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| author | Pjotr Prins | 2020-11-06 11:19:28 +0000 |
|---|---|---|
| committer | Pjotr Prins | 2020-11-06 11:19:28 +0000 |
| commit | 5fdfece97fb2d50a10eab5004a6467ec0097ece8 (patch) | |
| tree | 022eff03421416c082cd09e7c4d391b9527501e9 /doc/INSTALL.md | |
| parent | 951ebe949d88cdbfed028e0a2a420ce7921c3919 (diff) | |
| download | bh20-seq-resource-5fdfece97fb2d50a10eab5004a6467ec0097ece8.tar.gz bh20-seq-resource-5fdfece97fb2d50a10eab5004a6467ec0097ece8.tar.lz bh20-seq-resource-5fdfece97fb2d50a10eab5004a6467ec0097ece8.zip | |
Uploader script improvements
Diffstat (limited to 'doc/INSTALL.md')
| -rw-r--r-- | doc/INSTALL.md | 8 |
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 |