From 27d50093eecdac0c087ff766ae4da33b264c5c2a Mon Sep 17 00:00:00 2001 From: emiglietta Date: Tue, 12 Nov 2024 16:53:06 -0500 Subject: [PATCH 1/3] Update step_2_submit_jobs.md suggest edits to documentation: add default and clarification for --sites --- documentation/DCP-documentation/step_2_submit_jobs.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/documentation/DCP-documentation/step_2_submit_jobs.md b/documentation/DCP-documentation/step_2_submit_jobs.md index f26dfc8..5ac04a2 100644 --- a/documentation/DCP-documentation/step_2_submit_jobs.md +++ b/documentation/DCP-documentation/step_2_submit_jobs.md @@ -99,7 +99,7 @@ Separate values with commas and no spaces and surround with quotation marks (e.g * `--no-well-digit-pad`: Formats wells without well digit padding. Formats wells passed with `--plate format` or `--rows` and `--columns` but not `--wells`. (e.g. `A1` NOT `A01`) -* `--sites `: a custom list of sites (fields of view) to be analyzed. +* `--sites `: a custom list of sites (fields of view) to be analyzed. Default is 9 sites (1 to 9). Not used by `illum`, `qc`, or `assaydev` steps. Separate values with commas and no spaces and surround with quotation marks (e.g. `"1,2,3,4,5,6"`) ### Overwrite structural defaults From 1c1e1814cbd112721b7d1f066ea9ca2867cd56f0 Mon Sep 17 00:00:00 2001 From: Erin Weisbart <54687786+ErinWeisbart@users.noreply.github.com> Date: Wed, 13 Nov 2024 14:51:28 -0800 Subject: [PATCH 2/3] formatting --- documentation/DCP-documentation/step_2_submit_jobs.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/documentation/DCP-documentation/step_2_submit_jobs.md b/documentation/DCP-documentation/step_2_submit_jobs.md index 5ac04a2..0433078 100644 --- a/documentation/DCP-documentation/step_2_submit_jobs.md +++ b/documentation/DCP-documentation/step_2_submit_jobs.md @@ -99,7 +99,9 @@ Separate values with commas and no spaces and surround with quotation marks (e.g * `--no-well-digit-pad`: Formats wells without well digit padding. Formats wells passed with `--plate format` or `--rows` and `--columns` but not `--wells`. (e.g. `A1` NOT `A01`) -* `--sites `: a custom list of sites (fields of view) to be analyzed. Default is 9 sites (1 to 9). Not used by `illum`, `qc`, or `assaydev` steps. +* `--sites `: a custom list of sites (fields of view) to be analyzed. +Default is 9 sites (1 to 9). +Not used by `illum`, `qc`, or `assaydev` steps. Separate values with commas and no spaces and surround with quotation marks (e.g. `"1,2,3,4,5,6"`) ### Overwrite structural defaults From e135bc3e2983c7cf43af66e0e241215bee09e666 Mon Sep 17 00:00:00 2001 From: emiglietta Date: Tue, 20 Jan 2026 17:49:07 -0800 Subject: [PATCH 3/3] Fix missing arguments in call to killdeadAlarms in Monitor --- run.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/run.py b/run.py index 1beabeb..f1722e9 100644 --- a/run.py +++ b/run.py @@ -798,7 +798,7 @@ def monitor(cheapest=False): cloud.delete_alarms(AlarmNames=del_alarms) time.sleep(10) instancelist = instancelist[100:] - killdeadAlarms(fleetId,monitorapp) + killdeadAlarms(fleetId,monitorapp,ec2,cloud) except: pass