Update README and setup

README.md

@@ -1,14 +1,29 @@
-# srrTomat0
-
-[![Travis](https://travis-ci.org/cskokgibbs/srrTomat0.svg?branch=master)](https://travis-ci.org/cskokgibbs/srrTomat0)
+# inferelator-prior
 
 This is a set of pipelines to create expression and prior matrices for network inference. They are designed to create
-data that is compatible with the [inferelator](https://github.com/flatironinstitute/inferelator) package. In addition to
+data that is compatible with the [inferelator](https://github.com/flatironinstitute/inferelator) package. 
+
+### Usage
+
+    python -m inferelator_prior.network_from_motifs
+    usage: network_from_motifs.py -m motif_PWM_file.meme
+                                  -f genome_fasta_file.fasta
+                                  -g genome_annotation_file.gtf
+                                  -o ~/output/path/prefix
+                                  --species {yeast,fly,mouse,human}]
+                                  
+This requires a motif PWM database (`-m PATH`), 
+a genome to search (both sequence as a FASTA `-f PATH` and annotations `-g PATH`),
+and an output prefix for several files (`-o PATH`).
+In addition, default settings for a specific species can be set with (`--species`).
+
+### Requirements
+
+In addition to
 python dependencies, this package also requires 
 [STAR](https://github.com/alexdobin/STAR),
 [sra-tools](http://ncbi.github.io/sra-tools/), 
 [bedtools](https://bedtools.readthedocs.io/en/latest/),
-[samtools](http://www.htslib.org/),
-[homer](http://homer.ucsd.edu/homer/), and
+[samtools](http://www.htslib.org/), and
 [fimo](http://meme-suite.org/doc/fimo.html).
 

setup.py

@@ -3,24 +3,24 @@
 
 install_requires = ["numpy", "pandas", "HTSeq", "pybedtools", "scipy", "pathos"]
 tests_require = ["coverage", "nose", "pysam"]
-version = "0.1.1"
+version = "0.2.0"
 
 # Description from README.md
 base_dir = os.path.dirname(os.path.abspath(__file__))
 long_description = "\n\n".join([open(os.path.join(base_dir, "README.md"), "r").read()])
 
 setup(
-    name="srrTomat0",
+    name="inferelator_prior",
     version=version,
-    description="SRR Pipelines: Building matrixes from read data",
+    description="Inferelator-Prior Network Generation Tool",
     long_description=long_description,
     long_description_content_type="text/markdown",
-    url="https://github.com/flatironinstitute/srrTomat0",
+    url="https://github.com/flatironinstitute/inferelator-prior",
     author="Chris Jackson",
     author_email="[email protected]",
     maintainer="Chris Jackson",
     maintainer_email="[email protected]",
-    packages=find_packages(include=["srrTomat0", "srrTomat0.*"]),
+    packages=find_packages(include=["inferelator_prior", "inferelator_prior.*"]),
     zip_safe=False,
     install_requires=install_requires,
     tests_require=tests_require,