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fix: msi container #1486

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merged 16 commits into from
Oct 16, 2024
Merged

fix: msi container #1486

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852ac97
changelog
khurrammaqbool Oct 14, 2024
f5e357e
fix to version 1.2.0
khurrammaqbool Oct 14, 2024
60a4649
update to version 1.3.0
khurrammaqbool Oct 14, 2024
b4097d3
split tasks
khurrammaqbool Oct 14, 2024
d0b0c4b
merge tasks
khurrammaqbool Oct 14, 2024
d3f9db9
fix somalier container
khurrammaqbool Oct 14, 2024
01eae4d
fix nimble htslib bcftools version
khurrammaqbool Oct 14, 2024
32a5da7
fix depth
khurrammaqbool Oct 14, 2024
7e69688
update nim to 1.6.20
khurrammaqbool Oct 14, 2024
0f91063
update nim to 2.2.0
khurrammaqbool Oct 14, 2024
6f43126
update somalier to 0.2.19
khurrammaqbool Oct 14, 2024
1ee633a
fix nimble version to 1.6.6
khurrammaqbool Oct 14, 2024
aab049a
revert changes for somalier container
khurrammaqbool Oct 14, 2024
b0bfe27
refactor
khurrammaqbool Oct 14, 2024
ed52fcd
update software version information
khurrammaqbool Oct 15, 2024
6d4d190
Merge branch 'develop' into fix/msi_container
mathiasbio Oct 16, 2024
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22 changes: 11 additions & 11 deletions BALSAMIC/containers/msisensorpro/Dockerfile
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Expand Up @@ -4,26 +4,26 @@ LABEL base.image="ubuntu:22.04" \
maintainer="Clinical Genomics" \
about.contact="support@clinicalgenomics.se" \
software="msisensor-pro" \
software.version="1.2.0" \
software.version="1.3.0" \
about.summary="Microsatellite Instability (MSI) detection using high-throughput sequencing data" \
about.home="https://github.com/xjtu-omics/msisensor-pro" \
about.documentation="https://github.com/xjtu-omics/msisensor-pro/wiki" \
about.license="MIT License (MIT)"

ENV DEBIAN_FRONTEND noninteractive
ENV DEBIAN_FRONTEND=noninteractive
RUN apt-get update && apt-get -y upgrade && \
apt-get install -y --no-install-recommends git make build-essential \
liblzma-dev libbz2-dev zlib1g-dev libncurses5-dev libncursesw5-dev ca-certificates && \
apt-get clean && \
rm -rf /var/lib/apt/lists/*

RUN cd /tmp && \
git clone https://github.com/xjtu-omics/msisensor-pro && \
cd msisensor-pro && \
/tmp/msisensor-pro/INSTALL && \
cp -r /tmp/msisensor-pro/binary/msisensor-pro /usr/bin/ && \
cp -r /tmp/msisensor-pro/vendor/htslib-1.11/libhts.so* /lib/x86_64-linux-gnu && \
rm -rf /tmp/msisensor-pro
rm -rf /var/lib/apt/lists/* && \
cd /tmp && \
git clone https://github.com/xjtu-omics/msisensor-pro && \
cd /tmp/msisensor-pro && \
git checkout v1.3.0 && \
/tmp/msisensor-pro/INSTALL && \
cp -r /tmp/msisensor-pro/binary/msisensor-pro /usr/bin/ && \
cp -r /tmp/msisensor-pro/vendor/htslib-1.11/libhts.so* /lib/x86_64-linux-gnu && \
rm -rf /tmp/msisensor-pro

RUN adduser --disabled-password --gecos '' ubuntu && \
chsh -s /bin/bash && mkdir -p /home/ubuntu
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1 change: 0 additions & 1 deletion BALSAMIC/containers/somalier/Dockerfile
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Expand Up @@ -56,4 +56,3 @@ ENV somalier_ancestry_labels /ancestry_labels-1kg.tsv
RUN adduser -D defaultuser

USER defaultuser

3 changes: 2 additions & 1 deletion CHANGELOG.rst
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Expand Up @@ -52,7 +52,8 @@ Fixed:
* MSI table https://github.com/Clinical-Genomics/BALSAMIC/pull/1459
* Pin numpy version in CNVkit container https://github.com/Clinical-Genomics/BALSAMIC/pull/1457
* CNVkit incorrect version in the documentation https://github.com/Clinical-Genomics/BALSAMIC/pull/1457

* MSIsensor-pro container https://github.com/Clinical-Genomics/BALSAMIC/pull/

[15.0.1]
--------

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