{"id":2424,"date":"2015-04-20T15:00:41","date_gmt":"2015-04-20T15:00:41","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/?page_id=2424"},"modified":"2015-05-06T09:20:34","modified_gmt":"2015-05-06T09:20:34","slug":"ensembl","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/ensembl\/","title":{"rendered":"Ensembl"},"content":{"rendered":"<h2>Overview<\/h2>\n<p><a href=\"http:\/\/www.ensembl.org\/info\/docs\/tools\/vep\/index.html\">Ensembl<\/a> provides a Variant Effect Predictor script (written in perl) to determine the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.<\/p>\n<p>Version 79 of Ensembl Tools is installed on the CSF.<\/p>\n<h2>Restrictions on use<\/h2>\n<p>There are no restrictions on access this software on the CSF. The software is released under the <a href=\"http:\/\/www.ensembl.org\/info\/about\/legal\/code_licence.html\">Apache License<\/a> and all users are required to read and adhere to the license terms.<\/p>\n<h2>Set up procedure<\/h2>\n<p>To access the software you must first load the modulefile:<\/p>\n<pre>\r\nmodule load apps\/binapps\/ensembl\/79\/vep\r\n<\/pre>\n<p>This will automatically load the perl 5.20.2 modulefile.<\/p>\n<h2>Running the application<\/h2>\n<p>Please do not run Ensembl VEP on the login node. Jobs should be submitted to the compute nodes via batch.<\/p>\n<p>Please note that the VEP script will not be able to connect to an external MySQL database. Hence you should use the script in its <a href=\"http:\/\/www.ensembl.org\/info\/docs\/tools\/vep\/script\/vep_cache.html#offline\">offline<\/a> mode.<\/p>\n<h3>Serial batch job submission<\/h3>\n<p>Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n<pre>\r\n#!\/bin\/bash\r\n#$ -S \/bin\/bash\r\n#$ -cwd             # Job will run from the current directory\r\n#$ -V               # Job will inherit current environment settings\r\n\r\nvariant_effect_predictor.pl <em>args<\/em>\r\n<\/pre>\n<p>Submit the jobscript using: <\/p>\n<pre>qsub <em>scriptname<\/em><\/pre>\n<p>where <em>scriptname<\/em> is the name of your jobscript.<\/p>\n<h2>Further info<\/h2>\n<ul>\n<li><a href=\"http:\/\/www.ensembl.org\/info\/docs\/tools\/index.html\">Ensembl Tools website<\/a><\/li>\n<\/ul>\n<h2>Updates<\/h2>\n<p>None.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Overview Ensembl provides a Variant Effect Predictor script (written in perl) to determine the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. Version 79 of Ensembl Tools is installed on the CSF. Restrictions on use There are no restrictions on access this software on the CSF. The software is released under the Apache License and all users are required to read.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/ensembl\/\">Read more &raquo;<\/a><\/p>\n","protected":false},"author":2,"featured_media":0,"parent":31,"menu_order":0,"comment_status":"open","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-2424","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/2424","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/comments?post=2424"}],"version-history":[{"count":2,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/2424\/revisions"}],"predecessor-version":[{"id":2444,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/2424\/revisions\/2444"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/31"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/media?parent=2424"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}