Add instructions for offline use #1
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adamant-pwn
requested changes
Apr 17, 2025
README.md
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| #### Conda | ||
| ```sh | ||
| conda install -c bioconda -c conda-forge metagraph |
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Last time I checked, bioconda image was quite behind the git trunk. In particular, the query above wouldn't work due to incompatible CLI arguments. Should we do something about it before merging?
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yes, I'm creating the new release now
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I removed the conda instructions for now since there's still some work being done on upgrading the package.
Co-authored-by: Oleksandr Kulkov <[email protected]>
Co-authored-by: Oleksandr Kulkov <[email protected]>
Co-authored-by: Oleksandr Kulkov <[email protected]>
adamant-pwn
reviewed
Apr 17, 2025
adamant-pwn
reviewed
Apr 17, 2025
adamant-pwn
reviewed
Apr 17, 2025
Co-authored-by: Oleksandr Kulkov <[email protected]>
Co-authored-by: Oleksandr Kulkov <[email protected]>
Co-authored-by: Oleksandr Kulkov <[email protected]>
adamant-pwn
reviewed
Apr 22, 2025
adamant-pwn
reviewed
Apr 22, 2025
| --min-kmers-fraction-graph 0 \ | ||
| examples/100_studies_short.fq | ||
| ``` | ||
| replacing `${MNTDIR}` with the local mount path. |
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We should probably provide some specific examples on what should be used as ${MNTDIR}.
adamant-pwn
reviewed
Apr 22, 2025
Co-authored-by: Oleksandr Kulkov <[email protected]>
adamant-pwn
reviewed
Apr 25, 2025
adamant-pwn
reviewed
Apr 25, 2025
adamant-pwn
reviewed
Apr 25, 2025
adamant-pwn
reviewed
Apr 25, 2025
| ```sh | ||
| aws s3 sync s3://metagraph-data-public/all_sra/data/metagenome/0400 . --no-sign-request --region eu-central-2 | ||
| ``` | ||
| Currently, chunks numbered `0001` through to `0400` are available for download. The example query file is located in this repository under [`examples/100_studies_short.fq`](https://github.com/ratschlab/metagraph-open-data/blob/main/examples/100_studies_short.fq). |
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@akahles should we put "through to 4000 here?
Co-authored-by: Oleksandr Kulkov <[email protected]>
Co-authored-by: Oleksandr Kulkov <[email protected]>
Co-authored-by: Oleksandr Kulkov <[email protected]>
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