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:2
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Epic Link:
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Sprint:Spring 5, Spring 6, Spring 7, Spring 8, Spring 9
Description
mark-2022-timeseries experiment has been submitted to SRA and rerun with nextflow. A sanity check will need to be performed on the original data and the rerun SRA data to ensure the submission to NCBI was correct.
The next step is adding the SRA data to IGB Quickload. To do this a sample sheet is required.
Attachments
Activity
PR is merged. Ready for testing.
I did not try to run the new code as Molly Davis has already been able to run it, as noted above.
Moving to "ready for pull request."
Adding SRA submission to makeAnnotsXml.py
# Johnson lab mark-2022-timeseries SRA submission SRP441343
repo = "https://bitbucket.org/hotpollen/splicing-analysis"
branch = "main"
filename = "SRP441343_sample_sheet.xlsx"
path = "ExternalData/"+filename
getSampleSheetFromRepo(filename,repo,path,branch)
spreadsheet = pd.read_excel(filename)
sample_sheet = SampleSheet(spreadsheet)
sample_sheet.addGenome(SL5)
sample_sheet.addGenome(SL4)
to_return.append(sample_sheet)
export PYTHONPATH=/Users/mollydavis333/Desktop/igbquickload
python -m pip install requests
pip install openpyxl
conda create -c conda-forge -n name_of_my_env python pandas
source activate name_of_my_env
./makeAnnotsXml.py
Please check with makeAnnotsXml.py for the next step.
Sample sheet is good. Moving to DONE.