From 5b61a6901609b1b0c467c40681742ddb2e51592a Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Wed, 13 May 2020 10:09:17 -0500 Subject: Guix version of uploader works. Updated instructions. --- doc/INSTALL.md | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) (limited to 'doc') 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. -- cgit v1.2.3