root/galaxy-central/templates/webapps/community/tool/help.mako

リビジョン 2, 8.0 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<%namespace file="/message.mako" import="render_msg" />
2
3<%!
4   def inherit(context):
5       if context.get('use_panels'):
6           return '/webapps/community/base_panels.mako'
7       else:
8           return '/base.mako'
9%>
10<%inherit file="${inherit(context)}"/>
11
12<%def name="title()">Tool Help</%def>
13
14<h2>Tool Help</h2>
15
16%if message:
17    ${render_msg( message, status )}
18%endif
19
20<p/>
21<div class="toolFormTitle">Creating an archive containing a tool or a suite of tools</div>
22<p>
23    A tool or tool suite archive is a tar-format file (bzipped or gzipped tar are valid)
24    containing all the files necessary to load the tool(s) into a Galaxy instance.
25</p>
26<h3>Tool Suite Archive</h3>
27<p>
28    A tools suite must include a file named <code>suite_config.xml</code> which provides information about the id, name,
29    version and description of the tool suite, as well as the id, name, version and description of each tool
30    in the suite.  Here is an example <code>suite_config.xml</code> file.
31</p>
32<p>
33<pre>
34    &lt;suite id="lastz_toolsuite" name="Suite of Lastz tools" version="1.0.0"&gt;
35        &lt;description&gt;This suite contains all of my Lastz tools for Galaxy&lt;/description&gt;
36        &lt;tool id="lastz_wrapper_2" name="Lastz" version="1.1.0"&gt;
37            &lt;description&gt; map short reads against reference sequence&lt;/description&gt;
38        &lt;/tool&gt;
39        &lt;tool id="lastz_paired_reads_wrapper" name="Lastz paired reads" version="1.0.0"&gt;
40            &lt;description&gt; map short paired reads against reference sequence&lt;/description&gt;
41        &lt;/tool&gt;
42    &lt;/suite&gt;
43</pre>
44</p>
45</p>
46<p>
47    New versions of the suite can be uploaded, replacing an older version of the suite, but the version attribute
48    of the <suite> tag must be altered the same way that the version attribute of a single tool config must be altered
49    if uploading a new version of a tool.
50</p>
51<p>
52    The id, name and version attributes of each <tool> tag in the <code>suite_config.xml</code> file must exactly match the same
53    attributes in each associated tool config in the archive or you will not be allowed to upload the archive.
54</p>
55<p>
56    In addition to the <code>suite_config.xml</code> file, the archive must include all
57    <a href="http://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax" target="_blank">tool config files</a>,
58    executables, functional test data (if your tool config includes functional tests) and other files needed for each
59    of the tools in your suite to function within Galaxy.  See the information about single tool archives below for
60    additional hints to enable ease-of-use when others download your suite of tools.
61</p>
62<p>
63    For example, to package the above Lastz suite of tools:
64<pre>
65    user@host:~% tar jcvf ~/Desktop/galaxy_lastz_toolsuite.tar.bz2 lastzsuite
66    lastzsuite/
67    lastzsuite/README
68    lastzsuite/suite_config.xml
69    lastzsuite/lastz_paired_reads_wrapper.py
70    lastzsuite/lastz_paired_reads_wrapper.xml
71    lastzsuite/lastz_wrapper.py
72    lastzsuite/lastz_wrapper.xml
73    lastzsuite/lastz-distrib-1.02.00/
74    lastzsuite/lastz-distrib-1.02.00/src/
75    lastzsuite/lastz-distrib-1.02.00/src/Makefile
76    lastzsuite/lastz-distrib-1.02.00/src/version.mak
77    lastzsuite/lastz-distrib-1.02.00/src/lastz.c
78    lastzsuite/lastz-distrib-1.02.00/src/lastz.h
79    ...
80</pre>
81    ~/Desktop/galaxy_lastz_tool.tar.bz2 is now ready to be uploaded.
82</p>
83<h3>Single Tool Archive</h3>
84<p>
85    A single tool archive must include a
86    <a href="http://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax" target="_blank">tool config file</a>
87    and will probably also include a tool script.  If any steps are necessary to install your tool beyond the basic
88    instructions below, include a README file to provide details.  If the tool (or parts of it) are written in C,
89    the source code can be included (or put links to the source in the README).  Do not include pre-compiled binaries
90    without source since Galaxy is run on a wide variety of platforms.  Also, if you are only wrapping or providing a
91    Galaxy config for a tool that is not your own, be sure the license allows for redistribution before including any
92    part of that tool in the archive.
93</p>
94<p>
95    There are no requirements about the directory structure inside the archive, but for ease of use it's generally
96    a good idea to put everything inside a sub-directory, instead of directly at the top level.
97</p>
98<p>
99    For example, to package the Lastz tool's config file, Galaxy wrapper, and the C source:
100<pre>
101    user@host:~% tar jcvf ~/Desktop/galaxy_lastz_tool.tar.bz2 lastz
102    lastz/
103    lastz/README
104    lastz/lastz_wrapper.py
105    lastz/lastz_wrapper.xml
106    lastz/lastz-distrib-1.02.00/
107    lastz/lastz-distrib-1.02.00/src/
108    lastz/lastz-distrib-1.02.00/src/Makefile
109    lastz/lastz-distrib-1.02.00/src/version.mak
110    lastz/lastz-distrib-1.02.00/src/lastz.c
111    lastz/lastz-distrib-1.02.00/src/lastz.h
112    ...
113</pre>
114    ~/Desktop/galaxy_lastz_tool.tar.bz2 is now ready to be uploaded.
115</p>
116<h3>Editing Information, Categories, and Submitting For Approval</h3>
117<p>
118    Simply uploading a tool to the Galaxy too shed will not allow other users to find and download your tool.  It will
119    need to be approved by an administrator before it appears in the tool list.
120</p>
121<p>
122    After your archive has successfully uploaded, you will be redirected to the Edit Tool page.  Provide a detailed
123    description of what the tool does - this will be used by administrators to understand the tool before approving it
124    for display on the site.  Once approved, this information will be displayed to users who view your tool.  In addition,
125    the site administrators will have configured a number of categories with which you can associate your tool to make it
126    easy to find by users looking to solve specific problems.  Associate as many categories as are relevant to your tool.
127    You may change the description and associated categories as often as you'd like until you click the "<strong>Submit for
128    approval</strong>" button.  Once submitted, the tool will be approved or rejected by an administrator.  If the tool is
129    rejected, you will see information about why it was rejected, and you can make appropriate changes to the archive and
130    re-submit it for approval.  When it is approved, your archive will be visible to everyone.  At that point, the description
131    and associated categories can only be changed by an administrator.
132</p>
133<p>
134    When the tool has been approved or rejected, you may upload a new version by browsing to the tool's "View Tool" page,
135    clicking the "Tool actions" menu in the upper right corner of the page, and selecting "Upload a new version" from the
136    menu.
137</p>
138<hr/>
139<h3>Downloading and Installing Tools</h3>
140<p>
141    A tool's download link will send you the tool archive.  Once downloaded, unpack the tool on your local Galaxy instance's server:
142<pre>
143    user@host:~% tar xvf galaxy_lastz_tool.tar
144    ...
145    user@host:~% tar zxvf galaxy_lastz_tool.tar.gz
146    ...
147    user@host:~% tar jxvf galaxy_lastz_tool.tar.bz2
148    ...
149</pre>
150    If the archive includes a README file, consult it for installation instructions.  If not, follow these basic steps:
151    <ol>
152        <li>Create a directory under <code>galaxy_dist/tools/</code> to house downloaded tool(s).</li>
153        <li>In the new directory, place the XML and any script file(s) which were contained in the archive.</li>
154        <li>
155            If the tool includes binaries, you'll need to copy them to a directory on your <code>$PATH</code>.  If the tool depends on
156            C binaries but does not come with them (only source), you'll need to compile the source first.
157        </li>
158        <li>Add the tool to <code>galaxy_dist/tool_conf.xml</code>.</li>
159        <li>Restart your Galaxy server process.</li>
160    </ol>
161</p>
162<p>
163    In the near future, we plan to implement a more direct method to install tools via the Galaxy administrator user interface instead
164    of placing files on the filesystem and manually managing the <code>tool_conf.xml</code> file.
165</p>
166
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