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| author | Pjotr Prins | 2020-04-12 12:51:24 -0500 |
|---|---|---|
| committer | GitHub | 2020-04-12 12:51:24 -0500 |
| commit | 42ee1f77ca4a6e3a9c7dfc15e69b9de43f801c59 (patch) | |
| tree | e756eb01c166ab99f00019f997c8a6a67335412a /README.md | |
| parent | 0005a2544bdc48cd2ddc85e6cd6e0ddf51cc71df (diff) | |
| parent | a764f0496f47f5c93f2a6915d00c8a1e89df0712 (diff) | |
| download | bh20-seq-resource-42ee1f77ca4a6e3a9c7dfc15e69b9de43f801c59.tar.gz bh20-seq-resource-42ee1f77ca4a6e3a9c7dfc15e69b9de43f801c59.tar.lz bh20-seq-resource-42ee1f77ca4a6e3a9c7dfc15e69b9de43f801c59.zip | |
Merge pull request #8 from adamnovak/ui-improvements
Clarify support for FASTQ
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). |