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Diffstat (limited to 'doc/INSTALL.md')
| -rw-r--r-- | doc/INSTALL.md | 48 |
1 files changed, 47 insertions, 1 deletions
diff --git a/doc/INSTALL.md b/doc/INSTALL.md index df825c6..0367c63 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 @@ -67,3 +73,43 @@ penguin2:~/iwrk/opensource/code/vg/bh20-seq-resource$ env GUIX_PACKAGE_PATH=~/i ``` Note: see above on GUIX_PACKAGE_PATH. + +## Run country semantic enrichment script + + cd bh20-seq-resource/scripts/db_enrichment + edit input_location.csv + guix environment guix --ad-hoc git python nss-certs python-rdflib -- python3 country_enrichment.py + +## Run the tests + + guix package -i python-requests python-pandas python-jinja2 python -p ~/opt/python-dev + . ~/opt/python-dev/etc/profile + + +## Run Virtuoso-ose + +Guix has a package for virtuoso-ose we use + + guix package -i virtuoso-ose -p ~/opt/virtuoso + +Create a data dir + + mkdir -p /export/virtuoso/var/lib/virtuoso/db + chown $USER /export/virtuoso/var/lib/virtuoso/db + +Add an ini file + + cp ~/opt/virtuoso/var/lib/virtuoso/db/virtuoso.ini .config/ + +And run from the data dir + + cd /export/virtuoso/var/lib/virtuoso/db + guix environment --ad-hoc virtuoso-ose -- virtuoso-t -f + +Visit http://localhost:8890/sparql + +To update the turtle files do + + guix environment -C guix --ad-hoc python python-requests raptor2 curl --network -- python3 ./scripts/update_virtuoso/check_for_updates.py cache.txt dba dba + +where dba is the default password. |