{"id":4343,"date":"2019-12-11T16:51:40","date_gmt":"2019-12-11T16:51:40","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf3\/?page_id=4343"},"modified":"2019-12-11T16:51:40","modified_gmt":"2019-12-11T16:51:40","slug":"pplacer","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/applications\/pplacer\/","title":{"rendered":"pplacer"},"content":{"rendered":"<h2>Overview<\/h2>\n<p><a href=\"\">pplacer<\/a> is a program to place query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment.<\/p>\n<p>Version 1.1.alpha19 is installed on the CSF.<\/p>\n<h2>Restrictions on use<\/h2>\n<p>There are no restrictions on accessing this software on the CSF. It is released under the <a href=\"https:\/\/github.com\/matsen\/pplacer\/blob\/master\/COPYING\">GNU GPL v3.0 license<\/a> and all usage must adhere to that license.<\/p>\n<h2>Set up procedure<\/h2>\n<p>We now recommend loading modulefiles within your jobscript so that you have a full record of how the job was run. See the example jobscript below for how to do this. Alternatively, you may load modulefiles on the login node and let the job <abbr title=\"add '#$ -V' to your jobscript\">inherit these settings<\/abbr>.<\/p>\n<p>Load one of the following modulefiles:<\/p>\n<pre>\r\nmodule load apps\/binapps\/pplacer\/1.1.alpha19\r\n<\/pre>\n<h2>Running the application<\/h2>\n<p>Please do not run pplacer on the login node. Jobs should be submitted to the compute nodes via batch.<\/p>\n<h3>Serial batch job submission<\/h3>\n<p>Create a batch submission script (which will load the modulefile in the jobscript), for example:<\/p>\n<pre>\r\n#!\/bin\/bash --login\r\n#$ -cwd             # Job will run from the current directory\r\n                    # NO -V line - we load modulefiles in the jobscript\r\n\r\nmodule load apps\/path\/to\/module\/n.m\r\n\r\n# $NSLOTS will be set to 1 for a serial job. You <strong>must<\/strong> give the -j flag.\r\n# By default pplacer will use two cores. So a serial job must tell it to use 1 core.\r\npplacer -j $NSLOTS <em>args...<\/em>\r\n<\/pre>\n<p>Submit the jobscript using: <\/p>\n<pre>qsub <em>scriptname<\/em><\/pre>\n<p>where <em>scriptname<\/em> is the name of your jobscript.<\/p>\n<h3>Parallel batch job submission<\/h3>\n<p>Create a batch submission script (which will load the modulefile in the jobscript), for example:<\/p>\n<pre>\r\n#!\/bin\/bash --login\r\n#$ -pe smp.pe 8     # Number of cores, can be 2--32\r\n#$ -cwd             # Job will run from the current directory\r\n                    # NO -V line - we load modulefiles in the jobscript\r\n\r\nmodule load apps\/path\/to\/module\/n.m\r\n\r\n# $NSLOTS will be set to the number of cores requested above.\r\npplacer -j $NSLOTS <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:\/\/matsen.github.io\/pplacer\/\">pplacer online documentation<\/a><\/li>\n<li><a href=\"https:\/\/matsen.fhcrc.org\/pplacer\/\">pplacer website<\/a><\/li>\n<\/ul>\n<h2>Updates<\/h2>\n<p>None.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Overview pplacer is a program to place query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment. Version 1.1.alpha19 is installed on the CSF. Restrictions on use There are no restrictions on accessing this software on the CSF. It is released under the GNU GPL v3.0 license and all usage must adhere to that license. Set up procedure We now recommend loading modulefiles within your.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/applications\/pplacer\/\">Read more &raquo;<\/a><\/p>\n","protected":false},"author":2,"featured_media":0,"parent":86,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-4343","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/4343","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/comments?post=4343"}],"version-history":[{"count":1,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/4343\/revisions"}],"predecessor-version":[{"id":4344,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/4343\/revisions\/4344"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/86"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/media?parent=4343"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}