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| author | Pjotr Prins | 2020-04-06 16:42:00 -0500 |
|---|---|---|
| committer | Pjotr Prins | 2020-04-06 16:42:00 -0500 |
| commit | e8eb3d7eba3fdaa925b45bd914bf6b5d65682d7f (patch) | |
| tree | 9df61d1e63d74173808f021e46db23d40e2391d1 /README.md | |
| parent | c138b367229b5c0323984668315f369151668e32 (diff) | |
| download | bh20-seq-resource-e8eb3d7eba3fdaa925b45bd914bf6b5d65682d7f.tar.gz bh20-seq-resource-e8eb3d7eba3fdaa925b45bd914bf6b5d65682d7f.tar.lz bh20-seq-resource-e8eb3d7eba3fdaa925b45bd914bf6b5d65682d7f.zip | |
README and example
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| -rw-r--r-- | README.md | 35 |
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diff --git a/README.md b/README.md new file mode 100644 index 0000000..749121c --- /dev/null +++ b/README.md @@ -0,0 +1,35 @@ +# Sequence uploader + +This repository provides a sequence uploader for the + +# Run + +Run the uploader with a FASTA file and accompanying metadata: + + python3 bh20sequploader/main.py example/sequence.fasta example/metadata.json + +# Installation + +This tool requires the arvados Python module which can be installed +using .deb or .rpm packages through +https://doc.arvados.org/v2.0/sdk/python/sdk-python.html. The actual +code lives [here](https://github.com/arvados/arvados/tree/master/sdk/python) and +suggests a local install using + + apt-get install libcurl4-openssl-dev libssl1.0-dev + pip3 install --user arvados-python-client + +Next update + + export PATH=$PATH:$HOME/.local/bin + +## Install with GNU Guix + +Set up a container: + + ~/opt/guix/bin/guix environment -C guix --ad-hoc python openssl python-pycurl nss-certs + pip3 install --user arvados-python-client + +Pip installed the following modules + + arvados-python-client-2.0.1 ciso8601-2.1.3 future-0.18.2 google-api-python-client-1.6.7 httplib2-0.17.1 oauth2client-4.1.3 pyasn1-0.4.8 pyasn1-modules-0.2.8 rsa-4.0 ruamel.yaml-0.15.77 six-1.14.0 uritemplate-3.0.1 ws4py-0.5.1 |