{"id":398,"date":"2014-05-06T16:02:18","date_gmt":"2014-05-06T15:02:18","guid":{"rendered":"https:\/\/blogs.ncl.ac.uk\/igmit\/?p=398"},"modified":"2014-05-06T16:02:18","modified_gmt":"2014-05-06T15:02:18","slug":"hpc-lampredi-software-update-breakpointer-1-0-2","status":"publish","type":"post","link":"https:\/\/blogs.ncl.ac.uk\/igmit\/?p=398","title":{"rendered":"HPC \u2013 Lampredi \u2013 software update \u2013 Breakpointer 1.0"},"content":{"rendered":"<pre>$ module load apps\/breakpointer\/1.0\/bin\r\n apps\/breakpointer\/1.0\/bin\r\n | -- apps\/bwa\/0.6.2\/gcc-4.4.6\r\n | | -- libs\/gcc\/system\r\n | | * --&gt; OK\r\n | * --&gt; OK\r\n | -- apps\/samtools\/0.1.8\/gcc-4.4.6\r\n | | -- libs\/gcc\/system ... SKIPPED (already loaded)\r\n | * --&gt; OK\r\n |\r\n OK<\/pre>\n<pre>$ ls $BREAKPOINTERBIN\r\n BreakPointer BreakPointer.sh fh_BreakPointerScatter<\/pre>\n<pre>$ ls $BREAKPOINTERDIR\r\n bin doc lib share<\/pre>\n<pre>\r\n$ module whatis apps\/breakpointer\r\napps\/breakpointer    : \r\n\r\n            Title: BreakPointer\r\n          Summary: Pinpoint rearrangement breakpoints using paired end reads\r\n          License: NONFREE - For academic non-commercial research purposes only\r\n            Group: Bioinformatics\r\n              URL: http:\/\/www.broadinstitute.org\/cancer\/cga\/breakpointer\r\n\r\n             Name: breakpointer\r\n          Version: 1.0\r\n           Module: apps\/breakpointer\/1.0\/bin\r\n      Module path: \/opt\/gridware\/etc\/modules\/apps\/breakpointer\/1.0\/bin\r\n     Package path: \/opt\/gridware\/pkg\/apps\/breakpointer\/1.0\/bin\r\n\r\n       Repository: git+http:\/\/download.alces-software.com\/git\/packager-base@cdc9148\r\n          Package: ext\/breakpointer\/1.0@9068e192\r\n      Last update: 2014-05-02\r\n\r\n          Builder: root@headnode1.lampredi.cluster.local\r\n       Build date: 2014-05-02T15:29:09\r\n Build parameters: tarball=\/opt\/gridware\/ext\/BreakPointer_1.0.tar\r\n         Compiler: N\/A\r\n     Dependencies: apps\/bwa\/0.6.2\/gcc-4.4.6 (using: apps\/bwa\/0.6.2\/gcc-4.4.6)\r\n                   apps\/samtools\/0.1.8\/gcc-4.4.6 (using: apps\/samtools\/0.1.8\/gcc-4.4.6)\r\n\r\nFor further information, execute:\r\n\r\n\tmodule help apps\/breakpointer\/1.0\/bin\r\n\r\n&gt;&gt; GET STARTED &lt;&lt;\r\n\r\nPlease refer to the website for further details on usage of this\r\npackage.\r\n<\/pre>\n<pre>\r\n$ module show apps\/breakpointer\/1.0\/bin\r\n\r\n\/opt\/gridware\/etc\/modules\/apps\/breakpointer\/1.0\/bin:\r\n\r\nmodule-whatis\t \r\n\r\n            Title: BreakPointer\r\n          Summary: Pinpoint rearrangement breakpoints using paired end reads\r\n          License: NONFREE - For academic non-commercial research purposes only\r\n            Group: Bioinformatics\r\n              URL: http:\/\/www.broadinstitute.org\/cancer\/cga\/breakpointer\r\n\r\n             Name: breakpointer\r\n          Version: 1.0\r\n           Module: apps\/breakpointer\/1.0\/bin\r\n      Module path: \/opt\/gridware\/etc\/modules\/apps\/breakpointer\/1.0\/bin\r\n     Package path: \/opt\/gridware\/pkg\/apps\/breakpointer\/1.0\/bin\r\n\r\n       Repository: git+http:\/\/download.alces-software.com\/git\/packager-base@cdc9148\r\n          Package: ext\/breakpointer\/1.0@9068e192\r\n      Last update: 2014-05-02\r\n\r\n          Builder: root@headnode1.lampredi.cluster.local\r\n       Build date: 2014-05-02T15:29:09\r\n Build parameters: tarball=\/opt\/gridware\/ext\/BreakPointer_1.0.tar\r\n         Compiler: N\/A\r\n     Dependencies: apps\/bwa\/0.6.2\/gcc-4.4.6 (using: apps\/bwa\/0.6.2\/gcc-4.4.6)\r\n                   apps\/samtools\/0.1.8\/gcc-4.4.6 (using: apps\/samtools\/0.1.8\/gcc-4.4.6)\r\n\r\nFor further information, execute:\r\n\r\n\tmodule help apps\/breakpointer\/1.0\/bin\r\n \r\nmodule-prereq\t apps\/bwa\/0.6.2\/gcc-4.4.6 \r\nmodule-prereq\t apps\/samtools\/0.1.8\/gcc-4.4.6 \r\nmodule-conflict\t apps\/breakpointer \r\nsetenv\t\t BREAKPOINTERDIR \/opt\/gridware\/pkg\/apps\/breakpointer\/1.0\/bin \r\nsetenv\t\t BREAKPOINTERBIN \/opt\/gridware\/pkg\/apps\/breakpointer\/1.0\/bin\/bin \r\nprepend-path\t LD_LIBRARY_PATH \/opt\/gridware\/pkg\/apps\/breakpointer\/1.0\/bin\/lib\/mcr\/v710\/sys\/java\/jre\/glnxa64\/jre\/lib\/amd64 \r\nprepend-path\t LD_LIBRARY_PATH \/opt\/gridware\/pkg\/apps\/breakpointer\/1.0\/bin\/lib\/mcr\/v710\/sys\/java\/jre\/glnxa64\/jre\/lib\/amd64\/client \r\nprepend-path\t LD_LIBRARY_PATH \/opt\/gridware\/pkg\/apps\/breakpointer\/1.0\/bin\/lib\/mcr\/v710\/sys\/java\/jre\/glnxa64\/jre\/lib\/amd64\/server \r\nprepend-path\t LD_LIBRARY_PATH \/opt\/gridware\/pkg\/apps\/breakpointer\/1.0\/bin\/lib\/mcr\/v710\/sys\/java\/jre\/glnxa64\/jre\/lib\/amd64\/native_threads \r\nprepend-path\t LD_LIBRARY_PATH \/opt\/gridware\/pkg\/apps\/breakpointer\/1.0\/bin\/lib\/mcr\/v710\/sys\/os\/glnxa64 \r\nprepend-path\t LD_LIBRARY_PATH \/opt\/gridware\/pkg\/apps\/breakpointer\/1.0\/bin\/lib\/mcr\/v710\/bin\/glnxa64 \r\nprepend-path\t LD_LIBRARY_PATH \/opt\/gridware\/pkg\/apps\/breakpointer\/1.0\/bin\/lib\/mcr\/v710\/runtime\/glnxa64 \r\nsetenv\t\t XAPPLRESDIR \/opt\/gridware\/pkg\/apps\/breakpointer\/1.0\/bin\/lib\/mcr\/v710\/X11\/app-defaults \r\nprepend-path\t PATH \/opt\/gridware\/pkg\/apps\/breakpointer\/1.0\/bin\/bin \r\n<\/pre>\n<p>Lampredi HPC<br \/>\nigm-lampredi-users@ncl.ac.uk<\/p>\n<p>IGM IT<br \/>\nigmithelp@ncl.ac.uk<br \/>\nx8625<\/p>\n","protected":false},"excerpt":{"rendered":"<p>$ module load apps\/breakpointer\/1.0\/bin apps\/breakpointer\/1.0\/bin | &#8212; apps\/bwa\/0.6.2\/gcc-4.4.6 | | &#8212; libs\/gcc\/system | | * &#8211;&gt; OK | * &#8211;&gt; OK | &#8212; apps\/samtools\/0.1.8\/gcc-4.4.6 | | &#8212; libs\/gcc\/system &#8230; SKIPPED (already loaded) | * &#8211;&gt; OK | OK $ ls $BREAKPOINTERBIN BreakPointer BreakPointer.sh fh_BreakPointerScatter $ ls $BREAKPOINTERDIR bin doc lib share $ module whatis apps\/breakpointer <a href='https:\/\/blogs.ncl.ac.uk\/igmit\/?p=398' class='excerpt-more'>[&#8230;]<\/a><\/p>\n","protected":false},"author":1149,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[11,10,9,21],"class_list":["post-398","post","type-post","status-publish","format-standard","hentry","category-uncategorized","tag-cluster","tag-hpc","tag-lampredi","tag-lampredi2","category-1-id","post-seq-1","post-parity-odd","meta-position-corners","fix"],"_links":{"self":[{"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/posts\/398","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/users\/1149"}],"replies":[{"embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=398"}],"version-history":[{"count":13,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/posts\/398\/revisions"}],"predecessor-version":[{"id":418,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/posts\/398\/revisions\/418"}],"wp:attachment":[{"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=398"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=398"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=398"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}