{"id":4621,"date":"2018-03-20T16:56:45","date_gmt":"2018-03-20T16:56:45","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/?page_id=4621"},"modified":"2018-03-20T17:09:32","modified_gmt":"2018-03-20T17:09:32","slug":"metavelvet","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/metavelvet\/","title":{"rendered":"metaVelvet"},"content":{"rendered":"<h2>Overview<\/h2>\n<p><a href=\"http:\/\/metavelvet.dna.bio.keio.ac.jp\/\">metaVelvet<\/a> provides an extension of Velvet assembler to de novo metagenome assembly from short sequence reads.<\/p>\n<p>Version 1.2.02 is installed on the CSF.<\/p>\n<h2>Restrictions on use<\/h2>\n<p>There are no restrictions on accessing the software on the CSF. It is released under the GNU GPL v2 license and all use must adhere to that license.<\/p>\n<h2>Set up procedure<\/h2>\n<p>To access the software you must first load one of the modulefiles:<\/p>\n<pre>\r\n# Compiled with Intel compiler - app may run faster.\r\nmodule load apps\/intel-15.0\/metavelvet\/1.2.02\r\n\r\n# Compiled with GCC compiler.\r\nmodule load apps\/gcc\/metavelvet\/1.2.02\r\n<\/pre>\n<h2>Running the application<\/h2>\n<p>Please do not run metavelvet on the login node. Jobs should be submitted to the compute nodes via batch.<\/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#$ -cwd             # Job will run from the current directory\r\n#$ -V               # Job will inherit current environment settings\r\n\r\nmeta-velvetg <em>arg1 arg2 ...<\/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:\/\/metavelvet.dna.bio.keio.ac.jp\/\">MetaVelvet website<\/a><\/li>\n<\/ul>\n<h2>Updates<\/h2>\n<p>None.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Overview metaVelvet provides an extension of Velvet assembler to de novo metagenome assembly from short sequence reads. Version 1.2.02 is installed on the CSF. Restrictions on use There are no restrictions on accessing the software on the CSF. It is released under the GNU GPL v2 license and all use must adhere to that license. Set up procedure To access the software you must first load one of the modulefiles: # Compiled with Intel compiler.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/metavelvet\/\">Read more &raquo;<\/a><\/p>\n","protected":false},"author":15,"featured_media":0,"parent":31,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-4621","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/4621","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\/15"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/comments?post=4621"}],"version-history":[{"count":3,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/4621\/revisions"}],"predecessor-version":[{"id":4624,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/4621\/revisions\/4624"}],"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=4621"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}