{"id":2773,"date":"2015-10-28T14:06:16","date_gmt":"2015-10-28T14:06:16","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/?page_id=2773"},"modified":"2015-10-28T14:10:13","modified_gmt":"2015-10-28T14:10:13","slug":"rapmap","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/rapmap\/","title":{"rendered":"RapMap"},"content":{"rendered":"<h2>Overview<\/h2>\n<p>RapMap is a testing ground for ideas in lightweight \/ quasi \/ pseudo transcriptome alignment.<\/p>\n<p>Version 0.1.0 is installed on the CSF.<\/p>\n<h2>Restrictions on use<\/h2>\n<p>Open source, may be used by all CSF users.<\/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\/gcc\/rapmap\/0.1.0\r\n<\/pre>\n<h2>Running the application<\/h2>\n<p>Please do not run RapMap on the login node. Jobs should be submitted to the compute nodes via batch.<\/p>\n<h3>Serial batch job submission &#8211; details coming soon<\/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\nAPP arg1 arg2 > out.log\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=\"\">https:\/\/github.com\/COMBINE-lab\/RapMap<\/a><\/li>\n<\/ul>\n<h2>Updates<\/h2>\n<p>None.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Overview RapMap is a testing ground for ideas in lightweight \/ quasi \/ pseudo transcriptome alignment. Version 0.1.0 is installed on the CSF. Restrictions on use Open source, may be used by all CSF users. Set up procedure To access the software you must first load the modulefile: module load apps\/gcc\/rapmap\/0.1.0 Running the application Please do not run RapMap on the login node. Jobs should be submitted to the compute nodes via batch. Serial batch.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/rapmap\/\">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-2773","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/2773","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=2773"}],"version-history":[{"count":3,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/2773\/revisions"}],"predecessor-version":[{"id":2777,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/2773\/revisions\/2777"}],"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=2773"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}