{"id":827,"date":"2014-08-27T00:07:30","date_gmt":"2014-08-26T22:07:30","guid":{"rendered":"http:\/\/bioinfo2.ugr.es\/srnatoolbox\/?page_id=827"},"modified":"2022-03-30T10:31:47","modified_gmt":"2022-03-30T08:31:47","slug":"standalone","status":"publish","type":"page","link":"https:\/\/bioinfo2.ugr.es\/srnatoolbox\/standalone\/","title":{"rendered":"Standalone"},"content":{"rendered":"<table>\n<tbody>\n<tr>\n<td style=\"border-color: #a61b1b; text-align: center;\"><strong>We strongly recommend using the <a href=\"https:\/\/hub.docker.com\/r\/ugrbioinfo\/srnatoolbox\">docker<\/a> version instead of the standalone. See <a href=\"https:\/\/bioinfo2.ugr.es\/srnatoolbox\/srnatoolbox-docker\/\">this<\/a> page for more information.<\/strong><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<h4>Currently sRNAbench and sRNAde can be downloaded as standalone versions<\/h4>\n<h3>Dependencies<\/h3>\n<p>sRNAbench and sRNAde are implemented in JAVA and need apart from a JRE the following third party software that needs to be installed<strong> and placed in the PATH<\/strong> first.<\/p>\n<ul>\n<li>Vienna RNA package for RNA Secondary Structure Prediction and Comparison <a href=\"http:\/\/www.tbi.univie.ac.at\/~ronny\/RNA\/\">Vienna package 2<\/a>. <strong>sRNAbench will only work with Vienna 2.0 or higher! <\/strong><\/li>\n<li>Bowtie &#8211; An ultra-fast memory-efficient short read aligner (<a href=\"http:\/\/bowtie-bio.sourceforge.net\/index.shtml\">Bowtie<\/a>). <strong>sRNAbench will only work with Bowtie1 but not Bowtie2<\/strong>.<\/li>\n<li>For the differential expression program sRNAde: <a href=\"http:\/\/www.bioconductor.org\/packages\/2.12\/bioc\/html\/edgeR.html\">edgeR package<\/a> [4], <a href=\"http:\/\/bioconductor.org\/packages\/release\/bioc\/html\/DESeq.html\">DEseq<\/a> [5], <a href=\"https:\/\/www.bioconductor.org\/packages\/release\/bioc\/html\/NOISeq.html\">NOISeq<\/a> [6] (<a href=\"https:\/\/www.r-project.org\/\">R packages<\/a>) and <a href=\"http:\/\/commons.apache.org\/proper\/commons-math\/\">The Apache Commons Mathematics Library<\/a><\/li>\n<li><a href=\"http:\/\/www.ncbi.nlm.nih.gov\/books\/NBK158900\/\">SRA tool kit<\/a>: only if the user wants to use data from <a href=\"http:\/\/www.ncbi.nlm.nih.gov\/sra\">SRA<\/a> as input files as those need to be converted to fastq first.<\/li>\n<\/ul>\n<h3><a name=\"_Toc457468404\"><\/a>Get started with the standalone<\/h3>\n<p>sRNAbench and sRNAde rely on a local database where most of the library files, genome sequences, Rscripts and Bowtie indexes need to be stored. The database can have any arbitrary name and the easiest way to generate it is by means of the \u201cstart-up\u201d DB following the next steps:<\/p>\n<ol>\n<li>Download the \u201cstart-up\u201d database: <a href=\"http:\/\/bioinfo2.ugr.es\/sRNAtoolboxDB\/sRNAtoolboxDB.tgz\">sRNAtoolboxDB<\/a>. Please note that this does not generate a full database, i.e. it includes only microRNAs for <em>Human, human herpesvirus type 8 (HHV-8) and Epstein-Barr virus (EBV). <\/em>To populate the database, please see below.<\/li>\n<li>Extract it to the directory of your choice:<em> tar xvzf sRNAtoolboxDB.tgz . <\/em><strong>We recommend to use \/opt\/sRNAtoolboxDB<\/strong> (All programs take this directory as default value)<\/li>\n<li>Download the most recent version and replace the sRNAbench.jar and sRNAde.jar files form the database: <a href=\"http:\/\/bioinfo2.ugr.es\/sRNAtoolboxDB\/exec\/sRNAbench.jar\">sRNAbench.jar<\/a> &amp;&amp; <a href=\"http:\/\/bioinfo2.ugr.es\/sRNAtoolboxDB\/exec\/sRNAde.jar\">sRNAde.jar<\/a><\/li>\n<\/ol>\n<p>After extracting the database, you should see the following folders:<\/p>\n<ul>\n<li><strong>libs:<\/strong> The default location for all sequence libraries except the genome sequences<\/li>\n<li><strong>index:<\/strong> This folder contains the Bowtie indexes of the genome sequences<\/li>\n<li><strong>seqOBJ:<\/strong> This folder contains the prepared genome sequences in order to access them rapidly (the files can be generated by means of the <a href=\"http:\/\/bioinfo2.ugr.es\/sRNAtoolboxDB\/exec\/makeSeqObj.jar\">makeSeqObj<\/a> program).<\/li>\n<li><strong>exec<\/strong>: the programs, i.e. jar and other executable files<\/li>\n<\/ul>\n<p><strong>out<\/strong>: The default <em>output<\/em> folder. This directory is always used if the output= parameter is omitted<\/p>\n","protected":false},"excerpt":{"rendered":"<p>We strongly recommend using the docker version instead of the standalone. See this page for more information. Currently sRNAbench and sRNAde can be downloaded as standalone versions Dependencies sRNAbench and sRNAde are implemented in JAVA and need apart from a<span class=\"ellipsis\">&hellip;<\/span><\/p>\n<div class=\"read-more\"><a href=\"https:\/\/bioinfo2.ugr.es\/srnatoolbox\/standalone\/\">Read more &#8250;<\/a><\/div>\n<p><!-- end of .read-more --><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"open","template":"","meta":[],"_links":{"self":[{"href":"https:\/\/bioinfo2.ugr.es\/srnatoolbox\/wp-json\/wp\/v2\/pages\/827"}],"collection":[{"href":"https:\/\/bioinfo2.ugr.es\/srnatoolbox\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/bioinfo2.ugr.es\/srnatoolbox\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/bioinfo2.ugr.es\/srnatoolbox\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/bioinfo2.ugr.es\/srnatoolbox\/wp-json\/wp\/v2\/comments?post=827"}],"version-history":[{"count":13,"href":"https:\/\/bioinfo2.ugr.es\/srnatoolbox\/wp-json\/wp\/v2\/pages\/827\/revisions"}],"predecessor-version":[{"id":1147,"href":"https:\/\/bioinfo2.ugr.es\/srnatoolbox\/wp-json\/wp\/v2\/pages\/827\/revisions\/1147"}],"wp:attachment":[{"href":"https:\/\/bioinfo2.ugr.es\/srnatoolbox\/wp-json\/wp\/v2\/media?parent=827"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}