{"id":272,"date":"2013-10-28T15:49:54","date_gmt":"2013-10-28T15:49:54","guid":{"rendered":"https:\/\/blogs.ncl.ac.uk\/igmit\/?p=272"},"modified":"2013-10-28T15:52:02","modified_gmt":"2013-10-28T15:52:02","slug":"hpc-lampredi-software-update-famseq-1-0-0-2","status":"publish","type":"post","link":"https:\/\/blogs.ncl.ac.uk\/igmit\/?p=272","title":{"rendered":"HPC \u2013 Lampredi \u2013 software update \u2013 FamSeq 1.0.0-2"},"content":{"rendered":"

FamSeq 1.0.0-2 has been added to lampredi2. Details are:<\/p>\n

$ module load apps\/famseq
\napps\/famseq\/1.0.0-2\/gcc-4.4.6
\n| -- libs\/gcc\/system
\n| * --> OK
\n|
\nOK<\/p>\n

[...@node05(lampredi) ~]$ ls $FAMSEQDIR
\nbin doc sample<\/p>\n

[...@node05(lampredi) ~]$ ls $FAMSEQDIR\/doc
\nmanual.pdf<\/p>\n

[...@node05(lampredi) ~]$ FamSeq<\/p>\n

Program: FamSeq (Sequence calling using pedigree information)
\nVersion: 0.0.1<\/p>\n

Usage:\tFamSeq [options]<\/p>\n

Input type: vcf\t\tinput vcf file
\n\t\tLK\tinput likelihood file<\/code><\/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 whatis apps\/famseq
\napps\/famseq : <\/p>\n

Title: FamSeq
\n Summary: A computational tool for calculating probability of variants in family-based sequencing data
\n License: Public Domain
\n Group: Bioinformatics
\n URL: http:\/\/odin.mdacc.tmc.edu\/~wwang7\/FamSeqIndex.html<\/p>\n

Name: famseq
\n Version: 1.0.0-2
\n Module: apps\/famseq\/1.0.0-2\/gcc-4.4.6
\n Module path: \/opt\/gridware\/etc\/modules\/apps\/famseq\/1.0.0-2\/gcc-4.4.6
\n Package path: \/opt\/gridware\/pkg\/apps\/famseq\/1.0.0-2\/gcc-4.4.6<\/p>\n

Repository: git+http:\/\/download.alces-software.com\/git\/packager-base@ea64008
\n Package: apps\/famseq\/1.0.0-2@61f6fd9a
\n Last update: 2013-10-28<\/p>\n

Builder: root@headnode1.lampredi.cluster.local
\n Build date: 2013-10-28T14:52:15
\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\/famseq\/1.0.0-2\/gcc-4.4.6<\/code><\/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 help apps\/famseq\/1.0.0-2\/gcc-4.4.6<\/p>\n

----------- Module Specific Help for 'apps\/famseq\/1.0.0-2\/gcc-4.4.6' ---------------------------<\/p>\n

======== FamSeq ========
\n A computational tool for calculating probability of
\n variants in family-based sequencing data
\n ======================= <\/p>\n

This module sets up your environment for the use of the 'famseq'
\napplication. This module sets up version '1.0.0-2' 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\/famseq\/1.0.0-2\/gcc-4.4.6
\n-------------------------------------------------------------------
\n\/opt\/gridware\/etc\/modules\/apps\/famseq\/1.0.0-2\/gcc-4.4.6:<\/p>\n

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

Title: FamSeq
\n Summary: A computational tool for calculating probability of variants in family-based sequencing data
\n License: Public Domain
\n Group: Bioinformatics
\n URL: http:\/\/odin.mdacc.tmc.edu\/~wwang7\/FamSeqIndex.html<\/p>\n

Name: famseq
\n Version: 1.0.0-2
\n Module: apps\/famseq\/1.0.0-2\/gcc-4.4.6
\n Module path: \/opt\/gridware\/etc\/modules\/apps\/famseq\/1.0.0-2\/gcc-4.4.6
\n Package path: \/opt\/gridware\/pkg\/apps\/famseq\/1.0.0-2\/gcc-4.4.6<\/p>\n

Repository: git+http:\/\/download.alces-software.com\/git\/packager-base@ea64008
\n Package: apps\/famseq\/1.0.0-2@61f6fd9a
\n Last update: 2013-10-28<\/p>\n

Builder: root@headnode1.lampredi.cluster.local
\n Build date: 2013-10-28T14:52:15
\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\/famseq\/1.0.0-2\/gcc-4.4.6<\/p>\n

module-prereq\t libs\/gcc\/system
\nmodule-conflict\t apps\/famseq
\nsetenv\t\t FAMSEQDIR \/opt\/gridware\/pkg\/apps\/famseq\/1.0.0-2\/gcc-4.4.6
\nsetenv\t\t FAMSEQBIN \/opt\/gridware\/pkg\/apps\/famseq\/1.0.0-2\/gcc-4.4.6\/bin
\nsetenv\t\t FAMSEQDOC \/opt\/gridware\/pkg\/apps\/famseq\/1.0.0-2\/gcc-4.4.6\/doc
\nsetenv\t\t FAMSEQSAMPLE \/opt\/gridware\/pkg\/apps\/famseq\/1.0.0-2\/gcc-4.4.6\/sample
\nprepend-path\t PATH \/opt\/gridware\/pkg\/apps\/famseq\/1.0.0-2\/gcc-4.4.6\/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":"

FamSeq 1.0.0-2 has been added to lampredi2. Details are: $ module load apps\/famseq apps\/famseq\/1.0.0-2\/gcc-4.4.6 | — libs\/gcc\/system | * –> OK | OK […@node05(lampredi) ~]$ ls $FAMSEQDIR bin doc sample […@node05(lampredi) ~]$ ls $FAMSEQDIR\/doc manual.pdf […@node05(lampredi) ~]$ FamSeq Program: FamSeq (Sequence calling using pedigree information) Version: 0.0.1 Usage: FamSeq [options] Input type: vcf input vcf […]<\/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":[11,10,9,21,22],"class_list":["post-272","post","type-post","status-publish","format-standard","hentry","category-uncategorized","tag-cluster","tag-hpc","tag-lampredi","tag-lampredi2","tag-linux","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\/272","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=272"}],"version-history":[{"count":3,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/posts\/272\/revisions"}],"predecessor-version":[{"id":275,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/posts\/272\/revisions\/275"}],"wp:attachment":[{"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=272"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=272"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=272"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}