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Initial commit: adding latest HERVx pipeline and resources
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‎Dockerfile

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FROM ubuntu:18.04
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MAINTAINER Skyler Kuhn <[email protected]>
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RUN mkdir -p /data2
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RUN mkdir -p /opt2
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# Apt-get packages
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# Install python (3.6), bowtie2=2.3.4.1-1 (ubuntu:18.04 default)
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RUN apt-get update && apt-get -y upgrade
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RUN DEBIAN_FRONTEND=noninteractive apt-get install --yes \
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build-essential \
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apt-utils \
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git-all \
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python3 \
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python3-pip \
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bowtie2 \
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wget
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WORKDIR /opt2
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# Build Samtools 1.9, Telescope requires htslib=1.9 (must install SAMtools=1.9)
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# SAMtools installation information: https://github.com/samtools/samtools/blob/develop/INSTALL
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# HTSlib installation information: https://github.com/samtools/htslib/blob/1.9/INSTALL
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# Apt-get remaining dependencies
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RUN DEBIAN_FRONTEND=noninteractive apt-get install --yes \
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gcc \
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make \
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perl \
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bzip2 \
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zlibc \
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libssl-dev \
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libbz2-dev \
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zlib1g-dev \
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libncurses5-dev \
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libncursesw5-dev \
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libcurl4-gnutls-dev \
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liblzma-dev \
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locales \
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pigz && \
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apt-get clean && apt-get purge && \
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rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
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# Build SAMtools 1.9
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RUN wget https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2 && \
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tar -xjvf samtools-1.9.tar.bz2 && \
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rm samtools-1.9.tar.bz2 && \
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cd samtools-1.9 && \
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./configure --prefix $(pwd) && \
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make
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# Build HTSlib 1.9 (required by telescope)
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RUN wget https://github.com/samtools/htslib/releases/download/1.9/htslib-1.9.tar.bz2 && \
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tar -vxjf htslib-1.9.tar.bz2 && \
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rm htslib-1.9.tar.bz2 && \
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cd htslib-1.9 && \
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./configure --prefix $(pwd) && \
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make
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# Add SAMtools and HTSlib to PATH
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ENV PATH=${PATH}:/opt2/samtools-1.9
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ENV PATH=${PATH}:/opt2/htslib-1.9
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ENV HTSLIB_INCLUDE_DIR="/opt2/htslib-1.9"
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# pip install: Cutadapt, Telescope dependencies, and then Telescope
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RUN pip3 install --upgrade pip
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RUN pip3 install cutadapt==2.10
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# Python requirements from github page some are need for compiling telescope, installing now
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RUN pip3 install future pyyaml cython==0.29.7 numpy==1.16.3 scipy==1.2.1 pysam==0.15.2 intervaltree==3.0.2
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RUN pip3 install git+git://github.com/mlbendall/telescope.git
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# Adpater sequences for cutadapt and HERV reference files
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RUN mkdir -p /opt2/refs
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COPY refs/trimmonatic_TruSeqv3_adapters.fa /opt2/refs
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COPY refs/HERV_rmsk.hg38.v2.genes.gtf /opt2/refs
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COPY refs/HERV_rmsk.hg38.v2.transcripts.gtf /opt2/refs
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COPY refs/L1Base.hg38.v1.transcripts.gtf /opt2/refs
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COPY refs/retro.hg38.v1.transcripts.gtf /opt2/refs
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# hg38 bowtie2 indices
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RUN mkdir -p /opt2/bowtie2/
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COPY refs/hg38.1.bt2 /opt2/bowtie2/
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COPY refs/hg38.2.bt2 /opt2/bowtie2/
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COPY refs/hg38.3.bt2 /opt2/bowtie2/
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COPY refs/hg38.4.bt2 /opt2/bowtie2/
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COPY refs/hg38.rev.1.bt2 /opt2/bowtie2/
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COPY refs/hg38.rev.2.bt2 /opt2/bowtie2/
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# Set environment variable(s)
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# Configure "locale", see https://github.com/rocker-org/rocker/issues/19
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# Adding pigz for cutadapt
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RUN echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen \
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&& locale-gen en_US.utf8 \
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&& /usr/sbin/update-locale LANG=en_US.UTF-8
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# Add HERVx pipeline PATH
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RUN mkdir -p /opt2/HERVx/
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COPY src/HERVx /opt2/HERVx/
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ENV PATH=${PATH}:/opt2/HERVx
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# Copy the Dockerfile used to create image in /opt2
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COPY Dockerfile /opt2
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WORKDIR /data2

‎README.md

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# Telescope
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Characterization of Human Endogenous Retrovirus (HERV) expression within the transcriptomic landscape using RNA-seq is complicated by uncertainty in fragment assignment because of sequence similarity. Telescope is a computational method that provides accurate estimation of transposable element expression (retrotranscriptome) resolved to specific genomic locations. Telescope directly addresses uncertainty in fragment assignment by reassigning ambiguously mapped fragments to the most probable source transcript as determined within a Bayesian statistical model.
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Telescope can be installed from [Github](https://github.com/mlbendall/telescope). It can be installed using Conda, but I did not go down that route. This repository contains the Dockerfile to build Telescope from scratch along with a few other tools.
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The Dockerfile will install Cutadapt, bowtie2, SAMtools, HTSlib, and Telescope. Small reference files are located in `/opt2/refs/` in the container's filesystem.
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Currently, the following files are located in `/opt2/refs/`:
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- trimmonatic_TruSeqv3_adapters.fa
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- HERV_rmsk.hg38.v2.genes.gtf
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- HERV_rmsk.hg38.v2.transcripts.gtf
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- L1Base.hg38.v1.transcripts.gtf
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- retro.hg38.v1.transcripts.gtf
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> **Please Note:** Bowtie2 indices for `hg38` are bundled in the container's filesystem in `/opt2/bowtie2/`. Other indices can be provided by mounting the host filesystem to this PATH (overrides current hg38 indices).
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### Build from Dockerfile
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In the example below, change `skchronicles` with your DockerHub username.
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```bash
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# See listing of images on computer
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docker image ls
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# Build
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docker build --tag=ccbr_telescope:v0.0.1 .
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# Updating tag(s) before pushing to DockerHub
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docker tag ccbr_telescope:v0.0.1 skchronicles/ccbr_telescope:v0.0.1
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docker tag ccbr_telescope:v0.0.1 skchronicles/ccbr_telescope # latest
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docker tag ccbr_telescope:v0.0.1 nciccbr/ccbr_telescope:v0.0.1
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docker tag ccbr_telescope:v0.0.1 nciccbr/ccbr_telescope # latest
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# Check out new tag(s)
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docker image ls
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# Peak around the container: verify things run correctly
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docker run -ti ccbr_telescope:v0.0.1 /bin/bash
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# Push new tagged image to DockerHub
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docker push skchronicles/ccbr_telescope:v0.0.1
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docker push skchronicles/ccbr_telescope:latest
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docker push nciccbr/ccbr_telescope:v0.0.1
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docker push nciccbr/ccbr_telescope:latest
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```
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### Run using Singularity
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```bash
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module load singularity
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# Pull from DockerHub
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SINGULARITY_CACHEDIR=$PWD singularity pull -F docker://nciccbr/ccbr_telescope
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# Display usage and help information
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singularity exec -B $PWD:$PWD ccbr_telescope_latest.sif HERVx -h
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# Run HERVx pipeline
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singularity exec -B $PWD:$PWD ccbr_telescope_latest.sif HERVx -r1 small_S25_1.fastq -r2 small_S25_2.fastq -o ERV_hg38
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```
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### Build bowtie2 indices
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```bash
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# Get UCSC hg38 genome
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wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz
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zcat hg38.fa.gz > hg38.fa
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# Build the indices
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module load singularity
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SINGULARITY_CACHEDIR=$PWD singularity pull -F docker://nciccbr/ccbr_telescope
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singularity exec -B $PWD:$PWD ccbr_telescope_latest.sif bowtie2-build hg38.fa hg38
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```

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