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| author | Pjotr Prins | 2021-01-28 18:43:06 +0000 |
|---|---|---|
| committer | Pjotr Prins | 2021-01-28 18:43:06 +0000 |
| commit | 90470bc795a17a6ddf6dca156f507d02cb056ec3 (patch) | |
| tree | 6e765e2e92c84ce7dc9453beca217ec5192199fd | |
| parent | a54122023ef2bde4ef4fc39355b3491678bbf773 (diff) | |
| download | bh20-seq-resource-90470bc795a17a6ddf6dca156f507d02cb056ec3.tar.gz bh20-seq-resource-90470bc795a17a6ddf6dca156f507d02cb056ec3.tar.lz bh20-seq-resource-90470bc795a17a6ddf6dca156f507d02cb056ec3.zip | |
Adding support for Auspice
| -rw-r--r-- | doc/INSTALL.md | 24 |
1 files changed, 24 insertions, 0 deletions
diff --git a/doc/INSTALL.md b/doc/INSTALL.md index 0367c63..124aba0 100644 --- a/doc/INSTALL.md +++ b/doc/INSTALL.md @@ -113,3 +113,27 @@ 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. + +## Run the Auspice phylo-tree viewer + +Auspice is developed by the Nextstrain team and we use it for +exploring the phylogenetic tree. It does not scale well beyond 5,000 +SARS-CoV-2 virusses, so we need to limit the input set! + +Auspice runs on a separate port. + +Running on port 4001 using your repo: + +Install node with Guix + + ~/.config/guix/current/bin/guix package -i node -p ~/opt/node + +Load Guix environment variables + + . ~/opt/node/etc/profile + +Run server after fetching data in ./data + + cd auspice + npm install --global --prefix node_modules . + env PORT=4001 ./node_modules/bin/auspice view --datasetDir ./data |