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Upgrade delly to 1.5.0 #1036

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Upgrade delly to 1.5.0 #1036

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66d8c55
updated delly and htslib in delly-bcftools docker image
Jun 19, 2024
6eb9baa
update delly to 1.5.0
anoronh4 Aug 6, 2025
848fcfa
update delly docker label
anoronh4 Aug 6, 2025
5bfb9ce
fix LegacyKeyValueFormat warning
anoronh4 Aug 6, 2025
3e8122e
add --allow-unauthenticated flag
anoronh4 Aug 6, 2025
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6 changes: 3 additions & 3 deletions conf/containers.config
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Original file line number Diff line number Diff line change
Expand Up @@ -76,10 +76,10 @@
container = "cmopipeline/metadataparser:0.5.9"
}
withName:SomaticDellyCall {
container = "cmopipeline/delly-bcftools:0.0.1"
container = "cmopipeline/delly-bcftools:0.0.3"
}
withName:'.*DellyCombine' {
container = "cmopipeline/delly-bcftools:0.0.1"
container = "cmopipeline/delly-bcftools:0.0.3"
}
withName:SomaticRunManta {
container = "cmopipeline/strelka2-manta-bcftools-vt:2.0.1"
Expand Down Expand Up @@ -115,7 +115,7 @@
//------------------- Germline pipeline

withName:GermlineDellyCall {
container = "cmopipeline/delly-bcftools:0.0.1"
container = "cmopipeline/delly-bcftools:0.0.3"
}
withName:GermlineRunHaplotypecaller {
container = "broadinstitute/gatk:4.1.0.0"
Expand Down
18 changes: 12 additions & 6 deletions containers/delly-bcftools/Dockerfile
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Expand Up @@ -2,15 +2,21 @@ FROM halllab/bcftools:v1.9

LABEL maintainer="Anne Marie Noronha (noronhaa@mskcc.org)" \
version.ubuntu="18.04" \
version.delly="0.8.2" \
version.htslib="1.9"
version.delly="1.5.0" \
version.htslib="1.20" \
version.image="0.0.4"

# set the environment variables
ENV delly_version 0.8.2
ENV htslib_version 1.9
ENV delly_version=1.5.0
ENV htslib_version=1.20

# APT repository has moved to archive. Sources needs to change.
RUN sed -i /stretch-updates/d /etc/apt/sources.list
RUN sed -i "s/security.debian/archive.debian/g" /etc/apt/sources.list
RUN sed -i "s/deb.debian/archive.debian/g" /etc/apt/sources.list

# run update
RUN apt-get update -y && apt-get install -y \
RUN apt-get update -y && apt-get install -y --allow-unauthenticated \
libnss-sss \
curl \
less \
Expand All @@ -37,7 +43,7 @@ RUN tar -xjf /usr/local/bin/htslib-${htslib_version}.tar.bz2 -C /usr/local/bin/
RUN cd /usr/local/bin/htslib-${htslib_version}/ && ./configure
RUN cd /usr/local/bin/htslib-${htslib_version}/ && make
RUN cd /usr/local/bin/htslib-${htslib_version}/ && make install
ENV LD_LIBRARY_PATH /usr/local/bin/htslib-${htslib_version}/
ENV LD_LIBRARY_PATH=/usr/local/bin/htslib-${htslib_version}/

# install delly
WORKDIR /usr/local/bin
Expand Down