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Hangsu phasing #417

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12 changes: 12 additions & 0 deletions .dockstore.yml
Original file line number Diff line number Diff line change
Expand Up @@ -96,3 +96,15 @@ workflows:
- name: CleanupIntermediate
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/TechAgnostic/Utility/CleanupIntermediate.wdl
- name: StatisticalPhasing
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/PacBio/Assembly
- name: BandagePlotGraph
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/TechAgnostic/Utility/BandagePlotGraph.wdl
- name: ConvertToHailMTT2T
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/TechAgnostic/Utility/ConvertToHailMTT2T.wdl
- name: MergePhasedVCF
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/PacBio/Utility/MergePhasedVCF.wdl
31 changes: 31 additions & 0 deletions docker/lr-bandage/Dockerfile
Original file line number Diff line number Diff line change
@@ -0,0 +1,31 @@
FROM flowcraft/bandage:0.8.1

# ARG SAMTOOLS_VERSION=1.15.1
# ARG BCFTOOLS_VERSION=1.15.1

# ARG DEBIAN_FRONTEND=noninteractive
# RUN apt-get -qqy update --fix-missing && \
# apt-get -qqy dist-upgrade && \
# apt-get -qqy install --no-install-recommends \
# ca-certificates \
# libbz2-dev \
# libcurl4-openssl-dev \
# liblzma-dev \
# libncurses5-dev \
# autoconf \
# automake \
# bzip2 \
# gcc \
# g++ \
# make \
# wget \
# zlib1g-dev && \

# wget https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2 && \
# tar xjf samtools-${SAMTOOLS_VERSION}.tar.bz2 && \
# cd samtools-${SAMTOOLS_VERSION} && ./configure --without-curses --enable-libcurl && make -s all all-htslib && make install install-htslib && cd - && \
# rm -rf samtools-${SAMTOOLS_VERSION}* && \
# wget https://github.com/samtools/bcftools/releases/download/${BCFTOOLS_VERSION}/bcftools-${BCFTOOLS_VERSION}.tar.bz2 && \
# tar xjf bcftools-${BCFTOOLS_VERSION}.tar.bz2 && \
# cd bcftools-${BCFTOOLS_VERSION} && ./configure --without-curses && make -s && make install && cd - && \
# rm -rf bcftools-${BCFTOOLS_VERSION}*