[WIP] superenhancer-final

tools/superenhancer-docker.yml

@@ -0,0 +1,66 @@
+dockerFile: |
+  #################################################################
+  # Dockerfile
+  #
+  # Software:         Super Enhancer
+  # Software Version: 1a9bb86b5464
+  # Description:      Super Enhancer Image for Scidap
+  # Website:          https://bitbucket.org/young_computation/rose,http://scidap.com/
+  # Provides:         https://bitbucket.org/young_computation/rose/get/1a9bb86b5464.zip
+  # Base Image:       scidap/scidap:v0.0.1
+  # Build Cmd:        docker build --rm -t scidap/superenhancer .
+  # Pull Cmd:         docker pull scidap/superenhancer
+  # Run Cmd:          docker run --rm scidap/superenhancer
+  #################################################################
+  FROM scidap/samtools:v1.2-242-4d56437
+  MAINTAINER BHARATH MANICKA VASAGAM [email protected]
+  ENV DEBIAN_FRONTEND noninteractive
+  ################## BEGIN INSTALLATION ######################
+  WORKDIR /usr/local/bin/
+  ### Install required packages
+  #To configure the virtualbox with another DNS
+  #CMD "sh" "-c" "echo nameserver 8.8.8.8 > /etc/resolv.conf"
+  #change the nameserver in resolv.conf to current DNS server
+  #
+  RUN apt-get clean all && \
+    apt-get update && \
+    apt-get install -y  \
+    libncurses5-dev \
+    ed \
+    less \
+    locales \
+    wget \
+    ca-certificates &&\
+    apt-get clean && \
+    apt-get purge
+  ### Install the Super Enhancer Script
+  RUN wget -q -O edited-Super-Enhancer-master.zip https://github.com/bharath-cchmc/edited-Super-Enhancer/archive/master.zip && \
+    unzip edited-Super-Enhancer-master.zip && \
+    cp -r edited-Super-Enhancer-master /usr/local && \
+    rm -rf edited-Super-Enhancer-master && \
+    rm -f edited-Super-Enhancer-master.zip
+  ### patching the difference in script
+  RUN wget -q -O young_computation.zip https://bitbucket.org/young_computation/rose/get/1a9bb86b5464.zip && \
+    unzip young_computation.zip && \
+    #cp -r young_computation-rose-1a9bb86b5464 /usr/local/bin && \
+    ls &&\
+    rm -f young_computation.zip && \
+    rm -rf /usr/local/bin/young_computation-rose-1a9bb86b5464/annotation && \
+    rm /usr/local/bin/young_computation-rose-1a9bb86b5464/README.txt
+
+  RUN diff /usr/local/bin/young_computation-rose-1a9bb86b5464 /usr/local/edited-Super-Enhancer-master | > wow.patch
+
+  RUN patch < wow.patch && \
+    rm wow.patch && \
+    cp -r young_computation-rose-1a9bb86b5464/* /usr/local/bin
+
+  RUN rm -rf young_computation-rose-1a9bb86b5464
+  RUN rm -f /usr/local/edited-Super-Enhancer-master.zip
+  RUN chmod -R +x /usr/local/bin
+
+  ### Install R
+  RUN apt-get update
+  RUN apt-get -y install r-base
+  ### Cleanup
+
+  RUN rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* /usr/share/doc/* /var/lib/apt/lists/*

tools/superenhancer.cwl

@@ -3,6 +3,9 @@
 cwlVersion: "cwl:draft-3"
 
 class: CommandLineTool
+hints:
+- class: DockerRequirement
+  dockerPull: bharath90/superenhancer
 
 description: |
   Super Enhancer Workflow
@@ -18,8 +21,6 @@ description: |
 
 requirements:
 - $import: envvar-global.yml
-- $import: superenhancer.yml
-- class: InlineJavascriptRequirement
 
 inputs:
 - id: "genome"
@@ -95,7 +96,7 @@ s:mainEntity:
   class: s:SoftwareSourceCode
   s:name: "superenhnacer"
   s:about: >
-  PURPOSE: To create stitched enhancers, and to separate super-enhancers from typical enhancers using sequencing data (.bam) given a file of previously identified constituent enhancers (.gff)It makes use of the superenhancer script developed by Young Lab
+    PURPOSE: To create stitched enhancers, and to separate super-enhancers from typical enhancers using sequencing data (.bam) given a file of previously identified constituent enhancers (.gff)It makes use of the superenhancer script developed by Young Lab
 
   s:url: http://younglab.wi.mit.edu/super_enhancer_code.html
 
@@ -115,12 +116,10 @@ s:mainEntity:
   s:publication:
   - class: s:ScholarlyArticle
     id: http://dx.doi.org/10.1016/j.cell.2013.03.035
-    s:name: Warren A. Whyte, David A. Orlando, Denes Hnisz, Brian J. Abraham, Charles Y. Lin, Michael H. Kagey, Peter B. Rahl, Tong Ihn Lee and Richard A. Young Cell 
     s:url: http://www.cell.com/abstract/S0092-8674(13)00392-9
 
   - class: s:ScholarlyArticle
     id: http://dx.doi.org/10.1016/j.cell.2013.03.036
-    s:name: Jakob Lovén, Heather A. Hoke, Charles Y. Lin, Ashley Lau, David A. Orlando, Christopher R. Vakoc, James E. Bradner, Tong Ihn Lee, and Richard A. Young Cell
     s:url: http://www.cell.com/abstract/S0092-8674(13)00393-0
 
 s:downloadUrl: https://bitbucket.org/bharath-cchmc/se-docker-cwl-trial