{"id":4730,"date":"2018-06-25T13:29:14","date_gmt":"2018-06-25T13:29:14","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/?page_id=4730"},"modified":"2018-06-28T13:45:16","modified_gmt":"2018-06-28T13:45:16","slug":"corhmm","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/corhmm\/","title":{"rendered":"corHMM (R library)"},"content":{"rendered":"<h2>Overview<\/h2>\n<p><a href=\"https:\/\/cran.r-project.org\/web\/packages\/corHMM\/index.html\">corHMM<\/a> is an R package to fits a hidden rates model that allows different transition rate classes on different portions of a phylogeny by treating rate classes as hidden states in a Markov process and various other functions for evaluating models of binary character evolution.<\/p>\n<p>Version 1.22 is installed on the CSF. This will use R 3.4.3.<\/p>\n<h2>Restrictions on use<\/h2>\n<p>There are no restrictions on accessing the software on the CSF. The software is released under the GNU GPL-v3 <a href=\"https:\/\/cran.r-project.org\/web\/licenses\/GPL-3\">license<\/a> and all usage must adhere to that.<\/p>\n<h2>Set up procedure<\/h2>\n<p>To access the software you must first load the modulefile:<\/p>\n<pre>\r\n# This will automatically load the R v3.4.3 modulefile for you\r\n\r\nmodule load apps\/gcc\/R-packages\/3.4.3\/corhmm\/1.22\r\n<\/pre>\n<h2>Running the application<\/h2>\n<p>Please do not run corHMM on the login node. Jobs should be submitted to the compute nodes via batch.<\/p>\n<p>To load the corHMM library in to R once R has started, ensure you run the command:<\/p>\n<pre>\r\nlibrary(corHMM)\r\n<\/pre>\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\nR CMD BATCH my_script.R my_script.R.o$JOB_ID\r\n        #\r\n        # -- R must be called with both the \"CMD\" and \"BATCH\" options which tell it\r\n        #    to run an R *program*, in this case \"my_script.R\", instead of presenting\r\n        #    an interactive prompt\r\n        #\r\n        # -- Use the following R command in your script to load the scenic library:\r\n        #\r\n        #    library(\"corhmm\")\r\n        #\r\n        # -- the final argument, \"my_test.R.o$JOBID\", tells R to send output to a \r\n        #    file with this name (without, R sends output to \"my_test.Rout\", which\r\n        #    would be over-written by a second submission of \"my_test.R\" via\r\n        #    \"runmyRjob.qsub\")\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:\/\/cran.r-project.org\/web\/packages\/corHMM\/corHMM.pdf\">corHMM manual (PDF)<\/a><\/li>\n<\/ul>\n<h2>Updates<\/h2>\n<p>None.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Overview corHMM is an R package to fits a hidden rates model that allows different transition rate classes on different portions of a phylogeny by treating rate classes as hidden states in a Markov process and various other functions for evaluating models of binary character evolution. Version 1.22 is installed on the CSF. This will use R 3.4.3. Restrictions on use There are no restrictions on accessing the software on the CSF. The software is.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/corhmm\/\">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-4730","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/4730","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=4730"}],"version-history":[{"count":4,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/4730\/revisions"}],"predecessor-version":[{"id":4764,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/4730\/revisions\/4764"}],"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=4730"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}