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hepcat72 / completion_notifier.scpt
Last active Apr 2, 2020
Applescript to post webhooks triggered by newly completed iOS reminders in specific list(s)
View completion_notifier.scpt
--Look for newly completed reminders (since the last check) and if there is a new one, make a webhook post with date, title, and list JSON values
--by Robert W. Leach, based on scripts by Craig Eley, Samantha Hilton, and Nick Morris
--This is not foolproof. If you have more than 1 device you use to "complete" reminders and a reminder is completed while offline, after which, a reminder is completed from a second online device, the completion of the reminders in the offline device (once it comes online) will be missed. However, it's done this way so that the script doesn't take forever looking at all reminders each time.
--Schedule it to run as frequently as you would like using osascript in a cron job and forget about it. Run once manually in order to "allow" this script to run in the security settings by responding to the resulting dialog.
--Cron job every 30 minutes looking for newly completed reminders in list "MyReminders" example (execute `crontab -e` in terminal and enter): */30 * * * * osascript /Us
View splitseq_combine.sh
#!/bin/bash
#Run once for each sample to gather sequences from multiple sequencing runs that belong to that sample. Sample name must be exactly the same as in each sequencing run.
#USAGE: ./splitseq_combine.sh run1 v1 reference_directory "splitseq_all_out_directories" "sample_name A1:B6"
all_args=("$@")
run_id=$1
chemistry=$2 #v1 or v2
@hepcat72
hepcat72 / splitseq_run.sh
Created Jan 8, 2020
Sample SPLiT-Seq command shell scripts for running split-seq at Princeton
View splitseq_run.sh
#!/bin/bash
#USAGE: ./splitseq_run.sh run1 mrna.fq bcumi.fq v1 reference_directory "sample_name A1:B6" "sample2_name B7:C12" ...
all_args=("$@")
run_id=$1
mrna_fq=$2
bcumi_fq=$3
chemistry=$4 #v1 or v2
View tool_test_output.json
{"tests": [{"data": {"status": "failure", "tool_id": "barcode_splitter", "time_seconds": 38.440266132354736, "inputs": {"runinterface|seqfiles_0|nameinterface|readtype": "single", "runinterface|seqfiles_1|nameinterface|readtype": "singleindex", "runinterface|seqfiles_1|nameinterface|readname": "read2", "barcodes_at_end": false, "runinterface|seqfiles_0|input": {"src": "hda", "id": "5729865256bc2525"}, "runinterface|seqfiles_0|nameinterface|readname": "read1", "bcfile": {"src": "hda", "id": "2891970512fa2d5a"}, "runinterface|seqfiles_1|input": {"src": "hda", "id": "54f2a3a23292eb07"}, "runinterface|seqfiles_2|input": {"src": "hda", "id": "8155e4b4bf1581ff"}, "mismatches": "2", "runinterface|run_type": "flexible", "split_all": true, "runinterface|seqfiles_2|nameinterface|readname": "index2", "runinterface|seqfiles_2|nameinterface|readtype": "index"}, "tool_version": "0.18.4.0", "output_problems": [""], "job": {"inputs": {"runinterface|seqfiles_2|input": {"src": "hda", "id": "8155e4b4bf1581ff", "uuid": "0e1a53f5
@hepcat72
hepcat72 / Galaxy-Workflow-ChIP-Seq_Single_End_-_Step_2__Peaks_and_Motifs.ga
Created Oct 24, 2018
This workflow crashes the galaxy workflow editor, so I'l sharing it for debug purposes
View Galaxy-Workflow-ChIP-Seq_Single_End_-_Step_2__Peaks_and_Motifs.ga
{
"uuid": "b658f22b-96c9-46fb-9337-9beba3798044",
"tags": [],
"format-version": "0.1",
"name": "ChIP-Seq Single End - Step 2: Peaks and Motifs",
"steps": {
"0": {
"tool_id": null,
"tool_version": null,
"outputs": [],
View Calculate & Append Result.scpt
--Purpose: Calculate the result of a highlighted equation and append the result.
--How to use it:
-- 1. Highlight an equation in an editable text area.
-- 2. Right click the selection and select Services->Calculate & Append Result
--Author: Robert Leach, Genomics Group, Princeton, rleach@princeton.edu
on run {input, parameters}
tell application "System Events"
--Bring up spotlight
keystroke " " using {command down}
@hepcat72
hepcat72 / Count Nucleotides.scpt
Last active Aug 29, 2018
Automator services to determine sequence positions
View Count Nucleotides.scpt
--What is this: This is an applescript to use in an automator service that allows you to get the nucleotide and alignment length of a sequence, along with stats on the numbers of individual characters.
--Purpose: Determine the length of a selected nucleotide and alignment string in any application.
--Installation: Create an Automator service, paste this code into a "Run AppleScript" action, and save.
--How to use it: 1. Select a nucleotide string (newlines, numbers, spaces, and any other character are allowed). 2. Right-click the selection and select this service.
--Author: Robert Leach, Genomics Group, Princeton, rleach@princeton.edu
--Note, this counts "DNA characters"
on run {input, parameters}
tell application "System Events"
@hepcat72
hepcat72 / create_reminder_from_file.scpt
Last active Nov 5, 2016
Applescript Folder Action to create reminders from files added (for user with IFTTT's Google Calendar and Dropbox channels)
View create_reminder_from_file.scpt
--Download this file and put it in your ~/Library/Scripts/Folder Action Scripts folder, then attach it to a dropbox folder to run when items are added to it. Create those files using IFTTT recipes.
--This script creates a reminder from a file (e.g. when my wife adds a new event to her work calendar (containing the word "work" in the title) IFTTT creates a file inside dropbox which this script parses to create a static reminder(s) for a certain time that day, e.g. feed the cat and change the litter)
--Each line of the input file must be (Comments with # characters allowed):
-- Reminder List name to which to add the reminder
-- Due date (e.g. "August 31, 2016" optionally followed by " at 5:00am")
-- Due time (e.g. 9:00 AM)
-- Title (Name of the reminder)
-- Keyword (if found in the original title, reminder is created)
-- Original title (Title of the google calendar event)
--The file name have multiple events (every 6 lines)
@hepcat72
hepcat72 / New reminder from Launchbar
Last active Sep 23, 2016 — forked from mlgill/New reminder from Launchbar
A script for quickly adding reminders to the Reminders app in Mountain Lion from Launchbar and Alfred. Save this as a .scpt and drop it in ~/Library/Application\ Support/LaunchBar/Actions
View New reminder from Launchbar
--Script for setting Reminders for LaunchBar and Alfred
--For Alfred, Applescript must NOT be set to run in Background otherwise date parsing does not work
--For LaunchBar, place the script in ~/Library/Scripts/LaunchBar
--by Michelle L. Gill, 10/07/2012
--Inspired by https://gist.github.com/3187630
--A related Alfred version 2 workflow can be found here: https://github.com/mlgill/alfred-workflow-create-reminder
--Changes
--02/01/2013 * Fixed an issue with setting the time when the hour is 12 and AM/PM (12-hour clock) is used
-- * Removed the ability to set seconds for the time since Reminders doesn't recognize them