adding first version of code

Dockerfile

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+############################################################
+# Dockerfile to build a container that pulls KN subnetworks
+############################################################
+
+# Set the base image to python v3
+FROM python:3.4-slim
+
+# File Author / Maintainer
+MAINTAINER Charles Blatti <[email protected]>
+
+# Update the repository sources list
+RUN apt-get update && apt-get install -y \
+    curl \
+    time \
+    rsync \
+    wget \
+    s3cmd \
+    python3-pip
+
+RUN pip3 install awscli
+RUN wget -O /home/credentials http://knowcloud.cse.illinois.edu/index.php/s/E3OL5QpTj8SrOix/download
+COPY kn_fetcher.sh /home/
+RUN chmod 775 /home/kn_fetcher.sh
+
+
+# Set default contain command on run
+CMD /bin/bash
+
+# Set container execution behavior
+# ENTRYPOINT

kn_fetcher.cwl

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+class: CommandLineTool
+cwlVersion: v1.0
+id: "kn_fetcher"
+label: "Knowledge Network Fetcher"
+doc: "Retrieve appropriate subnetwork from KnowEnG Knowledge Network from AWS S3 storage"
+
+#dct:creator:
+#  "@id": "http://orcid.org/0000-0002-4683-6271"
+#  foaf:name: Charles Blatti
+#  foaf:mbox: "mailto:[email protected]"
+
+requirements:
+  - class: DockerRequirement
+    dockerPull: "quay.io/cblatti3/kn_fetcher:0.1"
+  - class: InlineJavascriptRequirement
+
+hints:
+  - class: ResourceRequirement
+    coresMin: 1
+    ramMin: 1024 #"the process requires at least 1G of RAM
+    outdirMin: 512000
+
+inputs:
+  - id: bucket
+    label: "AWS S3 Bucket Name"
+    doc: "the aws s3 bucket"
+    type: string
+    default: "KnowNets/KN-6rep-1611/userKN-6rep-1611"
+    inputBinding:
+      position: 1
+  - id: network_type
+    label: "Subnetwork Class"
+    doc: "the type of subnetwork"
+    type: string
+    default: Gene
+    inputBinding:
+      position: 2
+  - id: taxon
+    label: "Subnetwork Species ID"
+    doc: "the taxonomic id for the species of interest"
+    type: string
+    default: "9606"
+    inputBinding:
+      position: 3
+  - id: edge_type
+    label: "Subnetwork Edge Type"
+    doc: "the edge type keyword for the subnetwork of interest"
+    type: string
+    default: PPI_physical_association
+    inputBinding:
+      position: 4
+
+baseCommand: /home/kn_fetcher.sh
+
+outputs:
+  - id: output_file
+    label: "Subnetwork Edge File"
+    doc: "4 column format for subnetwork for single edge type and species"
+    outputBinding:
+      glob: "*.edge"
+    type: File

kn_fetcher.job

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+network_type: "Gene"
+taxon: "9606"
+edge_type: "STRING_textmining"

kn_fetcher.sh

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+#!/bin/bash
+
+BUCKET=$1
+NETWORKTYPE=$2
+TAXON=$3
+EDGETYPE=$4
+MYCMD="mkdir -p ~/.aws/ && cp /home/credentials ~/.aws/ && aws s3 cp s3://$BUCKET/$NETWORKTYPE/$TAXON/$EDGETYPE/ ./ --recursive"
+echo $MYCMD
+eval $MYCMD