blob: ec9afb1640108c693ed63e1a1fb38a512c2c1e95 (
plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
|
# 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
# 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
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
|
