generate variable PLATES without file plates_to_process.txt

cytomining / profiling-handbook

Image-based Profiling Handbook

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Closed cells2numbers closed 4 years ago

cells2numbers commented 6 years ago

We create the variable ${PLATES} in section 3.4 manually / using the text file plates_to_process.txt.

Instead, we could use the code

PLATES=$(ls ~/efs/${PROJECT_NAME}/${BATCH_ID}/images/ | cut -d '_' -f 1)

to create the variable; or we could create a text file containing the PLATE_IDs using

ls ~/efs/${PROJECT_NAME}/${BATCH_ID}/images/ | cut -d '_' -f 1 >>  ~/efs/${PROJECT_NAME}/workspace/scratch/${BATCH_ID}/platenames.txt

shntnu commented 4 years ago

It's not clear why I ended up with two PRs #48 and #47, but I think we are good here