toolshed added

docs/source/index.rst

@@ -32,6 +32,7 @@ MGEScan on Amazon Cloud (AWS EC2).
    workflow
    tutorial-cmd
    installation
+   toolshed
    aws
    ltr
    nonltr

docs/source/tooshed.rst

@@ -0,0 +1,72 @@
+MGEScan ToolShed
+===============================================================================
+
+MGEScan is available in Galaxy ToolShed to install MGEScan tools and
+dependencies from the public Galaxy Tool Shed (https://toolshed.g2.bx.psu.edu).
+A few clicks allow you to install MGEScan and required software easily e.g.
+HMMER, Tandem Repeat Finder, and EMBOSS. The following installation guide
+explains how to apply MGEScan to your existing or brand new Galaxy server using
+ToolShed.
+
+Installation Guide
+-------------------------------------------------------------------------------
+
+Prerequite
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+You need to make sure the following system packages are available on your
+system prior to install MGEScan.
+
+* Python pip
+* Python setuptools
+* Python dev package
+* MPI for parallel processing (i.e. openmpi-bin, libopenmpi-dev on Ubuntu)
+
+
+Admin Page
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+Admin user only is able to add a new Galaxy Tool from ToolShed. Find **Admin**
+link from the top menu tab. Click **Search Tool Shed** on the left menu tab of
+the Admin page.
+
+.. image:: images/toolshed-registration1.png
+
+If you can find 'Galaxy Main Tool Shed' select button on the right page, click
+**Browse valid repositories**.  It redirects the page to the public Galaxy
+toolshed page in which 3,728 tools available in 2016.
+
+.. image:: images/toolshed-registration2.png
+
+Type ``mgescan`` in the search box. Choose ``mgescan``, not
+``package_mgescan_3_0_0`` to preview and install.  You may find there are other
+dependencies to be installed as well. If you are ready to install, find
+**Install to Galaxy** button on top of the page. It goes to the confirmation page.
+
+.. image:: images/toolshed-registration-if-tool_dependency_dir_is_not_set.png
+
+.. note:: You need to make sure `repository dependencies` and `tool
+        dependencies` are checked in the page. Otherwise, necessary tools or
+        repositories may not be installed properly.
+
+You will find **Install** button at the bottom of the page. Once you click the
+button, your Galaxy server starts to download tools and repositories and
+install MGEScan on your Galaxy.
+
+.. image:: images/toolshed-registration3.png
+.. image:: images/toolshed-registration-installation.png
+
+You can find MGEScan from **Manage installed tools** page from the left menu
+tab in the admin page.  ``mgescan`` tool adds EMBSS, HMMER, Tandem Repeat
+Finder and MGEScan packages.  You need to find all these tools are successfully
+installed. *Installation Status* indicates whether is is installed properly
+with colors. *Installed* with light green box indicates the tool or package
+installation is succeeded, if you see grey box, there is some issue in the
+installation.
+
+.. image:: images/toolshed-registration-installation-after.png
+
+Go to the main page of your Galaxy. The new **MGEScan MGEScan** tool is
+available on your left tool menu tab.
+
+.. image:: images/toolshed-registration-mgescan-tool.png