Upload CellProfiler pipelines to S3 bucket (or this repo)

[shntnu]

Either at workspace/pipelines in S3 or 'pipelines` in this repo.

I believe they are all available at s3://imaging-platform/projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines but someone will need to create a README to document the mapping from pipelines to datasets (unless the folder structure is self-explanatory)

aws s3 ls --recursive s3://imaging-platform/projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines
2020-01-30 11:40:17          0 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/
2021-04-27 17:09:01          0 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/20210407_24W_CP251/
2021-04-28 14:35:23      17386 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/20210407_24W_CP251/1_CP_Illum.cppipe
2021-05-12 13:41:32      16154 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/20210407_24W_CP251/2_CP_Apply_Illum.cppipe
2021-05-12 17:00:26      23978 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/20210407_24W_CP251/3_CP_SegmentationCheck.cppipe
2021-04-27 17:09:13      17394 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/20210407_24W_CP251/5_BC_Illum.cppipe
2021-04-28 14:08:56      61518 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/20210407_24W_CP251/6_BC_Apply_Illum.cppipe
2021-05-13 16:51:47     132646 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/20210407_24W_CP251/7A_BC_PreprocessTroubleshoot.cppipe
2021-05-17 10:21:05      85679 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/20210407_24W_CP251/7_BC_Preprocess.cppipe
2021-05-24 11:56:48      62416 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/20210407_24W_CP251/9_Analysis.cppipe
2021-06-07 10:41:14          0 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2021_05_21_QualityControlPathwayArrayedScreen/
2021-06-11 15:19:22       5453 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2021_05_21_QualityControlPathwayArrayedScreen/ProjectionPipeline.cppipe
2021-06-22 16:11:43      22391 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2021_05_21_QualityControlPathwayArrayedScreen/analysis.cppipe
2021-06-14 14:48:53      13748 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2021_05_21_QualityControlPathwayArrayedScreen/illum_without_batchfile.cppipe
2021-06-22 14:40:07      17996 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2021_05_21_QualityControlPathwayArrayedScreen/segment_for_stitching.cppipe
2022-01-12 16:27:02          0 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch1/
2022-01-24 17:41:54       5535 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch1/ProjectionPipeline.cppipe
2022-01-12 16:27:21      22391 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch1/analysis.cppipe
2022-03-14 10:25:23      43270 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch1/analysis_batch1.cppipe
2022-03-14 10:25:23     110256 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch1/analysis_batch1.cpproj
2022-02-24 09:55:09    5905248 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch1/assaydev.cpproj
2022-03-01 12:29:36      22085 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch1/assaydev_BC.cppipe
2022-03-09 14:17:28      26585 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch1/assaydev_BC_2.cppipe
2022-03-10 10:22:31      94360 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch1/assaydev_BC_2.cpproj
2022-03-09 14:17:27      35409 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch1/assaydev_BC_3.cppipe
2022-03-09 14:17:28    5889432 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch1/assaydev_BC_3.cpproj
2022-03-10 10:42:02      41237 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch1/assaydev_BC_4.cppipe
2022-03-10 10:42:02    5895144 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch1/assaydev_BC_4.cpproj
2022-02-24 09:55:09    5895704 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch1/assaydev_dropgrow.cpproj
2022-02-24 09:55:09    5895800 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch1/assaydev_morethan1exp.cpproj
2022-03-07 14:58:49      26729 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch1/assaydev_v10.cppipe
2022-03-07 14:58:49    5880824 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch1/assaydev_v10.cpproj
2022-03-07 16:05:19      26946 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch1/assaydev_v11.cppipe
2022-03-07 16:05:19    5872847 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch1/assaydev_v11.cpproj
2022-03-07 16:57:50      26947 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch1/assaydev_v12.cppipe
2022-03-07 16:57:50    5867285 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch1/assaydev_v12.cpproj
2022-02-24 10:15:17      41518 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch1/assaydev_v3.cppipe
2022-02-24 10:15:17    5895312 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch1/assaydev_v3.cpproj
2022-02-24 19:29:19      53248 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch1/assaydev_v4.cppipe
2022-02-24 19:29:19    5906824 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch1/assaydev_v4.cpproj
2022-02-24 17:32:08    5906736 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch1/assaydev_v4_twoIDsecondaries.cpproj
2022-02-28 11:16:52      53414 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch1/assaydev_v5.cppipe
2022-02-28 11:16:52    5906992 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch1/assaydev_v5.cpproj
2022-03-01 11:10:22      31364 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch1/assaydev_v5_clean.cppipe
2022-03-01 11:10:22    5885384 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch1/assaydev_v5_clean.cpproj
2022-03-01 14:07:35      26437 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch1/assaydev_v6.cppipe
2022-03-01 14:07:35      20885 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch1/assaydev_v6_1IDSecondary.cppipe
2022-03-01 14:07:35    5880536 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch1/assaydev_v6_1IDSecondary.cpproj
2022-03-07 10:14:12      26604 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch1/assaydev_v7.cppipe
2022-03-07 10:57:30    5880569 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch1/assaydev_v7.cpproj
2022-03-07 10:57:30      26636 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch1/assaydev_v8.cppipe
2022-03-07 10:57:30    5880569 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch1/assaydev_v8.cpproj
2022-03-07 14:03:15      26731 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch1/assaydev_v9.cppipe
2022-03-07 14:02:05    5906894 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch1/assaydev_v9.cpproj
2022-03-09 14:17:28      13385 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch1/illum_without_batchfile.cppipe
2022-01-12 16:27:21      17996 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch1/segment_for_stitching.cppipe
2022-01-24 16:06:14          0 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch2/
2022-01-24 17:41:35       4311 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch2/ProjectionPipeline.cppipe
2022-03-14 15:56:36      42984 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch2/analysis_batch2.cppipe
2022-03-14 15:56:36     109976 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch2/analysis_batch2.cpproj
2022-03-09 14:20:18      35224 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch2/assaydev_BC_3.cppipe
2022-03-10 10:22:45    5889256 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch2/assaydev_BC_3.cpproj
2022-03-10 12:06:04      41050 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch2/assaydev_BC_4.cppipe
2022-03-10 12:06:04    4846923 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch2/assaydev_BC_4.cpproj
2022-03-14 09:41:51    4842618 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch2/assaydev_BC_5.cpproj
2022-03-09 14:20:18      10177 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch2/illum_without_batchfile.cppipe
2020-01-30 13:24:47          0 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/cellpainting_20x_TiE_bin1/
2020-06-29 12:53:18          0 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/cellpainting_20x_TiE_bin1/20200615_96W_CP173/
2020-06-29 12:53:22      34183 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/cellpainting_20x_TiE_bin1/20200615_96W_CP173/analysis.cppipe
2020-06-29 12:53:25      23279 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/cellpainting_20x_TiE_bin1/20200615_96W_CP173/illum.cppipe
2020-06-29 12:53:28       7089 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/cellpainting_20x_TiE_bin1/20200615_96W_CP173/qc.cppipe
2020-07-29 12:10:02          0 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/cellpainting_20x_TiE_bin1/20200727_96W_CP185/
2020-07-31 10:12:01      33045 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/cellpainting_20x_TiE_bin1/20200727_96W_CP185/analysis.cppipe
2020-07-29 12:13:05      23224 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/cellpainting_20x_TiE_bin1/20200727_96W_CP185/illum.cppipe
2020-07-29 17:16:39       7034 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/cellpainting_20x_TiE_bin1/20200727_96W_CP185/qc.cppipe
2020-08-07 10:50:13          0 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/cellpainting_20x_TiE_bin1/20200729_96W_CP183/
2020-08-07 16:45:48      33150 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/cellpainting_20x_TiE_bin1/20200729_96W_CP183/analysis.cppipe
2020-08-07 10:50:55      23224 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/cellpainting_20x_TiE_bin1/20200729_96W_CP183/illum.cppipe
2020-03-09 10:00:19          0 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/cellpainting_20x_TiE_bin1/Pilot_1/
2020-03-09 10:00:25      24053 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/cellpainting_20x_TiE_bin1/Pilot_1/analysis.cppipe
2020-06-21 00:11:10      14216 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/cellpainting_20x_TiE_bin1/Pilot_1/illum.cppipe
2020-03-09 10:00:32      18285 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/cellpainting_20x_TiE_bin1/Pilot_1/qc.cppipe

aws s3 ls --recursive s3://imaging-platform/projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines|grep analysis

2021-06-22 16:11:43      22391 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2021_05_21_QualityControlPathwayArrayedScreen/analysis.cppipe
2022-01-12 16:27:21      22391 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch1/analysis.cppipe
2022-03-14 10:25:23      43270 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch1/analysis_batch1.cppipe
2022-03-14 10:25:23     110256 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch1/analysis_batch1.cpproj
2022-03-14 15:56:36      42984 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch2/analysis_batch2.cppipe
2022-03-14 15:56:36     109976 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/2022_01_12_Batch2/analysis_batch2.cpproj
2020-06-29 12:53:22      34183 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/cellpainting_20x_TiE_bin1/20200615_96W_CP173/analysis.cppipe
2020-07-31 10:12:01      33045 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/cellpainting_20x_TiE_bin1/20200727_96W_CP185/analysis.cppipe
2020-08-07 16:45:48      33150 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/cellpainting_20x_TiE_bin1/20200729_96W_CP183/analysis.cppipe
2020-03-09 10:00:25      24053 projects/2017_10_19_Profiling_rare_ORFs/workspace/pipelines/cellpainting_20x_TiE_bin1/Pilot_1/analysis.cppipe