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Enable GCS, S3, and libdeflate support for bcftools #1019

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merged 6 commits into from
Aug 21, 2024
Merged

Enable GCS, S3, and libdeflate support for bcftools #1019

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c1feb6f
Enable AWS S3, GCS, and libdeflate support for bcftools by running ./…
pettyalex Jul 9, 2024
120ba57
Fix runtime deflate dependency with correct version for jammy.
pettyalex Jul 9, 2024
3777421
Add a test for bcftools that reads headers from a reference VCF hoste…
pettyalex Jul 10, 2024
38ed7a2
Update htslib, samtools, and bcftools to not include dev versions of …
pettyalex Jul 10, 2024
b5444c6
Move bcftools update into a new version. Incorporate feedback on Dock…
pettyalex Jul 18, 2024
95455e4
Add README to new version.
pettyalex Jul 18, 2024
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3 changes: 3 additions & 0 deletions bcftools/1.20/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 install --no-install-recommends -y \
libbz2-dev \
liblzma-dev \
libcurl4-gnutls-dev \
libdeflate-dev \
libssl-dev \
libperl-dev \
libgsl0-dev \
Expand All @@ -31,6 +32,7 @@ RUN wget https://github.com/samtools/bcftools/releases/download/${BCFTOOLS_VER}/
tar -xjf bcftools-${BCFTOOLS_VER}.tar.bz2 && \
rm -v bcftools-${BCFTOOLS_VER}.tar.bz2 && \
cd bcftools-${BCFTOOLS_VER} && \
./configure && \
make && \
make install && \
make test
Expand Down Expand Up @@ -63,6 +65,7 @@ RUN apt-get update && apt-get install --no-install-recommends -y \
bzip2 \
liblzma-dev \
libcurl4-gnutls-dev \
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Do these actually need to be -dev versions with headers in the runtime container? Do plugins somehow compile/link against them at runtime or can they just be liblzma libcurl4-gnutls?

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Not sure about compilation & linking, but I think the correct syntax is liblzma5 for Ubuntu Jammy: https://packages.ubuntu.com/search?suite=jammy&section=all&arch=any&keywords=liblzma&searchon=names

and libcurl4: https://packages.ubuntu.com/search?suite=jammy&section=all&arch=any&keywords=libcurl4&searchon=names

I believe when the samtools/bcftools/htslib dockerfiles were written we were following these instructions: https://github.com/samtools/samtools/blob/972c1889942a4f07d8f62e93330f723da919c271/INSTALL#L220

libdeflate \
procps \
&& apt-get autoclean && rm -rf /var/lib/apt/lists/* && \
mkdir /data
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