@7e80c4a4
\n Last update: 2013-10-31<\/p>\n

Builder: root@headnode1.lampredi.cluster.local
\n Build date: 2013-10-31T12:41:20
\n Build modules: apps\/bamtools\/2.3.0\/gcc-4.4.6
\n Compiler: compilers\/gcc\/system
\n System: Linux 2.6.32-279.2.1.el6_lustre.gc46c389.x86_64 x86_64
\n Arch: Intel(R) Xeon(R) CPU E5620 @ 2.40GHz, 2x4 (b6b89932)
\n Dependencies: libs\/gcc\/system (using: libs\/gcc\/system)<\/p>\n

For further information, execute:<\/p>\n

\tmodule help apps\/freebayes\/0.9.9.2.20131031\/gcc-4.4.6+bamtools-2.3.0
\n<\/code>
\n\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014-<\/p>\n

$ module help apps\/freebayes\/0.9.9.2.20131031\/gcc-4.4.6+bamtools-2.3.0<\/p>\n

----------- Module Specific Help for 'apps\/freebayes\/0.9.9.2.20131031\/gcc-4.4.6+bamtools-2.3.0' ---------------------------<\/p>\n

======== FreeBayes ========
\n Bayesian genetic variant detector designed to find small
\n polymorphisms
\n ========================== <\/p>\n

This module sets up your environment for the use of the 'freebayes'
\napplication. This module sets up version '0.9.9.2.20131031' of the
\napplication.<\/p>\n

>> SYNOPSIS <> LICENSING <> FURTHER INFORMATION <> GET STARTED <<<\/p>\n

Please refer to the website for further details on usage of this
\npackage.
\n<\/code>
\n\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014-<\/p>\n

$ module show apps\/freebayes\/0.9.9.2.20131031\/gcc-4.4.6+bamtools-2.3.0
\n-------------------------------------------------------------------
\n\/opt\/gridware\/etc\/modules\/apps\/freebayes\/0.9.9.2.20131031\/gcc-4.4.6+bamtools-2.3.0:<\/p>\n

module-whatis\t <\/p>\n

Title: FreeBayes
\n Summary: Bayesian genetic variant detector designed to find small polymorphisms
\n License: MIT
\n Group: Bioinformatics
\n URL: https:\/\/github.com\/ekg\/freebayes<\/p>\n

Name: freebayes
\n Version: 0.9.9.2.20131031
\n Module: apps\/freebayes\/0.9.9.2.20131031\/gcc-4.4.6+bamtools-2.3.0
\n Module path: \/opt\/gridware\/etc\/modules\/apps\/freebayes\/0.9.9.2.20131031\/gcc-4.4.6+bamtools-2.3.0
\n Package path: \/opt\/gridware\/pkg\/apps\/freebayes\/0.9.9.2.20131031\/gcc-4.4.6+bamtools-2.3.0<\/p>\n

Repository: git+http:\/\/download.alces-software.com\/git\/packager-base@8cca844
\n Package: apps\/freebayes\/0.9.9.2.20131031@7e80c4a4
\n Last update: 2013-10-31<\/p>\n

Builder: root@headnode1.lampredi.cluster.local
\n Build date: 2013-10-31T12:41:20
\n Build modules: apps\/bamtools\/2.3.0\/gcc-4.4.6
\n Compiler: compilers\/gcc\/system
\n System: Linux 2.6.32-279.2.1.el6_lustre.gc46c389.x86_64 x86_64
\n Arch: Intel(R) Xeon(R) CPU E5620 @ 2.40GHz, 2x4 (b6b89932)
\n Dependencies: libs\/gcc\/system (using: libs\/gcc\/system)<\/p>\n

For further information, execute:<\/p>\n

\tmodule help apps\/freebayes\/0.9.9.2.20131031\/gcc-4.4.6+bamtools-2.3.0<\/p>\n

module-prereq\t libs\/gcc\/system
\nmodule-conflict\t apps\/freebayes
\nsetenv\t\t FREEBAYESDIR \/opt\/gridware\/pkg\/apps\/freebayes\/0.9.9.2.20131031\/gcc-4.4.6+bamtools-2.3.0
\nsetenv\t\t FREEBAYESBIN \/opt\/gridware\/pkg\/apps\/freebayes\/0.9.9.2.20131031\/gcc-4.4.6+bamtools-2.3.0\/bin
\nsetenv\t\t FREEBAYESDOC \/opt\/gridware\/pkg\/apps\/freebayes\/0.9.9.2.20131031\/gcc-4.4.6+bamtools-2.3.0\/doc
\nprepend-path\t PATH \/opt\/gridware\/pkg\/apps\/freebayes\/0.9.9.2.20131031\/gcc-4.4.6+bamtools-2.3.0\/bin
\n<\/code>
\n\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014-<\/p>\n

Lampredi HPC
\nigm-lampredi-users@ncl.ac.uk<\/p>\n

IGM IT
\nigmithelp@ncl.ac.uk
\nx8625<\/p>\n","protected":false},"excerpt":{"rendered":"

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. \u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014- $ 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 $ […]<\/a><\/p>\n","protected":false},"author":1149,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":["post-291","post","type-post","status-publish","format-standard","hentry","category-uncategorized","category-1-id","post-seq-1","post-parity-odd","meta-position-corners","fix"],"_links":{"self":[{"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/posts\/291","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/users\/1149"}],"replies":[{"embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=291"}],"version-history":[{"count":4,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/posts\/291\/revisions"}],"predecessor-version":[{"id":295,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/posts\/291\/revisions\/295"}],"wp:attachment":[{"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=291"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=291"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=291"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}