Cleanup BWA.

Author: dthain

wq_bwa/README.md

@@ -0,0 +1,34 @@
+Work Queue BWA
+--------------
+
+The wq_bwa.py program aligns sequences of genomes listed in a fastq file using
+the Burrows-Wheeler Aligner. It aligns by partitioning the file into pieces
+containing one or more sequences and running BWA to align them individually.
+The program uses the Work Queue framework for distributed execution.
+
+Installation
+------------
+
+- Install the [Work Queue](http://ccl.cse.nd.edu/software/workqueue) framework.
+- Install BWA and its required dependencies from http://bio-bwa.sourceforge.net
+
+Example
+-------
+
+First start the manager program, which will divide up the queries
+and generate a large number of tasks:
+
+    ./wq_bwa <REFERENCE_FILE> <FASTQ_FILE>
+
+Then, run one or more remote workers:
+
+    work_queue_worker -d all <HOSTNAME> <PORT>
+
+where <HOSTNAME> is the name of the host on which the master is running
+	  <PORT> is the port number on which the master is listening.
+
+Alternatively, you can also specify a project name for the master and use that
+to start workers:
+
+    ./wq_bwa <REFERENCE_FILE> <FASTQ_FILE> -N WQBWA
+    work_queue_worker -d all -N WQBWA

wq_bwa/wq_bwa wq_bwa/wq_bwa.pywq_bwa/wq_bwa renamed to wq_bwa/wq_bwa.py

@@ -1,5 +1,4 @@
-#!/usr/bin/env cctools_python
-# CCTOOLS_PYTHON_VERSION 2.7
+#!/usr/bin/python
 
 # Copyright (c) 2019- The University of Notre Dame.
 # This software is distributed under the GNU General Public License.