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Unify host genome generation #182

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Unify host genome generation #182

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3eaaf70
Unify host genome generation
morsecodist Feb 1, 2023
86a0a38
add concat unzip step + docker_image_id
morsecodist Feb 2, 2023
03eade9
update docker
morsecodist Feb 2, 2023
558ff43
install docker dependencies
morsecodist Feb 2, 2023
4556f51
gzip inputs
morsecodist Feb 2, 2023
29a721e
fix file naming
morsecodist Feb 2, 2023
9921360
python path docker
morsecodist Feb 3, 2023
315c392
star gtf flag fix
morsecodist Feb 3, 2023
0639371
syntax
morsecodist Feb 4, 2023
54d98fe
fix name outputs
morsecodist Feb 4, 2023
0d92776
fix ercc gtf in host-genome generation (#202)
rzlim08 Apr 6, 2023
547a453
symlink bowtie2 directory (#229)
rzlim08 Apr 26, 2023
a9a57a4
create a relative symlink (#250)
rzlim08 May 23, 2023
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27 changes: 25 additions & 2 deletions workflows/host-genome-generation/Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -2,10 +2,33 @@
FROM ubuntu:22.04
ARG DEBIAN_FRONTEND=noninteractive

# this brings in python2.7
RUN apt-get update && apt-get install -y bowtie2 curl minimap2
RUN apt-get update && apt-get install -y wget bowtie2 curl minimap2 pigz dh-autoreconf nasm make git g++ unzip python3-pip

# nescessary for hisat2
RUN ln -s /usr/bin/python3 /usr/bin/python

# Install STAR, the package rna-star does not include STARlong
RUN curl -L https://github.com/alexdobin/STAR/archive/2.5.3a.tar.gz | tar xz
RUN mv STAR-2.5.3a/bin/Linux_x86_64_static/* /usr/local/bin
RUN rm -rf STAR-2.5.3a

# Install fastp (libdeflate libisal (dh-autoreconf nasm))
WORKDIR /tmp
RUN wget -nv -O - https://github.com/intel/isa-l/archive/refs/tags/v2.30.0.tar.gz | tar zx
RUN cd isa-l-* && ./autogen.sh && ./configure && make -j8 && make install
RUN wget -nv -O - https://github.com/ebiggers/libdeflate/archive/refs/tags/v1.12.tar.gz | tar zx
RUN cd libdeflate-* && make -j8 && make install
RUN ldconfig
RUN git clone https://github.com/mlin/fastp.git && git -C fastp checkout 37edd60
RUN cd fastp && make -j8 && ./fastp test && cp fastp /usr/local/bin

# Install hisat2
WORKDIR /hisat2
RUN wget -nv -O /tmp/HISAT2.zip https://cloud.biohpc.swmed.edu/index.php/s/oTtGWbWjaxsQ2Ho/download \
&& unzip /tmp/HISAT2.zip && mv hisat2-*/* . && rm /tmp/HISAT2.zip

# Install kallisto + python gtfparse
RUN curl -L https://github.com/pachterlab/kallisto/releases/download/v0.46.1/kallisto_linux-v0.46.1.tar.gz | tar xz -C /
RUN pip3 install gtfparse==1.2.1

WORKDIR /
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