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-rw-r--r--doc/INSTALL.md6
-rw-r--r--doc/blog/using-covid-19-pubseq-part1.org17
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