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authorPjotr Prins2020-11-06 11:19:28 +0000
committerPjotr Prins2020-11-06 11:19:28 +0000
commit5fdfece97fb2d50a10eab5004a6467ec0097ece8 (patch)
tree022eff03421416c082cd09e7c4d391b9527501e9 /doc/INSTALL.md
parent951ebe949d88cdbfed028e0a2a420ce7921c3919 (diff)
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Uploader script improvements
Diffstat (limited to 'doc/INSTALL.md')
-rw-r--r--doc/INSTALL.md8
1 files changed, 7 insertions, 1 deletions
diff --git a/doc/INSTALL.md b/doc/INSTALL.md
index f54c8f2..45aca0f 100644
--- a/doc/INSTALL.md
+++ b/doc/INSTALL.md
@@ -31,7 +31,7 @@ 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/maximum_metadata_example.yaml
+guix environment guix --ad-hoc git python openssl python-pycurl python-magic nss-certs python-pyshex -- python3 bh20sequploader/main.py example/maximum_metadata_example.yaml example/sequence.fasta
```
Note that python-pyshex is packaged in
@@ -44,6 +44,12 @@ repository. E.g.
env GUIX_PACKAGE_PATH=~/iwrk/opensource/guix/guix-bioinformatics/ ~/opt/guix/bin/guix environment -C guix --ad-hoc git python python-flask python-pyyaml python-pycurl python-magic nss-certs python-pyshex python-pyyaml --network openssl python-pyshex python-pyshexc minimap2 python-schema-salad python-arvados-python-client --share=/export/tmp -- env TMPDIR=/export/tmp python3 bh20sequploader/main.py --help
```
+Latest successful Guix run
+
+```sh
+env GUIX_PACKAGE_PATH=~/iwrk/opensource/guix/guix-bioinformatics/ ~/opt/guix/bin/guix environment guix --ad-hoc git python openssl python-pycurl python-magic nss-certs python-pyshex python-arvados-python-client python-schema-salad minimap2 -- python3 bh20sequploader/main.py scripts/uthsc_samples/yaml/AL_UT14.yaml scripts/uthsc_samples/yaml/AL_UT14.fa
+```
+
### Using the Web Uploader
To run the web uploader in a GNU Guix environment/container run it with something like