{"id":422,"date":"2013-04-26T14:13:08","date_gmt":"2013-04-26T14:13:08","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/?page_id=422"},"modified":"2013-04-26T14:13:08","modified_gmt":"2013-04-26T14:13:08","slug":"evm","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/evm\/","title":{"rendered":"EVM"},"content":{"rendered":"<h2>Overview<\/h2>\n<p>The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. EVM provides a flexible and intuitive framework for combining diverse evidence types into a single automated gene structure annotation system.<\/p>\n<p>Version r2012-06-25 is available on the CSF.<\/p>\n<h2>Restrictions on use<\/h2>\n<p>This software is opensource.<\/p>\n<p><a href=\"http:\/\/evidencemodeler.sourceforge.net\/#Referencing_EVM\">Referencing information.<\/a><\/p>\n<h2>Set up procedure<\/h2>\n<p>Please load the modulefile:<\/p>\n<pre class=\"in1\">\r\nmodule load apps\/binapps\/evm\/r2012-06-25\r\n<\/pre>\n<p>You may also require perl:<\/p>\n<pre class=\"in1\">\r\nmodule load apps\/gcc\/perl\/5.16.3\r\n<\/pre>\n<h2>Running the application<\/h2>\n<p>Please do not run EVM on the login node. Work should be submitted to batch.<\/p>\n<h3>Serial batch job submission<\/h3>\n<ul>\n<li>Make sure you have the required modulefiles loaded<\/li>\n<li>Ensure you have a weights file, the contents of which are driven by the software you have used to predict genes. For example:<\/li>\n<\/ul>\n<pre class=\"in1\">\r\nABINITIO_PREDICTION AUGUSTUS 1\r\nABINITIO_PREDICTION GeneMark 1\r\n<\/pre>\n<ul>\n<li>Create a batch submission script containing all the stages you need to run. For example:<\/li>\n<\/ul>\n<pre class=\"in1\">\r\n#!\/bin\/bash \r\n#$ -S \/bin\/bash\r\n#$ -cwd\r\n### The above uses the current directory. All relevant files should be in the directory.\r\n#$ -V\r\n### The above inherits the user environment from the login node so that commands can be found.\r\n\r\npartition_EVM_inputs.pl --genome AF300_all.fa --gene_predictions gene_predictions.gff3 --segmentSize=100000 \\\r\n--overlapSize=10000 --partition_listing partitions_list.out\r\n\r\nwrite_EVM_commands.pl --genome AF300_all.fa --weights ~\/scratch\/wt.txt --gene_predictions gene_predictions.gff3 \\\r\n--output_file_name evm.out --partitions partitions_list.out >commands.list\r\n\r\nexecute_EVM_commands.pl commands.list | tee run.log\r\n\r\nrecombine_EVM_partial_outputs.pl --partitions partitions_list.out --output_file_name evm.out\r\n\r\nconvert_EVM_outputs_to_GFF3.pl  --partitions partitions_list.out --output evm.out --genome AF300_all.fa\r\n<\/pre>\n<ul>\n<li>Submit the job: <code>qsub scriptname<\/code><\/li>\n<\/ul>\n<h3>Parallel batch job submission<\/h3>\n<p>Not currently supported for EVM on the CSF.<\/p>\n<h2>Further info<\/h2>\n<ul>\n<li><a href=\"http:\/\/evidencemodeler.sourceforge.net\/\">EVM website<\/a><\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Overview The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. EVM provides a flexible and intuitive framework for combining diverse evidence types into a single automated gene structure annotation system. Version r2012-06-25 is available on the CSF. Restrictions on use This software is opensource. Referencing information. Set up procedure Please load the modulefile: module load apps\/binapps\/evm\/r2012-06-25 You may also require perl: module load apps\/gcc\/perl\/5.16.3.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/evm\/\">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-422","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/422","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=422"}],"version-history":[{"count":2,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/422\/revisions"}],"predecessor-version":[{"id":3915,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/422\/revisions\/3915"}],"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=422"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}