Mercurial > repos > saml > semweb_tools
changeset 4:ee072a7d271b draft
Uploaded
author | saml |
---|---|
date | Wed, 21 Nov 2012 12:53:24 -0500 |
parents | 4b4bbcf5db31 |
children | eee537fd4600 |
files | galaxy_semwebtools |
diffstat | 1 files changed, 797 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_semwebtools Wed Nov 21 12:53:24 2012 -0500 @@ -0,0 +1,797 @@ +<!DOCTYPE html> +<html lang="en"> +<head> + <meta charset="utf-8"> + <meta http-equiv="X-UA-Compatible" content="IE=edge" /> + <title> + saml / galaxy_semwebtools — Bitbucket +</title> + <link rel="icon" type="image/png" href="https://dwz7u9t8u8usb.cloudfront.net/m/2219cd120e6a/img/favicon.png"> + <meta id="bb-canon-url" name="bb-canon-url" content="https://bitbucket.org"> + + +<link rel="stylesheet" href="https://dwz7u9t8u8usb.cloudfront.net/m/2219cd120e6a/compressed/css/0def6d819f1a.css" type="text/css" /> + + <!--[if lt IE 9]><link rel="stylesheet" href="https://dwz7u9t8u8usb.cloudfront.net/m/2219cd120e6a/css/aui/aui-ie.css" media="all"><![endif]--> + <!--[if IE 9]><link rel="stylesheet" href="https://dwz7u9t8u8usb.cloudfront.net/m/2219cd120e6a/css/aui/aui-ie9.css" media="all"><![endif]--> + <!--[if IE]><link rel="stylesheet" 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href="/saml/galaxy_semwebtools/changesets" id="repo-commits-link"> + Commits + </a> + </li> + + + <li> + <a href="/saml/galaxy_semwebtools/pull-requests" id="repo-pullrequests-link"> + Pull Requests + + + + </a> + </li> + + <li id="issues-tab" class=" + + hidden + + "> + <a href="/saml/galaxy_semwebtools/issues?status=new&status=open" id="repo-issues-link"> + Issues + + + + </a> + </li> + <li id="wiki-tab" class=" + + hidden + + "> + <a href="/saml/galaxy_semwebtools/wiki" id="repo-wiki-link">Wiki</a> + </li> + + <li> + <a href="/saml/galaxy_semwebtools/downloads" id="repo-downloads-link"> + Downloads + + + + </a> + </li> + + + </ul> + </div> + </nav> + + <div id="content" role="main"> + + <div id="repo-content"> + + <div id="repo-overview"> + + + + <div class="column"> + + + + <section id="readme"> + + <article class="readme file"> + <h1 id="semantic-web-tools-for-galaxy">Semantic Web Tools for Galaxy</h1> +<h2 id="sparql-import-tool">SPARQL Import tool</h2> +<p>This <a href="http://galaxyproject.org/">Galaxy (bioinformatics web portal)</a> toolkit currently just contains a tool that enables to specify an URL to a SPARQL endpoint, and a SPARQL query, and to save the returned data in tabular format, for further processing in Galaxy's tools.</p> +<h2 id="installation">Installation</h2> +<ol> +<li>Create a folder "semweb_tools" under [galaxy_root]/tools/ and add these files.</li> +<li>Add the following section right under the starting &lt;toolbox&gt; tag in [galaxy_root]/tool_conf.xml:</li> +</ol> +<div class="codehilite"><pre> <span class="nt"><section</span> <span class="na">name=</span><span class="s">"Semantic Web Tools"</span> <span class="na">id=</span><span class="s">"semweb_tools"</span><span class="nt">></span> + <span class="nt"><tool</span> <span class="na">file=</span><span class="s">"semweb_tools/sparql_import.xml"</span> <span class="nt">/></span> + <span class="nt"></section></span> +</pre></div> + + +<h2 id="change-log">Change log</h2> +<ul> +<li>2012-11-16: Now works properly (at least for my simple test case)!</li> +<li>2012-11-16: Created today, still under heavy development!</li> +</ul> + </article> + + </section> + + + + <section id="repo-activity"> + <h1> + Recent Activity + <a href="/saml/galaxy_semwebtools/rss" class="rss"><img src="https://dwz7u9t8u8usb.cloudfront.net/m/2219cd120e6a/img/icons/rss.png" alt="RSS feed for galaxy_semwebtools" title="RSS feed for galaxy_semwebtools" /></a> + </h1> + + + + + + + + + +<div class="newsfeed"> + + + + + + + + + <article class="news-item commit"> + <span class="icon commit"></span> + + + + <a href="/saml"><img alt="Samuel Lampa" src="https://secure.gravatar.com/avatar/87d770f5a0843a130b55572651e9d7d0?d=https%3A%2F%2Fdwz7u9t8u8usb.cloudfront.net%2Fm%2F2219cd120e6a%2Fimg%2Fdefault_avatar%2F32%2Fuser_blue.png&s=32" class="avatar avatar32" /></a> + + + <p> + + + <a href="/saml">Samuel Lampa</a> + + committed to + + +<a href="/saml/galaxy_semwebtools" title="saml/galaxy_semwebtools">saml/galaxy_semwebtools</a> + + + </p> + <time datetime="2012-11-21T17:52:02+00:00">a minute ago</time> + <div class="changeset"> + <a href="/saml/galaxy_semwebtools/changeset/ddc47ed3955c049a79c9407846f856ee" class="changeset-hash">ddc47ed</a> + - + + Initial check-in + + </div> + + + + + + + + + + + + + </article> + + + + + + + <article class="news-item create"> + <span class="icon create"></span> + + + + <a href="/saml"><img alt="Samuel Lampa" src="https://secure.gravatar.com/avatar/87d770f5a0843a130b55572651e9d7d0?d=https%3A%2F%2Fdwz7u9t8u8usb.cloudfront.net%2Fm%2F2219cd120e6a%2Fimg%2Fdefault_avatar%2F32%2Fuser_blue.png&s=32" class="avatar avatar32" /></a> + + + + <p> + + + <a href="/saml">Samuel Lampa</a> + + created + + +<a href="/saml/galaxy_semwebtools" title="saml/galaxy_semwebtools">saml/galaxy_semwebtools</a> + +</p> + + + <time datetime="2012-11-21T17:49:18+00:00">4 minutes ago</time> + + + + + + + </article> + + + + + +</div> + + + + + + + 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Level</dt> + <dd>Public</dd> + + <dt>Type</dt> + <dd>Mercurial</dd> + + + <dt>Language</dt> + <dd>Python</dd> + + + <dt>Last Updated</dt> + <dd><time datetime="2012-11-21T18:52:02.581101">a minute ago</time></dd> + + <dt>Created</dt> + <dd><time datetime="2012-11-21T18:49:18.906678">4 minutes ago</time></dd> + + <dt>Size</dt> + <dd> + 3.9 KB + <a rel="nofollow" + + href="/saml/galaxy_semwebtools/get/ddc47ed3955c.zip" + + >(download)</a> + </dd> + + + + </dl> + </section> + + + + + + </div> + <div class="clearfix"></div> + + + + </div> + + + + </div> + + </div> + </div> + <footer id="footer" role="contentinfo"> + <section class="footer-body"> + <ul> + <li><a href="http://blog.bitbucket.org">Blog</a></li> + <li><a href="//bitbucket.org/site/master/issues/new">Report a Bug</a></li> + <li><a href="/support">Support</a></li> + <li><a href="http://confluence.atlassian.com/display/BITBUCKET">Documentation</a></li> + <li><a href="http://confluence.atlassian.com/x/IYBGDQ">API</a></li> + <li><a 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