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| author | Peter Amstutz | 2020-04-06 17:54:37 -0400 |
|---|---|---|
| committer | GitHub | 2020-04-06 17:54:37 -0400 |
| commit | 9b1c125f91469074c7586a1278d89b85919e3eae (patch) | |
| tree | 6d6a69ef2ebf4a9481a2c350914373ad25f63d00 /README.md | |
| parent | 2c69ca48ce1a9ab431afcc891bdad8c495c9768e (diff) | |
| parent | 762b770eda79fd4006b767e2dd768746232995ba (diff) | |
| download | bh20-seq-resource-9b1c125f91469074c7586a1278d89b85919e3eae.tar.gz bh20-seq-resource-9b1c125f91469074c7586a1278d89b85919e3eae.tar.lz bh20-seq-resource-9b1c125f91469074c7586a1278d89b85919e3eae.zip | |
Merge pull request #1 from pjotrp/master
Installation notes
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| -rw-r--r-- | README.md | 48 |
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diff --git a/README.md b/README.md new file mode 100644 index 0000000..ec9afb1 --- /dev/null +++ b/README.md @@ -0,0 +1,48 @@ +# 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 |