{"id":4826,"date":"2018-08-01T16:59:55","date_gmt":"2018-08-01T16:59:55","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/?page_id=4826"},"modified":"2019-04-04T10:10:04","modified_gmt":"2019-04-04T10:10:04","slug":"maxbin","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/maxbin\/","title":{"rendered":"MaxBin"},"content":{"rendered":"<h2>Overview<\/h2>\n<p><a href=\"https:\/\/sourceforge.net\/projects\/maxbin2\/\">MaxBin2<\/a> is a program for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.<\/p>\n<p>Version 2.2.5 is installed on the CSF. Please note that the application incorrectly reports itself as version 2.2.4. This may be corrected in a future release but this is definitely version 2.2.5.<\/p>\n<p>It was compiled with the GCC 4.9.0 compiler.<\/p>\n<p>The auxiliary applications provided by MaxBin (IDBA-UD, HMMER3, Bowtie2, FragGeneScan) have been installed. While some of these already exists on the CSF (available via other modulefiles) the versions used by MaxBin are installed within the MaxBin installation and no further modulefiles are required.<\/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 ?BSD license and any use should fall within the restrictions of that license. Please see the <code>$MAXBINDIR\/License<\/code> text file on the CSF.<\/p>\n<h2>Set up procedure<\/h2>\n<p>To access the software you must first load the modulefile:<\/p>\n<pre>\r\nmodule load apps\/gcc\/maxbin\/2.2.5\r\n<\/pre>\n<h2>Running the application<\/h2>\n<p>Please do not run MaxBin on the login node. Jobs should be submitted to the compute nodes via batch.<\/p>\n<p>You may run the command without any args on the login node to display the help text:<\/p>\n<pre>\r\nrun_MaxBin.pl\r\n\r\nUsage:\r\n  run_MaxBin.pl\r\n    -contig (contig file)\r\n    -out (output file)\r\n  ...\r\n<\/pre>\n<h3>Serial batch job submission<\/h3>\n<p>Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n<pre>\r\n#!\/bin\/bash\r\n#$ -cwd             # Job will run from the current directory\r\n#$ -V               # Job will inherit current environment settings\r\n\r\n# $NSLOTS is automatically set to 1 in a serial job\r\nrun_MaxBin.pl -thread $NSLOTS -contig <em>contig_gile<\/em> -out <em>output_file<\/em> <em>other args...<\/em>\r\n<\/pre>\n<p>Submit the jobscript using: <\/p>\n<pre>qsub <em>scriptname<\/em><\/pre>\n<p>where <em>scriptname<\/em> is the name of your jobscript.<\/p>\n<h3>Parallel batch job submission<\/h3>\n<p>Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n<pre>\r\n#!\/bin\/bash\r\n#$ -cwd             # Job will run from the current directory\r\n#$ -V               # Job will inherit current environment settings\r\n#$ -pe smp.pe 8     # Number of cores (2-24 permitted)\r\n\r\n# $NSLOTS is automatically set to the number of cores requested above\r\nrun_MaxBin.pl -thread $NSLOTS -contig <em>contig_gile<\/em> -out <em>output_file<\/em> <em>other 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=\"https:\/\/sourceforge.net\/projects\/maxbin2\/\">MaxBin website<\/a><\/li>\n<\/ul>\n<h2>Updates<\/h2>\n<p>None.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Overview MaxBin2 is a program for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. Version 2.2.5 is installed on the CSF. Please note that the application incorrectly reports itself as version 2.2.4. This may be corrected in a future release but this is definitely version 2.2.5. It was compiled with the GCC 4.9.0 compiler. The auxiliary applications provided by MaxBin (IDBA-UD, HMMER3, Bowtie2, FragGeneScan) have been installed. While some of these already exists on.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/maxbin\/\">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-4826","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/4826","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=4826"}],"version-history":[{"count":5,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/4826\/revisions"}],"predecessor-version":[{"id":4997,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/4826\/revisions\/4997"}],"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=4826"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}