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# API Methods and Commands | ||
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# Commands | ||
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Pull API: | ||
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$ python manage.py api pull --help | ||
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optional arguments: | ||
-h, --help show this help message and exit | ||
-r, --recipes Pull recipes of --pid | ||
--url URL Site url. | ||
--key KEY API key. Required to access private projects. | ||
--rid RID Recipe uid to dump. | ||
--pid PID Project uid to dump. | ||
--dir DIR Directory to store in. | ||
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# Dump project from remote url (--url). | ||
$ python manage.py api pull --pid tutorial --dir tmp/remote/projects/ --url URL | ||
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# Dump recipes from remote url ( --url) | ||
$ python manage.py api pull --pid tutorial --dir tmp/remote/recipes/ --url URL --recipes | ||
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Push API: | ||
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$ python manage.py api push --help | ||
optional arguments: | ||
-h, --help show this help message and exit | ||
-u, --url_from_json Extract url from conf file instead of --url. | ||
--url URL Site url. | ||
--key KEY API key. Required to access private projects. | ||
--rid RID Recipe uid to load. | ||
--pid PID Project uid to load. | ||
--dir DIR Directory with json files to load in bulk. | ||
--json JSON Project or recipe JSON file to load. | ||
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# Load project tutorial from json file. | ||
$ python manage.py api push --json ../biostar-recipes/projects/tutorial.hjson | ||
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# Load recipe jsons in --dir to project --pid. Upload to remote host with -u flag. | ||
$ python manage.py api push --pid tutorial --dir ../biostar-recipes/recipes/ -u --key API_KEY | ||
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# Methods | ||
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## Listing | ||
GET /api/list/ | ||
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List projects and recipes in a tab delimited fashion with columns: **Project ID** , **Project Name**, **Recipe ID**, **Recipe Name**, **Privacy** | ||
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#### Example | ||
[/api/list/](https://www.bioinformatics.recipes/api/list/) | ||
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tutorial Recipe Tutorials environment Environment Check Public | ||
tutorial Recipe Tutorials interface Interface Elements Public | ||
tutorial Recipe Tutorials makefile Makefile Example Public | ||
tutorial Recipe Tutorials rscript R Script Public | ||
cookbook Bioinformatics Cookbook quality-check Improve the quality of sequencing reads Public | ||
cookbook Bioinformatics Cookbook fastqc Visualize FASTQ data quality Public | ||
cookbook Bioinformatics Cookbook pseudo-alignment RNA-Seq Transcript Abundance Estimation Public | ||
cookbook Bioinformatics Cookbook augustus Gene Prediction Public | ||
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## Project Information | ||
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GET /api/project/{id}/ | ||
PUT /api/project/{id}/ | ||
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#### Parameters | ||
* _id_: unique project ID | ||
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#### Example | ||
[/api/project/tutorials/](https://www.bioinformatics.recipes/api/project/tutorials/) | ||
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{ | ||
settings: | ||
{ | ||
uid: tutorial | ||
name: Recipe Tutorials | ||
image: tutorial.png | ||
privacy: Public | ||
help: | ||
''' | ||
This project contains simple analyses that demonstrate the process | ||
of creating a **recipe**. | ||
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Follow the **instructions,** investigate the **data** and **recipe code** | ||
to gain a deeper understanding of how recipes work. | ||
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Read the step by step instructions in the [How to write recipes](https://github.com/biostars/biostar-recipes/blob/master/docs/how-to-write-recipes.md). | ||
''' | ||
id: 2 | ||
project_uid: tutorial | ||
url: http://localhost:8000 | ||
} | ||
recipes: | ||
[ | ||
empty | ||
makefile | ||
starter | ||
interface | ||
hello-world | ||
environment | ||
rscript | ||
] | ||
} | ||
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## Project Image | ||
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GET /api/project/image/{id}/ | ||
PUT /api/project/image/{id}/ | ||
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#### Parameters | ||
* _id_: unique project ID | ||
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#### Example | ||
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[/api/project/image/tutorials/](https://www.bioinformatics.recipes/api/project/image/tutorials/) | ||
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Image in response: | ||
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![20% center](tutorial.png) | ||
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## Recipe Json | ||
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GET /api/recipe/json/{id}/ | ||
PUT /api/recipe/json/{id}/ | ||
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Recipe JSON used to generate interface | ||
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#### Parameters | ||
* _id_: Unique recipe ID | ||
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#### Fields in response | ||
Fields associated with the recipe JSON | ||
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#### Example | ||
[/api/recipe/json/starter/](https://www.bioinformatics.recipes/api/recipe/json/starter/) | ||
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{ | ||
readlen: | ||
{ | ||
label: Read Length | ||
display: INTEGER | ||
value: 250 | ||
range: | ||
[ | ||
70 | ||
100000 | ||
] | ||
} | ||
instrument: | ||
{ | ||
label: Select Instrument | ||
display: DROPDOWN | ||
choices: | ||
[ | ||
[ | ||
hiseq | ||
Illumina Hiseq | ||
] | ||
[ | ||
pacbio | ||
Pacific BioSciences Sequel | ||
] | ||
[ | ||
minion | ||
Oxford Nanopor Minion | ||
] | ||
] | ||
value: pacbio | ||
} | ||
reference: | ||
{ | ||
label: Reference Genome | ||
display: DROPDOWN | ||
type: FASTA | ||
source: PROJECT | ||
value: Genome.fa | ||
} | ||
settings: | ||
{ | ||
name: Starter Recipe | ||
image: starter.png | ||
help: | ||
''' | ||
This recipe can be a starting point for other recipes. | ||
# Help | ||
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Use this recipe to create new recipes. | ||
''' | ||
id: 12 | ||
uid: starter | ||
project_uid: tutorial | ||
url: http://localhost:8000 | ||
} | ||
} | ||
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## Recipe Template | ||
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GET /api/recipe/template/{id}/ | ||
PUT /api/recipe/template/{id}/ | ||
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Recipe template executed during analysis. | ||
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#### Parameters | ||
* _id_: Unique recipe ID | ||
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#### Example | ||
[/api/recipe/template/starter/](https://www.bioinformatics.recipes/api/recipe/template/starter/) | ||
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# | ||
# A starter recipe with examples. | ||
# | ||
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# | ||
# You can fill in shell variables | ||
# | ||
READLEN=250 | ||
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echo "Read length: $READLEN" | ||
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# | ||
# Substitute into content | ||
# | ||
echo "Referene genome: Genome.fa" | ||
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# | ||
# But you may also use Django Template constructs. | ||
# | ||
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echo "Yes, it is Pacific Biosciences!" | ||
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# | ||
# Generate a table of content with all files in the job directory. | ||
# | ||
find . -name '*' > files.txt | ||
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# | ||
# Print the contents to the screen | ||
# | ||
echo "****** File List: files.txt ****" | ||
cat files.txt | ||
# Make a nested directory | ||
mkdir -p foo/bar | ||
find . -name '*' > foo/bar/all.txt | ||
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## Recipe Image | ||
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GET /api/recipe/image/{id}/ | ||
PUT /api/recipe/image/{id}/ | ||
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#### Parameters | ||
* _id_: Unique recipe ID | ||
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#### Example | ||
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[api/recipe/image/starter/](https://www.bioinformatics.recipes/api/recipe/template/starter/) | ||
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Image in response: | ||
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![20%](starter.jpeg) |
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@@ -65,6 +65,7 @@ For more information see the documentation below: | |
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install | ||
recipes | ||
api | ||
deploy | ||
customize | ||
about | ||
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