Adding Dockerfile for custom iCLIP version

.tests/cluster_config.yaml

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+# cluster configuration
+__default__:
+    gres: lscratch:96
+    mem: 40g
+    partition: norm
+    time: 00-02:00:00
+    threads: 32
+    output: .%j.{wildcards}.out
+    error: .%j.{wildcards}.err
+
+qc_barcode:
+    threads: 3
+    mem: 3g
+    time: 00-04:00:00
+
+demultiplex:
+    threads: 3
+    mem: 3g
+    time: 04-00:00:00
+
+remove_adaptors:
+    threads: 3
+    time: 1-00:00:00
+    mem: 3g
+
+qc_fastq_pre:
+    threads: 3
+    mem: 3g
+    time: 00-03:00:00
+
+qc_fastq_post:
+    threads: 3
+    mem: 3g
+    time: 00-03:00:00
+
+qc_screen_validator:
+    mem: 15g
+    time: 00-03:00:00
+
+split_files:
+    threads: 3
+    mem: 3g
+    time: 00-03:00:00
+
+novoalign:
+    mem: 50g
+    time: 10-00:00:00
+
+cleanup_conversion:
+    threads: 5
+    mem: 30g
+    time: 00-3:00:00
+
+merge_unmapped_splits:
+    time: 01-00:00:00
+    mem: 75g
+
+create_bam_mm_unique:
+    threads: 6
+    gres: lscratch:256
+    mem: 30g
+    time: 04-00:00:00
+
+merge_splits_unique_mm:
+    mem: 512g
+    time: 02-06:00:00
+    partition: largemem
+
+merge_mm_and_unique:
+    threads: 2
+    gres: lscratch:256
+    mem: 5g
+    time: 02-00:00:00
+
+qc_alignment:
+    mem: 10g
+
+qc_troubleshoot:
+    threads: 3
+    mem: 3g
+
+dedup:
+    threads: 2
+    mem: 64g
+    gres: lscratch:256
+    time: 01-00:00:00
+
+create_beds_safs:
+    mem: 350g
+    gres: lscratch:256
+    threads: 4
+    partition: largemem
+
+project_annotations:
+    threads: 2
+    mem: 10g
+    time: 00-01:00:00
+
+peak_annotations:
+    threads: 3
+    gres: lscratch:128
+    mem: 30g
+    time: 00-12:00:00
+
+annotation_report:
+    mem: 10g
+
+MANORM_analysis:
+    threads: 4
+    mem: 30g
+
+MANORM_post_processing:
+    threads: 2
+    mem: 2g
+    time: 00-01:00:00
+
+MANORM_RMD:
+    threads: 2
+    mem: 3g
+    time: 00-01:00:00
+
+mapq_recalc:
+    mem: 1TB
+    gres: lscratch:256
+    partition: largemem
+    time: 00-06:00:00

docker/README.md

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+## Steps for Building Docker Images
+
+Directly below are instructions for building an image using the provided Dockerfile:
+
+```bash
+# See listing of images on computer
+docker image ls
+
+# Build from Dockerfile
+docker build --no-cache -f example.dockerfile --tag=ccbr_example:v0.1.0 .
+
+# Testing, take a peek inside
+docker run -ti ccbr_example:v0.1.0 /bin/bash
+
+# Updating Tag  before pushing to DockerHub
+docker tag ccbr_example:v0.1.0 skchronicles/ccbr_example:v0.1.0
+docker tag ccbr_example:v0.1.0 skchronicles/ccbr_example         # latest
+docker tag ccbr_example:v0.1.0 nciccbr/ccbr_example:v0.1.0
+docker tag ccbr_example:v0.1.0 nciccbr/ccbr_example              # latest
+
+# Check out new tag(s)
+docker image ls
+
+# Push new tagged image to DockerHub
+docker push skchronicles/ccbr_example:v0.1.0
+docker push skchronicles/ccbr_example:latest
+docker push nciccbr/ccbr_example:v0.1.0
+docker push nciccbr/ccbr_example:latest 
+```
+
+### Other Recommended Steps
+
+Scan your image for known vulnerabilities:
+
+```bash
+docker scan ccbr_example:v0.1.0
+```
+
+> **Please Note**: Any references to `skchronicles` should be replaced your username if you would also like to push the image to a non-org account.

docker/iCount/Dockerfile

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+# Custom version of iCount which contains an 
+# extra option to ultilize multiple threads 
+# in demultiplex and cutadapt sub commands:
+# https://github.com/skchronicles/iCount
+FROM ubuntu:18.04
+
+LABEL maintainer=kuhnsa@nih.gov
+
+# Create Container filesystem specific 
+# working directory and opt directories
+USER root
+RUN mkdir -p /opt2 && mkdir -p /data2
+WORKDIR /opt2 
+
+# Set time zone to US east coast 
+ENV TZ=America/New_York
+RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime \
+    && echo $TZ > /etc/timezone
+
+# This section installs system 
+# packages required for your 
+# project. If you need extra 
+# system packages add them here.
+# iCount requires argparse 
+# python package. Installs 
+# python/3.6, which includes 
+# argparse by default.
+# A child python dependency 
+# called 'Pillow', relies
+# on the following external
+# apt-get dependencies:
+# https://pillow.readthedocs.io/en/latest/installation.html#building-on-linux
+RUN apt-get update \
+    && apt-get -y upgrade \
+    && DEBIAN_FRONTEND=noninteractive apt-get install -y \
+        build-essential \
+        gfortran \
+        git \
+        g++ \
+        make \
+        libtiff5-dev \
+        libjpeg8-dev \
+        libopenjp2-7-dev \
+        libfreetype6-dev \
+        liblcms2-dev \
+        libwebp-dev \
+        libharfbuzz-dev \
+        libfribidi-dev \
+        libxcb1-dev \
+        libatlas-base-dev \
+        libncurses5-dev \
+        libncursesw5-dev \
+        libssl-dev \
+        libcurl4-gnutls-dev \
+        liblzma-dev \
+        libbz2-dev \
+        pigz \
+        python \
+        python3 \
+        python3-dev \
+        python3-pip \
+        python3-setuptools \
+        python3-tk \
+        pandoc \
+        tcl8.6-dev \
+        tk8.6-dev \
+        wget \
+        zlib1g-dev \
+    && apt-get clean && apt-get purge \
+    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+# Install htslib/1.10
+RUN wget https://github.com/samtools/htslib/releases/download/1.10/htslib-1.10.tar.bz2 \
+    && tar -vxjf htslib-1.10.tar.bz2 \
+    && rm htslib-1.10.tar.bz2 \
+    && cd htslib-1.10 \
+    && make \
+    && cd /opt2
+
+# Install samtools/1.10
+RUN wget https://github.com/samtools/samtools/releases/download/1.10/samtools-1.10.tar.bz2 \
+    && tar -vxjf samtools-1.10.tar.bz2 \
+    && rm samtools-1.10.tar.bz2 \
+    && cd samtools-1.10 \
+    && make \
+    && cd /opt2
+
+# Install BEDTools
+# Requires version>=2.26, where
+# merge command reports strand
+# Also, requires python (already 
+# satified) to build from source 
+RUN wget https://github.com/arq5x/bedtools2/releases/download/v2.27.1/bedtools-2.27.1.tar.gz \
+    && tar -xvf bedtools-2.27.1.tar.gz \
+    && rm bedtools-2.27.1.tar.gz \
+    && cd bedtools2/ \
+    && make \
+    && make install \
+    && cd /opt2
+
+# Install STAR
+RUN wget https://github.com/alexdobin/STAR/archive/2.6.1a.tar.gz \
+    && tar -xvzf 2.6.1a.tar.gz \
+    && rm 2.6.1a.tar.gz \
+    && cd STAR-2.6.1a/source/ \
+    && make STAR \
+    && cd /opt2
+
+# Install custom version of iCount
+# includes multithreading changes
+# demultiplex and cutadapt subcmds.
+# The output from the custom version 
+# and the orignial version should 
+# produce identical output. 
+# The changes that have been made
+# should only effect runtime, (i.e.
+# it should be significantly faster).
+RUN pip3 install numpy pandas pysam pybedtools numpydoc matplotlib
+RUN git clone https://github.com/skchronicles/iCount.git \
+    && cd iCount/ \
+    && pip3 install .[docs,test] \
+    && cd /opt2
+
+# Add Dockerfile to container FS
+# and export environment variables
+# and ensure proper permissions
+ADD Dockerfile /opt2/Dockerfile
+RUN chmod -R a+rX /opt2 \
+    && ln -sf /usr/bin/python3 /usr/bin/python
+ENV PATH="$PATH:/opt2/samtools-1.10:/opt2/htslib-1.10:/opt2/STAR-2.6.1a/source"
+
+# Reset working directory
+WORKDIR /data2

docker/iCount/build.sh

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+# Build image
+docker build --no-cache -f Dockerfile --tag=ccbr_icount:v1.0.0 .
+
+# Tag image with version and reset latest
+docker tag ccbr_icount:v1.0.0 skchronicles/ccbr_icount:v1.0.0
+docker tag ccbr_icount:v1.0.0 skchronicles/ccbr_icount
+docker tag ccbr_icount:v1.0.0 nciccbr/ccbr_icount:v1.0.0
+docker tag ccbr_icount:v1.0.0 nciccbr/ccbr_icount
+
+# Push image to DockerHub
+docker push skchronicles/ccbr_icount:v1.0.0
+docker push skchronicles/ccbr_icount:latest
+docker push nciccbr/ccbr_icount:v1.0.0
+docker push nciccbr/ccbr_icount:latest