From e8eb3d7eba3fdaa925b45bd914bf6b5d65682d7f Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Mon, 6 Apr 2020 16:42:00 -0500
Subject: README and example

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 README.md | 35 +++++++++++++++++++++++++++++++++++
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 create mode 100644 README.md

(limited to 'README.md')

diff --git a/README.md b/README.md
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+# Sequence uploader
+
+This repository provides a sequence uploader for the
+
+# Run
+
+Run the uploader with a FASTA file and accompanying metadata:
+
+    python3 bh20sequploader/main.py example/sequence.fasta example/metadata.json
+
+# Installation
+
+This tool requires the arvados Python module which can be installed
+using .deb or .rpm packages through
+https://doc.arvados.org/v2.0/sdk/python/sdk-python.html. The actual
+code lives [here](https://github.com/arvados/arvados/tree/master/sdk/python) and
+suggests a local install using
+
+    apt-get install libcurl4-openssl-dev libssl1.0-dev
+    pip3 install --user arvados-python-client
+
+Next update
+
+    export PATH=$PATH:$HOME/.local/bin
+
+## Install with GNU Guix
+
+Set up a container:
+
+    ~/opt/guix/bin/guix environment -C guix --ad-hoc python openssl python-pycurl nss-certs
+    pip3 install --user arvados-python-client
+
+Pip installed the following modules
+
+    arvados-python-client-2.0.1 ciso8601-2.1.3 future-0.18.2 google-api-python-client-1.6.7 httplib2-0.17.1 oauth2client-4.1.3 pyasn1-0.4.8 pyasn1-modules-0.2.8 rsa-4.0 ruamel.yaml-0.15.77 six-1.14.0 uritemplate-3.0.1 ws4py-0.5.1
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From 762b770eda79fd4006b767e2dd768746232995ba Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Mon, 6 Apr 2020 16:49:19 -0500
Subject: Add note on workflow

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 README.md | 13 +++++++++++++
 1 file changed, 13 insertions(+)

(limited to 'README.md')

diff --git a/README.md b/README.md
index 749121c..ec9afb1 100644
--- a/README.md
+++ b/README.md
@@ -8,6 +8,19 @@ Run the uploader with a FASTA file and accompanying metadata:
 
     python3 bh20sequploader/main.py example/sequence.fasta example/metadata.json
 
+# Add a workflow
+
+get your SARS-CoV-2 sequences from GenBank in seqs.fa
+
+```sh
+minimap2 -cx asm20 -X seqs.fa seqs.fa >seqs.paf
+seqwish -s seqs.fa -p seqs.paf -g seqs.gfa
+odgi build -g seqs.gfa -s -o seqs.odgi
+odgi viz -i seqs.odgi -o seqs.png -x 4000 -y 500 -R -P 5
+```
+
+from https://github.com/virtual-biohackathons/covid-19-bh20/wiki/Pangenome#pangenome-model-from-available-genomes
+
 # Installation
 
 This tool requires the arvados Python module which can be installed
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