Revert "temporarily empty repository"

This reverts commit 27cbb9c.

.gitignore

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+.settings
+.classpath
+.project
+target
+.DS_Store
+.springBeans
+/datanucleus.log

.opf.yml

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+name: Taverna Server
+vendor: The University of Manchester
+maintainer:
+	name: Donal Fellows
+	email: donal.k.fellows( AT )manchester.ac.uk
+platform: "Java 6+, Tomcat 6, POSIX"
+download: http://www.taverna.org.uk/download/server/
+# Really the documentation page as the overall home page is shared with the workbench but will do for now
+homepage: http://dev.mygrid.org.uk/wiki/display/taverna/Taverna+Server+2.4
+issues: http://dev.mygrid.org.uk/issues/browse/TAVSERV
+# Note, no anti-spam armouring required for this one
+support-contact: support@mygrid.org.uk

CITATION

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+Wolstencroft, K., Haines, R., Fellows, D., Williams, A., Withers, D.,
+  Owen, S., Soiland-Reyes, S., Dunlop, I., Nenadic, A., Fisher, P., Bhagat, J.,
+  Belhajjame, K., Bacall, F., Hardisty, A., Nieva de la Hidalga, A.,
+  Balcazar Vargas, M.P., Sufi, S., and Goble, C.  2013.
+The Taverna workflow suite: designing and executing workflows of Web Services
+on the desktop, web or in the cloud.  Nucl. Acids Res. gkt328v1
+http://doi.org/doi:10.1093/nar/gkt328
+
+@article{Wolstencroft02052013,
+  author = {Wolstencroft, Katherine and Haines, Robert and Fellows, Donal and Williams, Alan and Withers, David and Owen, Stuart and Soiland-Reyes, Stian and Dunlop, Ian and Nenadic, Aleksandra and Fisher, Paul and Bhagat, Jiten and Belhajjame, Khalid and Bacall, Finn and Hardisty, Alex and Nieva de la Hidalga, Abraham and Balcazar Vargas, Maria P. and Sufi, Shoaib and Goble, Carole}, 
+  title = {The {Taverna} workflow suite: designing and executing workflows of {Web Services} on the desktop, web or in the cloud},
+  year = {2013}, 
+  doi = {10.1093/nar/gkt328}, 
+  abstract ={The Taverna workflow tool suite (http://www.taverna.org.uk) is designed to combine distributed Web Services and/or local tools into complex analysis pipelines. These pipelines can be executed on local desktop machines or through larger infrastructure (such as supercomputers, Grids or cloud environments), using the Taverna Server. In bioinformatics, Taverna workflows are typically used in the areas of high-throughput omics analyses (for example, proteomics or transcriptomics), or for evidence gathering methods involving text mining or data mining. Through Taverna, scientists have access to several thousand different tools and resources that are freely available from a large range of life science institutions. Once constructed, the workflows are reusable, executable bioinformatics protocols that can be shared, reused and repurposed. A repository of public workflows is available at http://www.myexperiment.org. This article provides an update to the Taverna tool suite, highlighting new features and developments in the workbench and the Taverna Server.}, 
+  URL = {http://nar.oxfordjournals.org/content/early/2013/05/02/nar.gkt328.abstract}, 
+  eprint = {http://nar.oxfordjournals.org/content/early/2013/05/02/nar.gkt328.full.pdf+html}, 
+  journal = {Nucleic Acids Research} 
+}

README.md

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+A Beginner's Installation Guide to Taverna Server
+=================================================
+
+When installing Taverna Server 2.5, you *need* to decide whether to
+install in secure or insecure mode. In secure mode, the server
+enforces logins, ensures that they are done over HTTPS, and applies
+strong restrictions to what users can see of other users'
+workflows. In insecure mode, no restrictions are enforced which
+simplifies configuration but greatly reduces the overall system
+security. *Do not mix up installations between the two types.*
+
+You will need:
+
+* **Unix** (e.g., Linux, OSX). Running Linux inside a virtual machine
+  works. Running directly on Windows is not supported.
+
+* **Java 7** (or later) installed. See the Java requirements on the
+  [Taverna website](http://www.taverna.org.uk/download/workbench/system-requirements/).
+
+* **Tomcat 6** (recent version).
+
+* **Taverna Server 2.5**. Either the "full installation" or WAR will do
+  (the "full installation" zip contains a copy of the WAR) - see the
+  [Taverna website](http://www.taverna.org.uk/download/server/2-4/) for details on downloading the file.
+
+If you are installing in secured mode (default) you will also need:
+
+* **SSL** (i.e., HTTPS) **host certificate**. This should not be
+  self-signed and should have the hostname in the Common Name (CN)
+  field. (Self-signed certificates or ones without the hostname in are
+  exceptionally awkward for clients to work with, and proper
+  single-host certificates are in reality very cheap. Save yourself a
+  lot of work here!)
+
+* For the simplest operation, you should create a user `taverna` that is
+  a member of the group called `taverna`. This user will be used for
+  executing workflows, and does not need to allow anyone to log in as
+  it.
+
+Stick to the Factory Defaults
+-----------------------------
+
+Taverna Server 2.5 has a long list of things that may be configured,
+but it comes with “factory” settings that are correct in the majority
+of cases. Leave them alone for your first installation.
+
+Setting up Tomcat
+-----------------
+
+Note that the instructions below do not describe setting up Tomcat
+users. These are not necessary for Taverna Server, as that needs
+finer-grained permission control than is normal for a webapp.
+
+You can always find further information by searching the web for
+“_install tomcat6 YourOperatingSystem_”.
+
+### Installing on Debian Linux, Ubuntu
+
+On Debian Linux (and derivatives), you install Tomcat with:
+
+    sudo apt-get install tomcat6 tomcat6-admin tomcat6-common tomcat6-user
+
+You then start Tomcat with:
+
+    sudo /etc/init.d/tomcat6 start
+
+And stop it with:
+
+    sudo /etc/init.d/tomcat6 stop
+
+It's configuration file (called `conf/server.xml` in the instructions below) will be in:
+
+    /etc/tomcat6/server.xml
+
+It's webapp directory (`webapps` below) will be in:
+
+    /var/lib/tomcat6
+
+### Installing on RedHat Linux, Fedora, CentOS, Scientific Linux
+
+On RedHat Linux (and derivatives), you install Tomcat with:
+
+    yum install tomcat6-webapps
+
+You then start Tomcat with:
+
+    sudo service tomcat6 start
+
+And stop it with:
+
+    sudo service tomcat6 stop
+
+It's configuration file (called `conf/server.xml` in the instructions below) will be in:
+
+    /etc/tomcat6/server.xml
+
+It's webapp directory (`webapps` below) will be in:
+
+    /var/lib/tomcat6
+
+### Installing on MacOS X, and using a baseline Apache distribution
+
+On OSX (or if otherwise installing from a standard Apache
+distribution), you install Tomcat by downloading from the distribution
+page at:
+
+* http://tomcat.apache.org/download-60.cgi
+
+Both ZIP and `.tar.gz` download versions include a file `RUNNING.txt`
+that describes how to perform the installation, start the server, and
+stop it again.
+
+The normal location of the configuration file (`conf/server.xml` in
+the instructions below) is, for Tomcat 6.0.35:
+
+    /usr/local/tomcat6.0/apache-tomcat-6.0.35/conf/server.xml
+
+And its `webapps` directory is at:
+
+    /usr/local/tomcat6.0/apache-tomcat-6.0.35/webapps
+
+Installing an Unsecured Taverna Server
+--------------------------------------
+
+This is not the default configuration of Taverna Server because it is
+_insecure_; there is no attempt to verify the identity of users or to
+keep them from interfering with each other's workflows. _We recommend
+that you use the secured version if possible._
+
+The insecure version is installed by:
+
+### First, place the WAR into Tomcat's webapps directory
+
+Use a filename that relates to what URL you want Taverna Server to
+appear at within Tomcat (e.g., if you want it to be at
+`/tavernaserver`, use the filename `webapps/tavernaserver.war`).
+
+### Next, start Tomcat (if stopped), and shut it down again once it has unpacked the WAR.
+
+At this point, Taverna Server is installed but not usable.
+
+### Then configure for unsecure operation.
+
+Go to the unpacked WAR, find its `WEB-INF/web.xml` (with the above
+installation path, it would be
+`webapps/tavernaserver/WEB-INF/web.xml`), and change the lines:
+
+    <param-value>WEB-INF/secure.xml</param-value>
+    <!-- <param-value>WEB-INF/insecure.xml</param-value> -->
+
+to read:
+
+    <!-- <param-value>WEB-INF/secure.xml</param-value> -->
+    <param-value>WEB-INF/insecure.xml</param-value>
+
+This changes which part of the rest of the server configuration is
+used. It does so by altering what part of that XML file are commented
+out. One of those two `<param-value>` lines **must** be
+uncommented. The overall XML file **must** be valid.
+
+### Finally, start Tomcat.
+
+> **NB:** When accessing an unsecured Taverna Server, for most
+    operations (such as submitting a run) you will need to pass the
+    credentials for the default user. The default user has username
+    `taverna` and password `taverna`.
+
+Installing a Secured Taverna Server
+-----------------------------------
+Taverna Server 2.5 is installed in secure mode by doing this:
+
+### First you need to enable SSL on Tomcat.
+
+With Tomcat not running, make sure that its `conf/server.xml` file
+contains a `<Connector>` definition for SSL HTTP/1.1. The file should
+contain comments on how to do this. Here's an example:
+
+    <Connector port="8443" protocol="HTTP/1.1" SSLEnabled="true"
+        maxThreads="150" scheme="https" secure="true"
+        clientAuth="false" sslProtocol="TLS" keystorePass="tomcat"
+        keystoreFile="conf/tavserv.p12" keystoreType="PKCS12" />
+
+This configuration enables secure access on port 8443 (HTTPS-alt;
+strongly recommended) with the server using the key-pair that has been
+placed in a standard PKCS #12 format file in the file `tavserv.p12` in
+the same directory as the configuration file; the key-pair file will
+be unlocked with the (rather obvious) password “`tomcat`”.
+
+Note that if the configuration file is located below `/etc`, it is
+recommended that you specify the full path to the PKCS #12 file. You
+should also ensure that the file can only be read by the Unix user
+that will be running Tomcat.
+
+### Next, you need to grant permission to the Tomcat server to run code as other users.
+
+In particular, it needs to be able to run the Java executable it is
+using as other people via `sudo`. You _should_ take care to lock this
+down heavily. You do this by using the program visudo to add these
+parts to the sudo configuration. Note that each goes in a separate
+part of the overall file, and that we assume below that Tomcat is
+running as the user `tavserv`; you will probably need to change (e.g.,
+to `tomcat` or `nobody`) as appropriate.
+
+This defines some flags for the main server user:
+
+    Defaults:tavserv   !lecture, timestamp_timeout=0, passwd_tries=1
+
+This defines a rule for who the server can switch to. Let's say that
+they have to be a member of the Unix user group `taverna`; if a user
+isn't in that group, they cannot use Taverna Server. (Note that `root`
+should not be part of the group!)
+
+    Runas_Alias        TAV = %taverna
+
+This creates the actual permission, saying that the `tavserv` user may
+run anything as any user in the alias above (i.e., in the `taverna`
+group). The `NOPASSWD` is important because it allows Taverna Server
+to do the delegation even when running as a user that can't log in.
+
+    tavserv            ALL=(TAV) NOPASSWD: ALL
+
+### Now, place the WAR into Tomcat's `webapps` directory.
+
+Use a filename that relates to what URL you want Taverna Server to
+appear at within Tomcat (e.g., if you want it to be at
+`/tavernaserver`, use the filename `webapps/tavernaserver.war`).
+
+### Finally, start Tomcat.
+

context.sample.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<!-- Sample context.xml showing how to tweak logging and some parameters. -->
+<!-- See the Install Guide for more information about this file. -->
+<Context path="/taverna-server">
+	<!-- Sample logging configuration. -->
+	<Valve className="org.apache.catalina.valves.AccessLogValve" />
+
+	<!-- Controls whether URs are logged. -->
+	<Parameter name="usage.logFile" value="%{WEBAPPROOT}/usage.log"
+		description="Full path to name of file that usage records for executed workflow runs will be dumped to. To make it relative to the webapp root, prefix with '%{WEBAPPROOT}/'." />
+	<Parameter name="usage.disableDB" value="no"
+		description="Set to yes to disable writing of URs to the database." />
+
+	<!-- For email-dispatched notifications. -->
+	<Parameter name="email.host" value="localhost"
+		description="Where the SMTP server for sending notification emails is located."/>
+	<Parameter name="email.from" value="taverna.server@localhost"
+		description="Who to send notification emails as."/>
+</Context>