From bf93a6a2fec690eee4bff4891469cd5947102b3a Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Thu, 9 Apr 2020 17:02:38 -0500
Subject: Moved Guix documentation into separate file (as it confused people ;)

---
 README.md               | 21 +++++----------------
 bh20sequploader/main.py |  2 +-
 doc/INSTALL.md          | 31 +++++++++++++++++++++++++++++++
 3 files changed, 37 insertions(+), 17 deletions(-)
 create mode 100644 doc/INSTALL.md

diff --git a/README.md b/README.md
index a6fe052..3a8e5f0 100644
--- a/README.md
+++ b/README.md
@@ -122,19 +122,7 @@ It should print some instructions about how to use the uploader.
 
 ## Installation with GNU Guix
 
-Another way to install this tool is inside a [GNU Guix Environment](https://guix.gnu.org/manual/en/html_node/Invoking-guix-environment.html), which can handle installing dependencies for you even when you don't have root access on an Ubuntu system.
-
-1. **Set up and enter a container with the necessary dependencies.** After installing Guix as `~/opt/guix/bin/guix`, run:
-
-```sh
-~/opt/guix/bin/guix environment -C guix --ad-hoc git python openssl python-pycurl nss-certs
-```
-   
-2. **Install the tool.** From there you can follow the [user installation instructions](#installation-with-pip3---user). In brief:
-
-```sh
-pip3 install --user git+https://github.com/arvados/bh20-seq-resource.git@master
-```
+For running/developing the uploader with GNU Guix see [INSTALL.md](./doc/INSTALL.md)
 
 # Usage
 
@@ -148,7 +136,7 @@ bh20-seq-uploader example/sequence.fasta example/metadata.json
 
 All these uploaded sequences are being fed into a workflow to generate a [pangenome](https://academic.oup.com/bib/article/19/1/118/2566735) for the virus. You can replicate this workflow yourself.
 
-Get your SARS-CoV-2 sequences from GenBank in `seqs.fa`, and then run:
+An example is to get your SARS-CoV-2 sequences from GenBank in `seqs.fa`, and then run a series of commands
 
 ```sh
 minimap2 -cx asm20 -X seqs.fa seqs.fa >seqs.paf
@@ -157,6 +145,7 @@ odgi build -g seqs.gfa -s -o seqs.odgi
 odgi viz -i seqs.odgi -o seqs.png -x 4000 -y 500 -R -P 5
 ```
 
-For more information on building pangenome models, [see this wiki page](https://github.com/virtual-biohackathons/covid-19-bh20/wiki/Pangenome#pangenome-model-from-available-genomes).
-
+Here we convert such a pipeline into the Common Workflow Language (CWL) and
+sources can be found [here](https://github.com/hpobio-lab/viral-analysis/tree/master/cwl/pangenome-generate).
 
+For more information on building pangenome models, [see this wiki page](https://github.com/virtual-biohackathons/covid-19-bh20/wiki/Pangenome#pangenome-model-from-available-genomes).
diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py
index 56cbe22..bf74ea5 100644
--- a/bh20sequploader/main.py
+++ b/bh20sequploader/main.py
@@ -6,7 +6,7 @@ import json
 import urllib.request
 import socket
 import getpass
-from .qc_metadata import qc_metadata
+import qc_metadata
 
 ARVADOS_API_HOST='lugli.arvadosapi.com'
 ARVADOS_API_TOKEN='2fbebpmbo3rw3x05ueu2i6nx70zhrsb1p22ycu3ry34m4x4462'
diff --git a/doc/INSTALL.md b/doc/INSTALL.md
new file mode 100644
index 0000000..c5c486c
--- /dev/null
+++ b/doc/INSTALL.md
@@ -0,0 +1,31 @@
+# INSTALLATION
+
+Other options for running this tool.
+
+## GNU Guix
+
+Another way to install this tool is inside a [GNU Guix Environment](https://guix.gnu.org/manual/en/html_node/Invoking-guix-environment.html), which can handle installing dependencies for you even when you don't have root access on an Ubuntu system.
+
+1. **Set up and enter a container with the necessary dependencies.** After installing Guix as `~/opt/guix/bin/guix`, run:
+
+```sh
+~/opt/guix/bin/guix environment -C guix --ad-hoc git python openssl python-pycurl nss-certs
+```
+
+2. **Install the tool.** From there you can follow the [user installation instructions](#installation-with-pip3---user). In brief:
+
+```sh
+pip3 install --user schema-salad  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
+```
+
+3. Run the tool directly with
+
+```sh
+~/opt/guix/bin/guix environment guix --ad-hoc git python openssl python-pycurl nss-certs -- python3 bh20sequploader/main.py
+```
-- 
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