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| author | Pjotr Prins | 2020-04-09 17:02:38 -0500 |
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| committer | Pjotr Prins | 2020-04-09 17:02:38 -0500 |
| commit | bf93a6a2fec690eee4bff4891469cd5947102b3a (patch) | |
| tree | 103d82f4800aef14a66591341e19c5373a33d422 /README.md | |
| parent | 0670ac0644c1e7366952e254bdee2db62e673275 (diff) | |
| download | bh20-seq-resource-bf93a6a2fec690eee4bff4891469cd5947102b3a.tar.gz bh20-seq-resource-bf93a6a2fec690eee4bff4891469cd5947102b3a.tar.lz bh20-seq-resource-bf93a6a2fec690eee4bff4891469cd5947102b3a.zip | |
Moved Guix documentation into separate file (as it confused people ;)
Diffstat (limited to 'README.md')
| -rw-r--r-- | README.md | 21 |
1 files changed, 5 insertions, 16 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 +145,7 @@ 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). |