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| author | lltommy | 2020-04-13 02:38:26 +0200 |
|---|---|---|
| committer | lltommy | 2020-04-13 02:38:26 +0200 |
| commit | 51fc61bae3ed2eae9719c1aabf959d47468724b2 (patch) | |
| tree | 84c64e07db46034d88b1b48e033138b64ccc1f79 /README.md | |
| parent | bc62d3f4c9ed8d94e536d2dd67fedf40b3e011ab (diff) | |
| parent | aa93ecf387182896e6dc84bdd145ebce9aba3745 (diff) | |
| download | bh20-seq-resource-51fc61bae3ed2eae9719c1aabf959d47468724b2.tar.gz bh20-seq-resource-51fc61bae3ed2eae9719c1aabf959d47468724b2.tar.lz bh20-seq-resource-51fc61bae3ed2eae9719c1aabf959d47468724b2.zip | |
Merge branch 'master' of https://github.com/arvados/bh20-seq-resource
Diffstat (limited to 'README.md')
| -rw-r--r-- | README.md | 8 |
1 files changed, 4 insertions, 4 deletions
@@ -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). |