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| -rw-r--r-- | doc/INSTALL.md | 6 | ||||
| -rw-r--r-- | doc/blog/using-covid-19-pubseq-part1.org | 17 |
2 files changed, 19 insertions, 4 deletions
diff --git a/doc/INSTALL.md b/doc/INSTALL.md index d9948e6..6dcd72b 100644 --- a/doc/INSTALL.md +++ b/doc/INSTALL.md @@ -56,4 +56,10 @@ guix environment guix --ad-hoc git python python-flask python-pyyaml python-pycu WIP: add gunicorn container +Currently the full webserver container deploy command looks like + +``` +penguin2:~/iwrk/opensource/code/vg/bh20-seq-resource$ env GUIX_PACKAGE_PATH=~/iwrk/opensource/guix/guix-bioinformatics/ ~/iwrk/opensource/guix/guix/pre-inst-env 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 clustalw python-schema-salad python-arvados-python-client --share=/export/tmp -- env TMPDIR=/export/tmp FLASK_ENV=development FLASK_APP=bh20simplewebuploader/main.py flask run +`` + Note: see above on GUIX_PACKAGE_PATH. diff --git a/doc/blog/using-covid-19-pubseq-part1.org b/doc/blog/using-covid-19-pubseq-part1.org index bca885d..8d3dae5 100644 --- a/doc/blog/using-covid-19-pubseq-part1.org +++ b/doc/blog/using-covid-19-pubseq-part1.org @@ -1,6 +1,5 @@ -* COVID-19 PubSeq (part 1) - -/by Pjotr Prins/ +#+TITLE: COVID-19 PubSeq (part 1) +#+AUTHOR: Pjotr Prins As part of the COVID-19 Biohackathon 2020 we formed a working group to create a COVID-19 Public Sequence Resource (COVID-19 PubSeq) for @@ -12,7 +11,16 @@ most importantly, providing standardised workflows that get triggered on upload, so that results are immediately available in standardised data formats. -** What does this mean? +* Table of Contents :TOC: + - [[#what-does-this-mean][What does this mean?]] + - [[#fetch-sequence-data][Fetch sequence data]] + - [[#predicates][Predicates]] + - [[#fetch-submitter-info-and-other-metadata][Fetch submitter info and other metadata]] + - [[#fetch-all-sequences-from-washington-state][Fetch all sequences from Washington state]] + - [[#discussion][Discussion]] + - [[#acknowledgements][Acknowledgements]] + +* What does this mean? This means that when someone uploads a SARS-CoV-2 sequence using one of our tools (CLI or web-based) they add some metadata which is @@ -55,6 +63,7 @@ graph in triples. Soon we will at multi sequence alignments (MSA) and more. Anyone can contribute data, tools and workflows to this initiative! + * Fetch sequence data The latest run of the pipeline can be viewed [[https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca][here]]. Each of these |