Merge pull request #273 from SeqWare/feature/seqware_1967

Feature/seqware 1967

Author: denis-yuen

seqware-distribution/docs/site/content/docs/6-pipeline.md

@@ -15,8 +15,12 @@ monitoring workflows.
 
 <img width="600" src="/assets/images/seqware_hpc_oozie.png"/>
 
-We currently support one workflow languages (Java) and four 
-workflow engines (oozie, oozie-sge, whitestar, and whitestar-sge). Our current recommended combination is
+We currently support one workflow language (Java) and four 
+workflow engines (oozie, oozie-sge, whitestar, and whitestar-sge). 
+
+(Previously, we also supported Pegasus/Condor/Globus as a workflow engine). 
+
+Our current recommended combination is
 Java workflows with the Oozie-sge engine.
 
 * Oozie uses the Hadoop Workflow Scheduler to schedule steps in workflows on the Hadoop ecosystem (JobTrackers and TaskTrackers). 
@@ -74,8 +78,6 @@ run on a randomly chosen cluster node.
 
 * [Java Workflows](/docs/6-pipeline/java-workflows/)
 : This is our newer workflow language that is much simpler than the FTL and more expressive. We recommend this for all new workflow development.
-* [Deprecated FTL Workflows](/docs/6-pipeline/legacy-ftl-workflows/)
-: This is our older, more verbose workflow language based on FreeMarker. This provides information on the structure of a typical workflow descriptor written in this language. FTL is deprecated, do not use it for new workflows.
 * [Workflow Bundle Conventions](/docs/6-pipeline/workflow_bundles/)
 : We rely on a bundle format for packaging up and exchanging workflows. This document describes the format and directory structure.
 * [Workflow Config Files](/docs/6-pipeline/config_files/)
@@ -88,7 +90,7 @@ run on a randomly chosen cluster node.
 ## Developer Tutorials
 
 * [Debugging, Troubleshooting, & Restarting Workflow](/docs/6-pipeline/debug-workflows/)
-: A guide to debugging, troubleshooting, and restarting failed workflows for both workflow engines (Pegasus and Oozie).
+: A guide to debugging, troubleshooting, and restarting failed workflows for the Oozie workflow engine.
 
 * [Developing in Partial SeqWare Environments with Whitestar](/docs/6-pipeline/partial_environments/)
 : A guide to developing without dependencies such as Oozie, SGE/Hadoop, and metadata (via the SeqWare webservice).  

seqware-distribution/docs/site/content/docs/6-pipeline/connecting-to-cluster.md

@@ -51,23 +51,6 @@ From the SeqWare perspective you will need to tell SeqWare which HDFS/MapReduce
 cluster to talk to, see the Oozie and Hadoop sections of the [SeqWare
 Configuration Guide](/docs/6-pipeline/user-configuration/).  
 
-## Pegasus Workflow Engine
-
-How to connect the Pipeline's Pegasus Workflow Engine to a real SGE cluster.
-
-### Importing the VM
-
-This really depends on your organization and how they want to run a virtualized
-server.  For information on VirtualBox see their
-[website](https://www.virtualbox.org/).  For information on importing our
-VirtualBox image into KVM see [this
-link](http://cheznick.net/main/content/converting-a-virtual-machine-from-virtualbox-to-kvm).
-If you use Xen as your server virtualization see [this
-link](http://roymic.blogspot.ca/2012/02/how-to-convert-virtual-box-image-to-xen.html).
-You can also just use VirtualBox to run your virtual SeqWare server, in which
-case you will find the command line tools useful, see [this
-link](http://www.ubuntugeek.com/how-to-control-virtual-machines-virtualbox-using-vboxmanage.html).
-
 ### Install the Corresponding SGE Version
 
 This is really up to your local sysadmin.  You will need to use a common
@@ -77,31 +60,6 @@ Consult the [GridEngine
 wiki](http://wiki.gridengine.info/wiki/index.php/Main_Page) for more
 information about obtaining and configuring SGE.  
 
-### Configuring GRAM on the VM
-
-This is the key step in the whole process.  The GRAM layer from the Globus Toolkit
-actually handles the submission of workflow step to the cluster as a job.  This is
-done via a Perl module that knows how to talk with SGE. We need to modify that
-Perl module so it knows 1) where the SGE tools are located and 2) the settings particular
-to the cluster being connected to.
-
-#### Perl Submission Module
-
-On the VM, this Perl module lives in: <tt>/usr/share/perl5/vendor_perl/Globus/GRAM/JobManager/sge.pm</tt>. 
-
-You may have seen this document mentioned in the [Install from Scratch](/docs/2a-installation-from-scratch/) guide where we patched it.  Now, you need to ensure you setup the parallel environment (<tt>-pe</tt>) and max memory (<tt>-l vf=</tt>) correctly for your new cluster.  Annoyingly, the parameters used for this are actually configurable in SGE so you will need to discuss with your cluster Sys Admin to see what is right for your environment.  See the code snippet patches below.
-
-<%= render '/includes/setup_gram_1/' %>
-
-<%= render '/includes/setup_gram_2/' %>
-
-You will also need to modify the following settings files:
-
-  /etc/sysconfig/gridengine
-  /etc/globus/globus-sge.conf
-
-These contain file paths and cluster name parameters that you need to update to point to the correct values for the real cluster.
-
 ### Testing
 
 Finally you can submit and run a workflow just as you normally do following the

seqware-distribution/docs/site/content/docs/6-pipeline/debug-workflows.md

@@ -433,18 +433,3 @@ Fix the error, rebuild, and relaunch. The workflow should now proceed onto the n
 	-----------------------------------------------------------------------
 
 Fix the two errors and your workflow should now run to completion. 
-
-
-## The Pegasus Engine - Unsupported
-
-The Pegasus engine is deprecated in 1.0.X and is no longer supported in 11.0.
-The Pegasus Engine used <tt>pegasus-status</tt> as the primary command for monitoring the status of workflows.
-
-### Debugging Workflows
-
-<%= render '/includes/debug/pegasus_debug/' %>
-
-### Restarting Workflows 
-
-<%= render '/includes/debug/pegasus_restart/' %>
-