adding for making a release

.gitmodules

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+[submodule "SciEDPipeR"]
+	path = SciEDPipeR
+	url = https://github.com/SciEDPipeR/SciEDPipeR.git

LICENSE.txt

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+Copyright (c) 2015, The Broad Institute, Inc. All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+·         Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+
+·         Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+
+·         Neither the name of the Broad Institute nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.**
+
+THIS SOFTWARE IS PROVIDED BY THE BROAD INSTITUTE  ''AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, 
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE BROAD INSTITUTE 
+BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES(INCLUDING, BUT NOT LIMITED TO, 
+PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, 
+EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.md

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+For foreign transcript detection, we leverage Centrifuge and Kraken, leveraging RNA-Seq reads and Trinity-reconstructed transcripts. Our efforts here are being carried out in collaboration with the group of Steven Salzberg at JHU.

metagenomics.py

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+#!/usr/bin/env python
+
+
+__author__ = "Asma Bankapur, Timothy Tickle"
+__copyright__ = "Copyright 2014"
+__credits__ = [ "Timothy Tickle", "Brian Haas" ]
+__license__ = "MIT"
+__maintainer__ = "Asma Bankapur"
+__email__ = "[email protected]"
+__status__ = "Development"
+
+#import inspect
+import os,sys
+sys.path.append(os.path.sep.join([os.path.dirname(os.path.realpath(__file__)), "SciEDPipeR"]))
+sys.path.append(os.path.sep.join([os.path.dirname(os.path.realpath(__file__)), "SciEDPipeR", "sciedpiper"]))
+import sciedpiper.Command as Command
+import sciedpiper.PipelineRunner as PipelineRunner
+
+class MetagenomicsScript( PipelineRunner.PipelineRunner ):
+
+    def func_update_arguments(self, arg_raw ):
+        """
+        Updates to the arg parser, command line options
+        
+        * arg_raw : Arguments ( not yet parsed )
+                  : Arguments
+        * return  : Updated Arguments
+                  : Arguments
+        """
+
+        arg_raw.prog = "metagenomics.py "
+        arg_raw.description = "Metagenomics - Centrifuge"
+        arg_raw.add_argument("--threads", dest = "threads", default = "1", required = True ,help = "Launch NTHREADS parallel search threads - default: 1" )
+        arg_raw.add_argument("--format",dest="format",choices=["fastq","fasta"],default="fastq" ,help="Choose format")
+        arg_raw.add_argument("--num_primary_assign",dest="distinct_primary_assignments",default="1",help="It searches for at most <int> distinct, primary assignments for each read or pair.Default=5") 
+        arg_raw.add_argument("--index", dest="centrifuge_index",help="The basename of the index for the reference genomes")
+        arg_raw.add_argument("--read_type", dest="read_type", choices=["single","paired"], default="paired", help="Choose read type, skip if using Trinity assembles reads")
+        arg_raw.add_argument("--right_fq", dest="right_fq" ,help="Right_fq (only when fastq format is used for read_type paired)")
+        arg_raw.add_argument("--left_fq", dest="left_fq", help="Left_fq (only when fastq format is used for read_type paired)")
+        arg_raw.add_argument("--unpaired_reads", dest="unpaired_reads",help="Comma-separated list of files containing unpaired reads to be aligned (for Trinity runs and single end reads)")
+        return(arg_raw)
+
+    def func_make_commands( self, args_parsed, cur_pipeline ):
+
+
+        #For trinity assembled reads
+        if args_parsed.format=="fasta":
+            cur_pipeline.func_check_files_exist( [ args_parsed.unpaired_reads ] )
+        #Direct route: paired or single end fastq 
+        elif args_parsed.format=="fastq":
+            if args_parsed.read_type=="single":
+                cur_pipeline.func_check_files_exist( [ args_parsed.unpaired_reads ] )
+            else:
+                cur_pipeline.func_check_files_exist( [ args_parsed.right_fq,args_parsed.left_fq ] )
+        else:
+            cur_pipeline.logr_logger.error("Choose either --fasta or --fastq and provide appropriate inputs")
+
+        # Make all output files 
+        classification_results = os.path.join(args_parsed.str_out_dir,"classification.results.txt") 
+        classification_report = os.path.join(args_parsed.str_out_dir,"classification.report.txt")
+        report_kraken = os.path.join(args_parsed.str_out_dir,"kraken_style_report.txt") 
+
+        #Trinity centrifuge command
+        if args_parsed.format=="fasta":
+            centrifige_cmd=["centrifuge",
+                            "-p",args_parsed.threads,
+                            "-k",args_parsed.distinct_primary_assignments,
+                            "-f","-x",args_parsed.centrifuge_index,
+                            "-U",args_parsed.unpaired_reads,
+                            "-S",classification_results,
+                            "--report-file",classification_report]
+
+        #Direct fastq run with centrifuge
+        elif args_parsed.format=="fastq":
+            if args_parsed.read_type=="single":
+                centrifige_cmd=["centrifuge",
+                                "-p",args_parsed.threads,
+                                "-k",args_parsed.distinct_primary_assignments,
+                                "-q","-x",args_parsed.centrifuge_index,
+                                "-U",args_parsed.unpaired_reads,
+                                "-S",classification_results,
+                                "--report-file",classification_report]
+            else:
+                centrifige_cmd=["centrifuge",              
+                                 "-p",args_parsed.threads,
+                                 "-q","-x",args_parsed.centrifuge_index,
+                                 "-k",args_parsed.distinct_primary_assignments,
+                                 "-1",args_parsed.left_fq,
+                                 "-2",args_parsed.right_fq,
+                                 "-S",classification_results,
+                                 "--report-file",classification_report] 
+        else:
+            cur_pipeline.logr_logger.error("Choose either --fasta or --fastq and provide appropriate inputs")
+
+
+        #Generate kraken style report
+        kreport_cmd=["centrifuge-kreport",
+                      "-x",args_parsed.centrifuge_index,
+                      classification_results,">",report_kraken]
+
+
+        lcmd_commands = []
+        lcmd_commands.extend( [ Command.Command( str_cur_command = " ".join(centrifige_cmd),
+                                                 lstr_cur_dependencies = [ args_parsed.centrifuge_index ], 
+                                                 lstr_cur_products = [ classification_results,
+                                                                       classification_report ] ) ] )
+
+        lcmd_commands.extend( [ Command.Command( str_cur_command = " ".join(kreport_cmd),
+                                                 lstr_cur_dependencies = [ args_parsed.centrifuge_index,classification_results],
+                                                 lstr_cur_products = [ report_kraken ] ) ] )
+        return(lcmd_commands)
+
+
+if __name__ == "__main__":
+
+    # Needed to run, calls the script
+    MetagenomicsScript( ).func_run_pipeline( )