{"id":4371,"date":"2017-11-27T15:56:10","date_gmt":"2017-11-27T15:56:10","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/?page_id=4371"},"modified":"2017-11-27T15:56:10","modified_gmt":"2017-11-27T15:56:10","slug":"pysnptools","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/pysnptools\/","title":{"rendered":"PySnpTools"},"content":{"rendered":"<h2>Overview<\/h2>\n<p><a href=\"https:\/\/github.com\/MicrosoftGenomics\/PySnpTools\">PySnpTools<\/a> from Microsoft Research, is a set of python tools for processing SNP genomic data files.<\/p>\n<p>Version 0.3.12 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\/PySnpTools\/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\/pysnptools\/0.3.12\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 PySnpTools python scripts 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\/PySnpTools\">PySnpTools website<\/a><\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Overview PySnpTools from Microsoft Research, is a set of python tools for processing SNP genomic data files. Version 0.3.12 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\/pysnptools\/0.3.12 Note: this will automatically load anaconda python 2.5.0 (which provided Python 2.7) for you. Running.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/pysnptools\/\">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-4371","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/4371","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=4371"}],"version-history":[{"count":1,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/4371\/revisions"}],"predecessor-version":[{"id":4372,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/4371\/revisions\/4372"}],"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=4371"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}