From 8118c9365c3663632d927e56cfafadccdca15ce1 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Wed, 20 May 2020 14:09:27 -0500
Subject: BLOG

---
 doc/INSTALL.md                           |  6 ++++++
 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
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