{"id":4739,"date":"2018-06-26T10:45:19","date_gmt":"2018-06-26T10:45:19","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/?page_id=4739"},"modified":"2018-06-26T10:47:02","modified_gmt":"2018-06-26T10:47:02","slug":"picard","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/picard\/","title":{"rendered":"Picard (tools)"},"content":{"rendered":"<h2>Overview<\/h2>\n<p><a href=\"https:\/\/broadinstitute.github.io\/picard\/\">Picard<\/a> is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM\/BAM\/CRAM and VCF.<\/p>\n<p>Version 2.18.7 is installed on the CSF.<\/p>\n<h2>Restrictions on use<\/h2>\n<p>There are no restrictions on accessing Picard on the CSF. The software is released under the MIT <a href=\"https:\/\/github.com\/broadinstitute\/picard\/blob\/2.18.7\/LICENSE.txt\">license<\/a> and all usage should adhere to that license.<\/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\/binapps\/picard\/2.18.7\r\n<\/pre>\n<h2>Running the application<\/h2>\n<p>Please do not run Picard tools on the login node. Jobs should be submitted to the compute nodes via batch.<\/p>\n<p>You <em>may<\/em> run the following command on the login node to see a list of tools provided by Picard:<\/p>\n<pre>\r\npicard -h\r\n<\/pre>\n<p>To see the help text specific to a particular tool, run:<\/p>\n<pre>\r\npicard <em>toolname<\/em> -h\r\n<\/pre>\n<p>For example:<\/p>\n<pre>\r\npicard CheckIlluminaDirectory -h\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#$ -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\npicard <em>toolname<\/em> <em>args...<\/em>\r\n         #\r\n         # Name of picard tool to run\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:\/\/broadinstitute.github.io\/picard\/command-line-overview.html\">Picard individual tool documentation<\/a><\/li>\n<li><a href=\"https:\/\/broadinstitute.github.io\/picard\/\">Picard website<\/a><\/li>\n<\/ul>\n<h2>Updates<\/h2>\n<p>None.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Overview Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM\/BAM\/CRAM and VCF. Version 2.18.7 is installed on the CSF. Restrictions on use There are no restrictions on accessing Picard on the CSF. The software is released under the MIT license and all usage should adhere to that license. Set up procedure To access the software you must first load the modulefile: module load apps\/binapps\/picard\/2.18.7 Running.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/picard\/\">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-4739","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/4739","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=4739"}],"version-history":[{"count":2,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/4739\/revisions"}],"predecessor-version":[{"id":4742,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/4739\/revisions\/4742"}],"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=4739"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}