{"id":2495,"date":"2015-05-22T10:53:12","date_gmt":"2015-05-22T10:53:12","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/?page_id=2495"},"modified":"2015-06-29T11:50:12","modified_gmt":"2015-06-29T11:50:12","slug":"sickle","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/sickle\/","title":{"rendered":"sickle"},"content":{"rendered":"<h2>Overview<\/h2>\n<p>sickle &#8211; A windowed adaptive trimming tool for FASTQ files using quality<\/p>\n<p>Version 1.33 is installed on the CSF.<\/p>\n<h2>Restrictions on use<\/h2>\n<p>Details of the licence, restrictions, links to licence docs etc<\/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\/sickle\/1.33\r\n<\/pre>\n<h2>Running the application<\/h2>\n<p>Please do not run sickle on the login node. Jobs should be submitted to the compute nodes via batch.<\/p>\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#$ -S \/bin\/bash\r\n#$ -cwd             # Job will run from the current directory\r\n#$ -V               # Job will inherit current environment settings\r\n\r\nsickle arg1 arg2 &gt; out.log\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>Given an example parallel jobscript, including suitable PE<\/p>\n<h2>Further info<\/h2>\n<ul>\n<li><a href=\"https:\/\/github.com\/najoshi\/sickle\">sickle website<\/a><\/li>\n<\/ul>\n<h2>Updates<\/h2>\n<p>None.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Overview sickle &#8211; A windowed adaptive trimming tool for FASTQ files using quality Version 1.33 is installed on the CSF. Restrictions on use Details of the licence, restrictions, links to licence docs etc Set up procedure To access the software you must first load the modulefile: module load apps\/gcc\/sickle\/1.33 Running the application Please do not run sickle on the login node. Jobs should be submitted to the compute nodes via batch. Serial batch job submission.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/sickle\/\">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-2495","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/2495","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=2495"}],"version-history":[{"count":5,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/2495\/revisions"}],"predecessor-version":[{"id":2629,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/2495\/revisions\/2629"}],"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=2495"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}