Add in License.

LICENSE.md

+MIT License
+
+Copyright (c) 2019, University of Texas Southwestern Medical Center.
+All rights reserved.
+Contributors: Spencer D. Barnes, Holly Ruess, Beibei Chen, Venkat S. Malladi
+Department: Bioinformatic Core Facility, Department of Bioinformatics
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

workflow/scripts/call_peaks_macs.py

 #!/usr/bin/env python3
 
+#
+# * --------------------------------------------------------------------------
+# * Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/LICENSE.md)
+# * --------------------------------------------------------------------------
+#
+
 '''Generate peaks from data.'''
 
 import os

workflow/scripts/check_design.py

 #!/usr/bin/env python3
 
+#
+# * --------------------------------------------------------------------------
+# * Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/LICENSE.md)
+# * --------------------------------------------------------------------------
+#
+
 '''Check if design file is correctly formatted and matches files list.'''
 
 import argparse

workflow/scripts/convert_reads.py

 #!/usr/bin/env python3
 
+#
+# * --------------------------------------------------------------------------
+# * Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/LICENSE.md)
+# * --------------------------------------------------------------------------
+#
+
 '''Convert tagAlign files for further processing.'''
 
 import os

workflow/scripts/experiment_design.py

 #!/usr/bin/env python3
 
+#
+# * --------------------------------------------------------------------------
+# * Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/LICENSE.md)
+# * --------------------------------------------------------------------------
+#
+
 '''Generate experiment design files for downstream processing.'''
 
 import argparse

workflow/scripts/experiment_qc.py

 #!/usr/bin/env python3
 
+#
+# * --------------------------------------------------------------------------
+# * Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/LICENSE.md)
+# * --------------------------------------------------------------------------
+#
+
 '''Experiment correlation and enrichment of reads over genome-wide bins.'''
 
 

workflow/scripts/generate_references.py

 #!/usr/bin/env python
 
+#
+# * --------------------------------------------------------------------------
+# * Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/LICENSE.md)
+# * --------------------------------------------------------------------------
+#
+
 '''Make header for HTML of references.'''
 
 import argparse

workflow/scripts/generate_versions.py

 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 
+#
+# * --------------------------------------------------------------------------
+# * Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/LICENSE.md)
+# * --------------------------------------------------------------------------
+#
+
 '''Make YAML of software versions.'''
 
 from __future__ import print_function

workflow/scripts/map_qc.py

 #!/usr/bin/env python3
 
+#
+# * --------------------------------------------------------------------------
+# * Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/LICENSE.md)
+# * --------------------------------------------------------------------------
+#
+
 '''Remove duplicates and filter unmapped reads.'''
 
 import os

workflow/scripts/map_reads.py

 #!/usr/bin/env python3
 
+#
+# * --------------------------------------------------------------------------
+# * Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/LICENSE.md)
+# * --------------------------------------------------------------------------
+#
+
 '''Align reads to reference genome.'''
 
 import os

workflow/scripts/motif_search.py

 #!/usr/bin/env python3
 
+#
+# * --------------------------------------------------------------------------
+# * Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/LICENSE.md)
+# * --------------------------------------------------------------------------
+#
+
 '''Call Motifs on called peaks.'''
 
 import os

workflow/scripts/overlap_peaks.py

 #!/usr/bin/env python3
 
+#
+# * --------------------------------------------------------------------------
+# * Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/LICENSE.md)
+# * --------------------------------------------------------------------------
+#
+
 '''Generate naive overlap peak files and design file for downstream processing.'''
 
 import os

workflow/scripts/pool_and_psuedoreplicate.py

 #!/usr/bin/env python3
 
+#
+# * --------------------------------------------------------------------------
+# * Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/LICENSE.md)
+# * --------------------------------------------------------------------------
+#
+
 '''Generate pooled and pseudoreplicate from data.'''
 
 import argparse

workflow/scripts/trim_reads.py

 #!/usr/bin/env python3
 
+#
+# * --------------------------------------------------------------------------
+# * Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/LICENSE.md)
+# * --------------------------------------------------------------------------
+#
+
 '''Trim low quality reads and remove sequences less than 35 base pairs.'''
 
 import subprocess

workflow/scripts/utils.py

 #!/usr/bin/env python3
 
+#
+# * --------------------------------------------------------------------------
+# * Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/LICENSE.md)
+# * --------------------------------------------------------------------------
+#
+
 '''General utilities.'''
 
 

workflow/scripts/xcor.py

 #!/usr/bin/env python3
 
+#
+# * --------------------------------------------------------------------------
+# * Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/LICENSE.md)
+# * --------------------------------------------------------------------------
+#
+
 '''Compute cross-correlation analysis.'''
 
 import os