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ratschlab
Docker issue: No version information available: libhts.so.3:
Hello! I've tried to pull two different metagraph Docker images for Metagraph using the following:
docker pull ghcr.io/ratschlab/metagraph:latest
docker pull ghcr.io/ratschlab/metagraph:master
In both cases, I'm able to run the Docker container with a /bin/bash entrypoint, but receive the following when I run any Metagraph commands:
metagraph: /lib/x86_64-linux-gnu/libhts.so.3: no version information available (required by metagraph)
It appears that libhts.so.3 is installed at /usr/lib/x86_64-linux-gnu/libhts.so.1.10.2-3ubuntu0.1, but I'm not sure how to go about providing the version to MetaGraph.
If it's relevant, I'm working with an Apple silicon laptop running MacOSX Sonoma 14.4.1 and Docker engine 24.0.6. Any insights you can offer are very much appreciated!
Hi @bbowles1! Does the issue still occur to you? I tried to do the following:
sudo docker pull ghcr.io/ratschlab/metagraph:latest
sudo docker run -it --entrypoint /bin/bash ghcr.io/ratschlab/metagraph:latest
Then, in the docler image, I have
root@825172b7a726:/# metagraph
Usage: metagraph <command> [command specific options]
Available commands:
build construct a graph object from input sequence
files in fast[a|q] formats into a given graph
clean clean an existing graph and extract sequences from it
in fast[a|q] formats
transform given a graph, transform it to other formats
align align sequences provided in fast[a|q] files to graph
annotate given a graph and a fast[a|q] file, annotate
the respective kmers
relax_brwt optimize the tree structure in brwt annotator
transform_anno change representation of the graph annotation
assemble given a graph, extract sequences from it
query annotate sequences from fast[a|q] files
server_query annotate received sequences and send annotations back
stats print graph statistics for given graph(s) or annotation
General options:
--advanced show other advanced and legacy options [off]
--version print version
So, I can not reproduce the error that you describe at the moment. I tested it on Docker version 26.1.4, and then also downgraded to 24.0.6, but it didn't change anything.
Hey Adamant, thanks for the quick response! I followed up on your recommendations and unfortunately I'm receiving an error "Illegal instruction" after I run the container and enter a simple metagraph command like you recommended.
This seems to be a MacOS-specific issue, as the Metagraph container works flawlessly when I run it in a Linux environment. On Mac, I see an AMD64 warning "Image may have poor performance, or fail, if run via emulation" when I pull the Docker image. Adding a --platform linux/amd64 flag to the Docker run command to explicitly run the container via emulation does not change the error or resolve my issue.
Since this appears related to MacOS, and you may be unable to replicate the error as a result, I understand if you wish to close this issue. In the meantime, I'm happy to update if I have any further insights into this error. Thanks again for your recommendations.
Checking in with a quick update, I'm also unable to build the Docker image locally. I receive an error related to a missing install.sh:
(base) bbowles@Bradleys-MBP metagraph % docker build .
[+] Building 124.0s (16/22) docker:desktop-linux
=> [internal] load build definition from Dockerfile 0.0s
=> => transferring dockerfile: 3.13kB 0.0s
=> [internal] load .dockerignore 0.0s
=> => transferring context: 225B 0.0s
=> [internal] load metadata for docker.io/library/ubuntu:20.04 1.2s
=> [internal] load build context 0.1s
=> => transferring context: 38.28kB 0.1s
=> CACHED [metagraph_dev_env 1/8] FROM docker.io/library/ubuntu:20.04@sha256:0b897358ff6624825fb50d20ffb605ab0eaea77ced0adb8c6a4b756513dec6fc 0.0s
=> CACHED [stage-2 2/8] RUN apt-get update && apt-get install -y libatomic1 libcurl4-nss-dev libgomp1 libhts-dev libjemalloc2 python3 0.0s
=> [metagraph_dev_env 2/8] RUN export DEBIAN_FRONTEND="noninteractive" && apt-get update && apt-get install -y autoconf automake binutils-dev 89.6s
=> [metagraph_dev_env 3/8] RUN pip3 install parameterized==0.7.1 "cmake>=3.19" 3.3s
=> [metagraph_dev_env 4/8] WORKDIR /opt 0.0s
=> [metagraph_dev_env 5/8] RUN git clone https://github.com/curl/curl.git && mkdir curl/_build && cd curl/_build && cmake -DBUILD_SHARED_LIBS=on 20.9s
=> [metagraph_dev_env 6/8] RUN wget https://github.com/samtools/htslib/releases/download/1.10.2/htslib-1.10.2.tar.bz2 && tar -vxjf htslib-1.10.2.tar.bz2 8.2s
=> [metagraph_dev_env 7/8] RUN mkdir -p /opt/metagraph/build_docker /opt/ccache_docker 0.3s
=> [metagraph_dev_env 8/8] RUN chmod o+rwx /opt/metagraph /opt/ccache_docker 0.3s
=> [metagraph_bin 1/3] COPY . /opt/metagraph 0.1s
=> [metagraph_bin 2/3] WORKDIR /opt/metagraph 0.0s
=> ERROR [metagraph_bin 3/3] RUN make build-sdsl-lite && make build-metagraph alphabet=Protein && make build-metagraph alphabet=DNA 0.1s
------
> [metagraph_bin 3/3] RUN make build-sdsl-lite && make build-metagraph alphabet=Protein && make build-metagraph alphabet=DNA:
0.088 bash -c 'cd /opt/metagraph/metagraph/external-libraries/sdsl-lite && ./install.sh ${PWD}'
0.092 bash: ./install.sh: No such file or directory
0.093 make: *** [Makefile:72: build-sdsl-lite] Error 127
------
Dockerfile:80
--------------------
79 | WORKDIR ${CODE_BASE}
80 | >>> RUN make build-sdsl-lite \
81 | >>> && make build-metagraph alphabet=Protein \
82 | >>> && make build-metagraph alphabet=DNA
83 |
--------------------
ERROR: failed to solve: process "/bin/sh -c make build-sdsl-lite && make build-metagraph alphabet=Protein && make build-metagraph alphabet=DNA" did not complete successfully: exit code: 2
Hi @bbowles1, the Docker container is fixed now (the previous release where it worked for me was v0.3.6. Now the latest images (ghcr.io/ratschlab/metagraph:master) are working on MacOS again, and will be supported in the next release). All other issues mentioned in this thread should also be fixed now. Please let me know if you have any questions.
