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| author | Pjotr Prins | 2020-05-13 10:09:17 -0500 |
|---|---|---|
| committer | Pjotr Prins | 2020-05-13 10:09:50 -0500 |
| commit | 5b61a6901609b1b0c467c40681742ddb2e51592a (patch) | |
| tree | 3fcfc35a11c2ff3d9c5942c995f61f4dfaeeaeac /doc | |
| parent | e48ab6fcfd24e98b76b588545c5ab6b595524f25 (diff) | |
| download | bh20-seq-resource-5b61a6901609b1b0c467c40681742ddb2e51592a.tar.gz bh20-seq-resource-5b61a6901609b1b0c467c40681742ddb2e51592a.tar.lz bh20-seq-resource-5b61a6901609b1b0c467c40681742ddb2e51592a.zip | |
Guix version of uploader works. Updated instructions.
Diffstat (limited to 'doc')
| -rw-r--r-- | doc/INSTALL.md | 9 |
1 files changed, 8 insertions, 1 deletions
diff --git a/doc/INSTALL.md b/doc/INSTALL.md index 8f4b2f0..d9948e6 100644 --- a/doc/INSTALL.md +++ b/doc/INSTALL.md @@ -1,3 +1,5 @@ +#+OPTIONS: ^:nil + # INSTALLATION Other options for running this tool. @@ -29,12 +31,15 @@ arvados-python-client-2.0.1 ciso8601-2.1.3 future-0.18.2 google-api-python-clien 3. Run the tool directly with ```sh -guix environment guix --ad-hoc git python openssl python-pycurl python-magic nss-certs python-pyshex -- python3 bh20sequploader/main.py example/sequence.fasta example/metadata.yaml +guix environment guix --ad-hoc git python openssl python-pycurl python-magic nss-certs python-pyshex -- python3 bh20sequploader/main.py example/sequence.fasta example/maximum_metadata_example.yaml ``` Note that python-pyshex is packaged in http://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics +so you'll need it to the GUIX_PACKAGE_PATH - see the README in that +repository. + ### Using the Web Uploader To run the web uploader in a GNU Guix environment/container @@ -50,3 +55,5 @@ guix environment guix --ad-hoc git python python-flask python-pyyaml python-pycu ``` WIP: add gunicorn container + +Note: see above on GUIX_PACKAGE_PATH. |