{"id":4366,"date":"2017-11-27T15:44:11","date_gmt":"2017-11-27T15:44:11","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/?page_id=4366"},"modified":"2017-11-27T16:01:55","modified_gmt":"2017-11-27T16:01:55","slug":"fast-lmm","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/fast-lmm\/","title":{"rendered":"Fast-LMM"},"content":{"rendered":"<h2>Overview<\/h2>\n<p><a href=\"https:\/\/github.com\/MicrosoftGenomics\/FaST-LMM\">Fast-LMM<\/a> [Factored Spectrally Transformed Linear Mixed Models] from Microsoft Research, is a Python module for performing both single-SNP and SNP-set genome-wide association studies (GWAS) on extremely large data sets.<\/p>\n<p>Version 0.2.31 is installed on the CSF.<\/p>\n<h2>Restrictions on use<\/h2>\n<p>This software is open source (via the <a href=\"https:\/\/github.com\/MicrosoftGenomics\/FaST-LMM\/blob\/master\/LICENSE.md\">Apache License 2.0<\/a>) so all CSF users may access it.<\/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\/python-packages\/anaconda-2.5.0\/fastlmm\/0.2.31\r\n<\/pre>\n<p>Note: this will automatically load anaconda python 2.5.0 (which provided Python 2.7) for you.<\/p>\n<h2>Running the application<\/h2>\n<p>Please do not run Fast-LMM on the login node. Jobs should be submitted to the compute nodes via batch.<\/p>\n<h3>Batch job submission<\/h3>\n<p>After loading the moduelfile above, please write a job submission script and use <code>qsub<\/code> to submit it to the system. For example:<\/p>\n<pre>\r\n#!\/bin\/bash\r\n#$ -cwd\r\n#$ -V\r\npython myscript.py\r\n<\/pre>\n<h2>Further info<\/h2>\n<ul>\n<li><a href=\"https:\/\/github.com\/MicrosoftGenomics\/FaST-LMM\">Fast-LMM website<\/a><\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Overview Fast-LMM [Factored Spectrally Transformed Linear Mixed Models] from Microsoft Research, is a Python module for performing both single-SNP and SNP-set genome-wide association studies (GWAS) on extremely large data sets. Version 0.2.31 is installed on the CSF. Restrictions on use This software is open source (via the Apache License 2.0) so all CSF users may access it. Set up procedure To access the software you must first load the modulefile: module load apps\/gcc\/python-packages\/anaconda-2.5.0\/fastlmm\/0.2.31 Note: this.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/fast-lmm\/\">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-4366","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/4366","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=4366"}],"version-history":[{"count":2,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/4366\/revisions"}],"predecessor-version":[{"id":4376,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/4366\/revisions\/4376"}],"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=4366"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}