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authorlltommy2020-04-13 02:38:26 +0200
committerlltommy2020-04-13 02:38:26 +0200
commit51fc61bae3ed2eae9719c1aabf959d47468724b2 (patch)
tree84c64e07db46034d88b1b48e033138b64ccc1f79 /README.md
parentbc62d3f4c9ed8d94e536d2dd67fedf40b3e011ab (diff)
parentaa93ecf387182896e6dc84bdd145ebce9aba3745 (diff)
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Merge branch 'master' of https://github.com/arvados/bh20-seq-resource
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1 files changed, 4 insertions, 4 deletions
diff --git a/README.md b/README.md
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@@ -59,7 +59,7 @@ sudo apt install -y virtualenv git libcurl4-openssl-dev build-essential python3-
pip3 install --user git+https://github.com/arvados/bh20-seq-resource.git@master
```
-3. **Make sure the tool is on your `PATH`.** THe `pip3` command will install the uploader in `.local/bin` inside your home directory. Your shell may not know to look for commands there by default. To fix this for the terminal you currently have open, run:
+3. **Make sure the tool is on your `PATH`.** The `pip3` command will install the uploader in `.local/bin` inside your home directory. Your shell may not know to look for commands there by default. To fix this for the terminal you currently have open, run:
```sh
export PATH=$PATH:$HOME/.local/bin
@@ -126,10 +126,10 @@ For running/developing the uploader with GNU Guix see [INSTALL.md](./doc/INSTALL
# Usage
-Run the uploader with a FASTA file and accompanying metadata file in [JSON-LD format](https://json-ld.org/):
+Run the uploader with a FASTA or FASTQ file and accompanying metadata file in JSON or YAML:
```sh
-bh20-seq-uploader example/sequence.fasta example/metadata.json
+bh20-seq-uploader example/sequence.fasta example/metadata.yaml
```
## Workflow for Generating a Pangenome
@@ -174,7 +174,7 @@ pip3 install gunicorn
gunicorn bh20simplewebuploader.main:app
```
-This runs on [http://127.0.0.1:8000/](http://127.0.0.1:8000/) by default, but can be adjusted with various [gunicorn options](http://docs.gunicorn.org/en/latest/run.html#commonly-used-arguments)
+This runs on [http://127.0.0.1:8000/](http://127.0.0.1:8000/) by default, but can be adjusted with various [gunicorn options](http://docs.gunicorn.org/en/latest/run.html#commonly-used-arguments).