{"id":179,"date":"2013-10-01T12:38:48","date_gmt":"2013-10-01T11:38:48","guid":{"rendered":"https:\/\/blogs.ncl.ac.uk\/igmit\/?p=179"},"modified":"2013-10-01T12:43:01","modified_gmt":"2013-10-01T11:43:01","slug":"hpc-lampredi-update-trinity-20130814","status":"publish","type":"post","link":"https:\/\/blogs.ncl.ac.uk\/igmit\/?p=179","title":{"rendered":"HPC – Lampredi – software update – Trinity 20130814"},"content":{"rendered":"

Trinity has been updated to version 2013-08-14. Details are:<\/p>\n

$ module load apps\/trinity\/20130814
\napps\/trinity\/20130814\/gcc-4.4.6
\n | -- libs\/gcc\/system
\n | * --> OK
\n |
\n OK<\/p>\n

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

$ ls $TRINITYDIR
\nAnalysis docs install_tests.sh notes PerlLibAdaptors sample_data util
\nButterfly galaxy-plugin LICENSE.txt perl README Trinity.pl
\nChrysalis Inchworm Makefile PerlLib Release.Notes trinity-plugins<\/p>\n

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

$ module whatis apps\/trinity\/20130814
\napps\/trinity\/20130814: <\/p>\n

Title: trinity
\n Summary: A novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data
\n License: BSD
\n Group: Bioinformatics
\n URL: http:\/\/trinityrnaseq.sourceforge.net\/<\/p>\n

Name: trinity
\n Version: 20130814
\n Module: apps\/trinity\/20130814\/gcc-4.4.6
\n Module path: \/opt\/gridware\/etc\/modules\/apps\/trinity\/20130814\/gcc-4.4.6
\n Package path: \/opt\/gridware\/pkg\/apps\/trinity\/20130814\/gcc-4.4.6<\/p>\n

Repository: git+http:\/\/download.alces-software.com\/git\/packager-base@0fda8da
\n Package: apps\/trinity\/20130814@8c2c4fe7
\n Last update: 2013-10-01<\/p>\n

Builder: root@headnode1.lampredi.cluster.local
\n Build date: 2013-10-01T12:04:20
\n Build modules: apps\/cpanminus\/1.5017\/noarch
\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\/trinity\/20130814\/gcc-4.4.6<\/p>\n

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

$ module help apps\/trinity\/20130814\/gcc-4.4.6<\/p>\n

----------- Module Specific Help for 'apps\/trinity\/20130814\/gcc-4.4.6' -----------<\/p>\n

======== trinity ========
\n A novel method for the efficient and robust de novo
\n reconstruction of transcriptomes from RNA-seq data
\n ======================== <\/p>\n

This module sets up your environment for the use of the 'trinity'
\napplication. This module sets up version '20130814' 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.<\/p>\n

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

$ module show apps\/trinity\/20130814\/gcc-4.4.6
\n-------------------------------------------------------------------
\n\/opt\/gridware\/etc\/modules\/apps\/trinity\/20130814\/gcc-4.4.6:<\/p>\n

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

Title: trinity
\n Summary: A novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data
\n License: BSD
\n Group: Bioinformatics
\n URL: http:\/\/trinityrnaseq.sourceforge.net\/<\/p>\n

Name: trinity
\n Version: 20130814
\n Module: apps\/trinity\/20130814\/gcc-4.4.6
\n Module path: \/opt\/gridware\/etc\/modules\/apps\/trinity\/20130814\/gcc-4.4.6
\n Package path: \/opt\/gridware\/pkg\/apps\/trinity\/20130814\/gcc-4.4.6<\/p>\n

Repository: git+http:\/\/download.alces-software.com\/git\/packager-base@0fda8da
\n Package: apps\/trinity\/20130814@8c2c4fe7
\n Last update: 2013-10-01<\/p>\n

Builder: root@headnode1.lampredi.cluster.local
\n Build date: 2013-10-01T12:04:20
\n Build modules: apps\/cpanminus\/1.5017\/noarch
\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\/trinity\/20130814\/gcc-4.4.6<\/p>\n

module-prereq\t libs\/gcc\/system
\nmodule-conflict\t apps\/trinity
\nsetenv\t\t TRINITYDIR \/opt\/gridware\/pkg\/apps\/trinity\/20130814\/gcc-4.4.6
\nsetenv\t\t TRINITYBIN \/opt\/gridware\/pkg\/apps\/trinity\/20130814\/gcc-4.4.6
\nprepend-path\t PERL5LIB \/opt\/gridware\/pkg\/apps\/trinity\/20130814\/gcc-4.4.6\/perl\/lib\/perl5
\nprepend-path\t MANPATH \/opt\/gridware\/pkg\/apps\/trinity\/20130814\/gcc-4.4.6\/perl\/man
\nprepend-path\t PATH \/opt\/gridware\/pkg\/apps\/trinity\/20130814\/gcc-4.4.6\/perl\/bin
\nprepend-path\t PATH \/opt\/gridware\/pkg\/apps\/trinity\/20130814\/gcc-4.4.6\/util
\nprepend-path\t PATH \/opt\/gridware\/pkg\/apps\/trinity\/20130814\/gcc-4.4.6
\n----------------------------------------------------------------------------------
\n<\/code><\/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":"

Trinity has been updated to version 2013-08-14. Details are: $ module load apps\/trinity\/20130814 apps\/trinity\/20130814\/gcc-4.4.6 | — libs\/gcc\/system | * –> OK | OK ———————————————————————————- $ ls $TRINITYDIR Analysis docs install_tests.sh notes PerlLibAdaptors sample_data util Butterfly galaxy-plugin LICENSE.txt perl README Trinity.pl Chrysalis Inchworm Makefile PerlLib Release.Notes trinity-plugins ———————————————————————————- $ module whatis apps\/trinity\/20130814 apps\/trinity\/20130814: Title: trinity Summary: […]<\/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],"class_list":["post-179","post","type-post","status-publish","format-standard","hentry","category-uncategorized","tag-cluster","tag-hpc","tag-lampredi","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\/179","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=179"}],"version-history":[{"count":19,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/posts\/179\/revisions"}],"predecessor-version":[{"id":198,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/posts\/179\/revisions\/198"}],"wp:attachment":[{"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=179"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=179"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=179"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}