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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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1 change: 1 addition & 0 deletions BALSAMIC/containers/msisensorpro/Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,7 @@ RUN apt-get update && apt-get -y upgrade && \
RUN cd /tmp && \
git clone https://github.com/xjtu-omics/msisensor-pro && \
cd msisensor-pro && \
git checkout v1.2.2 \
/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 && \
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3 changes: 2 additions & 1 deletion CHANGELOG.rst
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Expand Up @@ -27,7 +27,8 @@ 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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