Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:1
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Epic Link:
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Sprint:Spring 2 2021 Apr 5 - Apr 16, Spring 3 2021 Apr 19 - Apr 30, Spring 4 2021 May 3 - May 14, Spring 5 2021 May 17 - May 28, Spring 6 2021 May 31 - June 11, Summer 1 2021 Jun 14 - Jun 25, Summer 2 2021 Jun 28 - Jul 9
Description
To investigate scRNA tools website (https://www.scrna-tools.org/) and how it is implemented so that we can create a similar tool for genome browsers and visualization tools. Related issue IGBF-2699
Attachments
Activity
The virtual environment is python - correct? If yes, which version? (3 or 2?)
In my system, the python version is 3.7.0 the virtual environment version is 16.5.0
To set up scRNA-tools https://github.com/scRNA-tools/scRNA-tools/wiki/Setting-up
Discussed during scrum on July 1. We have extracted sufficient value from examining the code. Moving to Done.
scRNA-tools
Delete the renv folder and create a new virtual environment using the command: virtualenv renv
Activate the virtual environment by going renv/Scripts and running the activate command
The application development server can be run in Flask by running test_server.py in 'docs' folder (Requires installation of a few packages)
URL: http://127.0.0.1:8765/index.html
Database schema: the database is a set of '.tsv' files in the database folder
categories-idx.tsv -> Tool and Category
categores.tsv -> Categories, Phase, Description (of the category)
doi-idx.tsv -> Tool and their DOI links
ignored.tsv -> Tool, Type, Name (purpose unclear)
references.tsv -> DOI, arXiv(T/F), Preprint(T/F), Date(of publication), Title(of the publication)
tools.tsv -> Tool, Platform(in which the tool is designed in), Code(repository link), Description, License, Added(date), Updated(date)
These files are read and loaded in the app using app/load.R. 'scrnatools' (home directory) is a command-line application for interacting with the database. The CRUD operations and other database functions that are in the 'app' folder are mapped in 'scrnatools'.