# 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