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correct role handling and S3FS bypass #130

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Merged
ErinWeisbart merged 22 commits into from
Jan 21, 2023
Merged

correct role handling and S3FS bypass #130

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0417e7d
correct role handling
ErinWeisbart Jun 16, 2022
526411d
update generate_task_definition
ErinWeisbart Aug 2, 2022
38df4c9
import configparser in run.py
ErinWeisbart Aug 2, 2022
80a8c5b
enable separate source and destination buckets
ErinWeisbart Aug 2, 2022
5498710
oops shouldnt have deleted those
ErinWeisbart Aug 2, 2022
e657f11
fix multibucket handling
ErinWeisbart Aug 3, 2022
cefd9e0
move source destination buckets to config
ErinWeisbart Aug 3, 2022
865d515
switched in and not in
ErinWeisbart Aug 3, 2022
f7919b8
fix s3fs bybass
ErinWeisbart Aug 4, 2022
b9f8916
remove multibucket from job file
ErinWeisbart Aug 4, 2022
3d8cc82
remove changes to run_batch_general
ErinWeisbart Aug 4, 2022
fad0284
csv handling to keep structure
ErinWeisbart Aug 4, 2022
c840b44
pipelines path and run command fixes
ErinWeisbart Aug 5, 2022
8f57047
output, destination, same difference
ErinWeisbart Aug 5, 2022
4ff6463
add upload flags
ErinWeisbart Aug 5, 2022
22abe35
but what if it doesn't exist
ErinWeisbart Aug 5, 2022
e774d41
more things in task definition
ErinWeisbart Aug 5, 2022
7d8f4c8
stash changes
ErinWeisbart Sep 15, 2022
e907c6a
update to AWS CLI2
ErinWeisbart Sep 21, 2022
c66de9e
the right way to check for variable, finally
ErinWeisbart Oct 5, 2022
8cb1390
Merge branch 'master' into role_fix
ErinWeisbart Jan 6, 2023
2b95a36
Update exampleJob.json
ErinWeisbart Jan 21, 2023
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remove multibucket from job file
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@ErinWeisbart
ErinWeisbart committed Aug 4, 2022
commit b9f89162c94a63f214ee7d34b6a9a5c5fbd1e67f
5 changes: 2 additions & 3 deletions files/exampleJob.json
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@@ -1,10 +1,9 @@
{
"_comment1": "Paths in this file are relative to the root of your S3 bucket",
"_comment1": "Paths in this file are relative to the root of S3 buckets",
"_comment2": "pipeline, data_file, and input are relative to INPUT_BUCKET; output to OUTPUT_BUCKET",
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"pipeline": "projects/analysis.cppipe",
"data_file": "projects/list_of_images.csv",
"input_bucket": "SOURCE_BUCKET",
"input": "projects/input/",
"output_bucket": "DESTINATION_BUCKET",
"output": "projects/output/",
"output_structure": "Metadata_Plate-Metadata_Well-Metadata_Site",
"_comment2": "The following groups are tasks, and each will be run in parallel",
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