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authorPjotr Prins2020-05-13 10:09:17 -0500
committerPjotr Prins2020-05-13 10:09:50 -0500
commit5b61a6901609b1b0c467c40681742ddb2e51592a (patch)
tree3fcfc35a11c2ff3d9c5942c995f61f4dfaeeaeac
parente48ab6fcfd24e98b76b588545c5ab6b595524f25 (diff)
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Guix version of uploader works. Updated instructions.
-rw-r--r--doc/INSTALL.md9
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.