{"id":377,"date":"2014-04-11T14:42:38","date_gmt":"2014-04-11T13:42:38","guid":{"rendered":"https:\/\/blogs.ncl.ac.uk\/igmit\/?p=377"},"modified":"2014-04-11T14:51:30","modified_gmt":"2014-04-11T13:51:30","slug":"hpc-lampredi-software-update-annovar-529-2012-09-20","status":"publish","type":"post","link":"https:\/\/blogs.ncl.ac.uk\/igmit\/?p=377","title":{"rendered":"HPC &#8211; Lampredi &#8211; software update &#8211; Annovar 529 (2012-09-20)"},"content":{"rendered":"<pre>\r\n$ module load apps\/annovar\/529\r\napps\/annovar\/529\/noarch\r\n |\r\n OK\r\n\r\n$ ls $ANNOVARBIN\r\nannotate_variation.pl  coding_change.pl \r\nconvert2annovar.pl  retrieve_seq_from_fasta.pl\r\nsummarize_annovar.pl  table_annovar.pl \r\nvariants_reduction.pl\r\n\r\n$ ls $ANNOVARDIR\r\nbin  db  example\r\n<\/pre>\n<pre>\r\n$ module whatis apps\/annovar\/529\/noarch\r\n\r\n apps\/annovar\/529 :\r\n\r\nTitle: ANNOVAR\r\n Summary: Functional annotation of genetic variants from high-throughput sequencing data\r\n License: NONFREE - Free for non-profit use; see http:\/\/www.openbioinformatics.org\/annovar\/annovar_faq.html#license\r\n Group: Bioinformatics\r\n URL: http:\/\/www.openbioinformatics.org\/annovar\/\r\n\r\nName: annovar\r\n Version: 529\r\n Module: apps\/annovar\/529\/noarch\r\n Module path: \/opt\/gridware\/etc\/modules\/apps\/annovar\/529\/noarch\r\n Package path: \/opt\/gridware\/pkg\/apps\/annovar\/529\/noarch\r\n\r\nRepository: git+http:\/\/download.alces-software.com\/git\/packager-base@c0cb517\r\n Package: ext\/annovar\/@094f23e0\r\n Last update: 2012-09-20\r\n\r\nBuilder: root@headnode1.lampredi.cluster.local\r\n Build date: 2014-04-11T13:12:32\r\n Build parameters: tarball=\/opt\/gridware\/ext\/annovar-20130823.tar.gz\r\n Compiler: N\/A\r\n\r\nFor further information, execute:\r\nmodule help apps\/annovar\/529\/noarch\r\n<\/pre>\n<pre>\r\n$ module help apps\/annovar\/529\/noarch\r\n\r\n----------- Module Specific Help for 'apps\/annovar\/529\/noarch' ---------------------------\r\n\r\n\r\n                      ======== ANNOVAR ========                      \r\n           Functional annotation of genetic variants from            \r\n                   high-throughput sequencing data                   \r\n                      ========================                      \r\n\r\nThis module sets up your environment for the use of the 'annovar'\r\napplication. This module sets up version '529' of the\r\napplication.\r\n\r\n\r\n&gt;&gt; SYNOPSIS &lt;1%) in the\r\n    1000 Genome Project, or identify subset of non-synonymous SNPs\r\n    with SIFT score&gt;0.05, or many other annotations on specific\r\n    mutations.\r\n  * Other functionalities: Retrieve the nucleotide sequence in any\r\n    user-specific genomic positions in batch, identify a candidate\r\n    gene list for Mendelian diseases from exome data, identify a\r\n    list of SNPs from 1000 Genomes that are in strong LD with a GWAS\r\n    hit, and many other creative utilities.\r\n\r\n\r\n&gt;&gt; LICENSING &lt;&gt; FURTHER INFORMATION &lt;&gt; GET STARTED &lt;&lt;\r\n\r\nPlease refer to the website for further details on usage of this\r\npackage.\r\n<\/pre>\n<pre>\r\n$ module show apps\/annovar\/529\/noarch\r\n\r\n-------------------------------------------------------------------\r\n\/opt\/gridware\/etc\/modules\/apps\/annovar\/529\/noarch:\r\n\r\nmodule-whatis\t \r\n\r\n            Title: ANNOVAR\r\n          Summary: Functional annotation of genetic variants from high-throughput sequencing data\r\n          License: NONFREE - Free for non-profit use; see http:\/\/www.openbioinformatics.org\/annovar\/annovar_faq.html#license\r\n            Group: Bioinformatics\r\n              URL: http:\/\/www.openbioinformatics.org\/annovar\/\r\n\r\n             Name: annovar\r\n          Version: 529\r\n           Module: apps\/annovar\/529\/noarch\r\n      Module path: \/opt\/gridware\/etc\/modules\/apps\/annovar\/529\/noarch\r\n     Package path: \/opt\/gridware\/pkg\/apps\/annovar\/529\/noarch\r\n\r\n       Repository: git+http:\/\/download.alces-software.com\/git\/packager-base@c0cb517\r\n          Package: ext\/annovar\/@094f23e0\r\n      Last update: 2012-09-20\r\n\r\n          Builder: root@headnode1.lampredi.cluster.local\r\n       Build date: 2014-04-11T13:12:32\r\n Build parameters: tarball=\/opt\/gridware\/ext\/annovar-20130823.tar.gz\r\n         Compiler: N\/A\r\n\r\n\r\nFor further information, execute:\r\n\r\n\tmodule help apps\/annovar\/529\/noarch\r\n \r\nmodule-conflict\t apps\/annovar \r\nsetenv\t\t ANNOVARDIR \/opt\/gridware\/pkg\/apps\/annovar\/529\/noarch \r\nsetenv\t\t ANNOVARBIN \/opt\/gridware\/pkg\/apps\/annovar\/529\/noarch\/bin \r\nprepend-path\t PATH \/opt\/gridware\/pkg\/apps\/annovar\/529\/noarch\/bin \r\nprepend-path\t MANPATH \/opt\/gridware\/pkg\/apps\/annovar\/529\/noarch\/share\/man \r\n-------------------------------------------------------------------\r\n<\/pre>\n<p>Lampredi HPC<br \/>\nigm-lampredi-users@ncl.ac.uk<\/p>\n<p>IGM IT<br \/>\nigmithelp@ncl.ac.uk<br \/>\nx8625<\/p>\n","protected":false},"excerpt":{"rendered":"<p>$ module load apps\/annovar\/529 apps\/annovar\/529\/noarch | OK $ ls $ANNOVARBIN annotate_variation.pl coding_change.pl convert2annovar.pl retrieve_seq_from_fasta.pl summarize_annovar.pl table_annovar.pl variants_reduction.pl $ ls $ANNOVARDIR bin db example $ module whatis apps\/annovar\/529\/noarch apps\/annovar\/529 : Title: ANNOVAR Summary: Functional annotation of genetic variants from high-throughput sequencing data License: NONFREE &#8211; Free for non-profit use; see http:\/\/www.openbioinformatics.org\/annovar\/annovar_faq.html#license Group: Bioinformatics URL: http:\/\/www.openbioinformatics.org\/annovar\/ Name: <a href='https:\/\/blogs.ncl.ac.uk\/igmit\/?p=377' class='excerpt-more'>[&#8230;]<\/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-377","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\/377","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=377"}],"version-history":[{"count":13,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/posts\/377\/revisions"}],"predecessor-version":[{"id":393,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/posts\/377\/revisions\/393"}],"wp:attachment":[{"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=377"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=377"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=377"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}