Comments (4)
from gaptools.
Dear Mike,
Thank you for your reply. While I got gaptools to run just fine on the provided 1000 Genomes example file, it is not running on this made-up example data (link below) and I have no idea why. All it produces in the 'metrics' folder is:
$ more metrics-CHECK_METADATA_FILES.json
[
{
"dag_id": "GapTools",
"run_id": "2023-02-08-16-23-10",
"dag_task": "CHECK_METADATA_FILES",
"metric_name": "dag_run_start_time",
"metric_value": "2023-02-08 16:23:23",
"metric_object": ""
}
]
I tried it with different variations of the json, first with just the phenotype files, and then with the phenotype, consent, and sample subject map files, and now with more. All of those variations generate only the metrics-CHECK_METADATA_FILES.json
file as seen above.
Thanks,
Dan
Link to made-up example data:
from gaptools.
I found my mistake:
I didn't notice this line in the instructions:
"The file has to be named metadata.json"
so it was failing because I had named it 'Example1.json' instead.
Suggestion:
I made this mistake in part because I assumed this option in the example command:
-m ./input_files/1000_Genomes_Study/metadata.json
would allow me to change the name of the json meta data file.
Since the -m
option is only meant to allow the user to change the path to the metadata.json
file and not to allow them to change the name itself, it would be better if you changed the option to only ask the user the path by shortening it to:
-m ./input_files/1000_Genomes_Study/
from gaptools.
from gaptools.
Related Issues (5)
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from gaptools.