diff options
| author | Adam Novak | 2020-04-09 15:57:37 -0700 |
|---|---|---|
| committer | Adam Novak | 2020-04-09 15:58:56 -0700 |
| commit | d9a24cfb81a028fcd901abd08fc02b9140d5e78b (patch) | |
| tree | b08ac8d559a263381703ce14c06e144e6f48912c /README.md | |
| parent | 2cd6623aa0ddfe4e42b2d434e0523773bb3536ef (diff) | |
| parent | b1039ff369ee88770e42d1bbbdc402b1181c2aa5 (diff) | |
| download | bh20-seq-resource-d9a24cfb81a028fcd901abd08fc02b9140d5e78b.tar.gz bh20-seq-resource-d9a24cfb81a028fcd901abd08fc02b9140d5e78b.tar.lz bh20-seq-resource-d9a24cfb81a028fcd901abd08fc02b9140d5e78b.zip | |
Merge remote-tracking branch 'upstream/master' into add-web-ui
Diffstat (limited to 'README.md')
| -rw-r--r-- | README.md | 19 |
1 files changed, 5 insertions, 14 deletions
@@ -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 +145,9 @@ odgi build -g seqs.gfa -s -o seqs.odgi odgi viz -i seqs.odgi -o seqs.png -x 4000 -y 500 -R -P 5 ``` +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). # Web Interface |