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0e0c349c
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Confirming commit 922844e, and past signatures
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A. Karl Kornel <a****l@s****u>
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almost 9 years ago
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922844e6
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No longer using key 14A7B2A56335B8D5
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A. Karl Kornel <a****l@s****u>
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almost 9 years ago
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69fe86f0
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Convert tabs to spaces
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A. Karl Kornel <a****l@s****u>
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about 9 years ago
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54356122
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Better checking of search output
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A. Karl Kornel <a****l@s****u>
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about 9 years ago
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94464c19
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Move file creation to right before writing
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A. Karl Kornel <a****l@s****u>
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about 9 years ago
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e0eb32ab
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Do proper select/read loop for the drive download
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A. Karl Kornel <a****l@s****u>
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about 9 years ago
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dc939d51
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Some more drive search output
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A. Karl Kornel <a****l@s****u>
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about 9 years ago
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89e6985f
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Add some logging
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A. Karl Kornel <a****l@s****u>
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about 9 years ago
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8bab242b
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Forgot to handle the buffer properly
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A. Karl Kornel <a****l@s****u>
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about 9 years ago
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16c3991d
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Forgot the -q for gdrive
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A. Karl Kornel <a****l@s****u>
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about 9 years ago
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812f7e50
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Fix some syntax bugs
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A. Karl Kornel <a****l@s****u>
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about 9 years ago
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3ddf9769
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Switch from drive to gdrive.
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A. Karl Kornel <a****l@s****u>
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about 9 years ago
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db78a1ee
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Ignore email-recipients.txt
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A. Karl Kornel <a****l@s****u>
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about 9 years ago
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60c59f4a
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Bump up the NextSeq second timeout to 3 hours
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A. Karl Kornel <a****l@s****u>
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about 9 years ago
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164a1f18
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Change the hard-coded home directory for spyros.
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A. Karl Kornel <a****l@s****u>
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over 9 years ago
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a49ba894
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Ignore drive conflict in a few more places
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A. Karl Kornel <a****l@s****u>
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almost 10 years ago
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64e9c75d
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Use same handle for stdout and stderr on drive call
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A. Karl Kornel <a****l@s****u>
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almost 10 years ago
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a847872d
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Ignore drive conflicts
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A. Karl Kornel <a****l@s****u>
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almost 10 years ago
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af280ac3
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Return on drive program error
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A. Karl Kornel <a****l@s****u>
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almost 10 years ago
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7ee4ca88
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Catch other non-zero exit codes from the drive program.
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A. Karl Kornel <a****l@s****u>
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almost 10 years ago
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2b5f94a9
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Remove duplicate declaration.
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A. Karl Kornel <a****l@s****u>
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almost 10 years ago
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5d2e6547
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nextseq: Only copy sample sheet if one doesn't exist already
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A. Karl Kornel <a****l@s****u>
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almost 10 years ago
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1bb5c1e0
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Move workflow-complete creation into a separate function.
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A. Karl Kornel <a****l@s****u>
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almost 10 years ago
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312a3c5c
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Change up the subject line for emails
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A. Karl Kornel <a****l@s****u>
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almost 10 years ago
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d42819d3
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Add folder_name function, to return the last component of a path
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A. Karl Kornel <a****l@s****u>
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almost 10 years ago
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b5c5912a
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Fix escaping regex
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A. Karl Kornel <a****l@s****u>
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about 10 years ago
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e9859035
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Escape spaces in samplesheet path
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A. Karl Kornel <a****l@s****u>
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about 10 years ago
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b4583df2
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Add SampleSheet code
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A. Karl Kornel <a****l@s****u>
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about 10 years ago
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66598df0
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Fix lots of places calling nonexistant log_failure
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A. Karl Kornel <a****l@s****u>
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about 10 years ago
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116717ba
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Rename the file containing Karl's notes.
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A. Karl Kornel <a****l@s****u>
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about 10 years ago
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ae4816a0
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Small text fix
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A. Karl Kornel <a****l@s****u>
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about 10 years ago
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75a93906
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Fix permissions
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A. Karl Kornel <a****l@s****u>
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about 10 years ago
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d1d9ad2b
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Started the nextseq code
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A. Karl Kornel <a****l@s****u>
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about 10 years ago
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ccc75e27
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Use the full path for bcl2fastq
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A. Karl Kornel <a****l@s****u>
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about 10 years ago
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72fc9de2
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Catch problems starting bcl2fastq
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A. Karl Kornel <a****l@s****u>
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about 10 years ago
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0af0280f
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Use scalar refs in a few places
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A. Karl Kornel <a****l@s****u>
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about 10 years ago
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e269a9f1
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Don't quote in use lib
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A. Karl Kornel <a****l@s****u>
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about 10 years ago
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0a5558d4
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Return the lock handle from lock_get
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A. Karl Kornel <a****l@s****u>
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about 10 years ago
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c2348e93
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Fix another use of lock_get and log_open
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A. Karl Kornel <a****l@s****u>
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about 10 years ago
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03c44b0e
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Set perms on email-recipients.txt
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A. Karl Kornel <a****l@s****u>
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about 10 years ago
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da132fa3
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Move misc. code into a separate file
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A. Karl Kornel <a****l@s****u>
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about 10 years ago
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19cd82fc
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Add copyright notice
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A. Karl Kornel <a****l@s****u>
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about 10 years ago
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ce6b1332
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Add copyright notice
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A. Karl Kornel <a****l@s****u>
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about 10 years ago
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fd7c40aa
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Forgot to end on true
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A. Karl Kornel <a****l@s****u>
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about 10 years ago
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c430a853
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Move locking and logging code into a different file
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A. Karl Kornel <a****l@s****u>
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about 10 years ago
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28e03ae7
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Move delivery code into a separate file
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A. Karl Kornel <a****l@s****u>
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about 10 years ago
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43f8067b
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Text cleanup
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A. Karl Kornel <a****l@s****u>
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about 10 years ago
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2e03cf4c
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Move the email-related code into a separate file
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A. Karl Kornel <a****l@s****u>
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about 10 years ago
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5d71f27b
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Add delivery-related email code
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A. Karl Kornel <a****l@s****u>
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about 10 years ago
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85e62cb8
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Output octal numbers properly
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A. Karl Kornel <a****l@s****u>
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about 10 years ago
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6b8eec4c
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Use correct array index for mode
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A. Karl Kornel <a****l@s****u>
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about 10 years ago
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7db63f51
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Add missing newline
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A. Karl Kornel <a****l@s****u>
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about 10 years ago
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5f6ebdb1
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Forgot to pass uid/gid when recursing
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A. Karl Kornel <a****l@s****u>
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about 10 years ago
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21e4e084
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Add copying code to the delivery action
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A. Karl Kornel <a****l@s****u>
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about 10 years ago
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84a64694
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Add manual delivery email
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A. Karl Kornel <a****l@s****u>
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about 10 years ago
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f868bc40
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Small fixed
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A. Karl Kornel <a****l@s****u>
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about 10 years ago
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5a8e772f
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Start delivery code
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A. Karl Kornel <a****l@s****u>
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about 10 years ago
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9e356f3b
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Add file explaining how to set up crontab
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A. Karl Kornel <a****l@s****u>
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about 10 years ago
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f62ebce3
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Rename bbox-workflow to bbox-workflow-miseq
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A. Karl Kornel <a****l@s****u>
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about 10 years ago
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ebd14ccf
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Use while loop, not foreach
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A. Karl Kornel <a****l@s****u>
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about 10 years ago
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691f5bbc
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Add more logging
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A. Karl Kornel <a****l@s****u>
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about 10 years ago
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8eb6d534
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Move log messages around
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A. Karl Kornel <a****l@s****u>
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about 10 years ago
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289abf2b
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Add code to scan
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A. Karl Kornel <a****l@s****u>
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about 10 years ago
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bc83ad7b
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Small text fixes
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A. Karl Kornel <a****l@s****u>
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about 10 years ago
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be474b77
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Remove the Help Goes Here marker
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A. Karl Kornel <a****l@s****u>
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about 10 years ago
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2f6d851a
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Stupid @ symbol
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A. Karl Kornel <a****l@s****u>
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about 10 years ago
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a821e801
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Added help text
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A. Karl Kornel <a****l@s****u>
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about 10 years ago
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e8652e0a
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Remove unused variable from email_analysis
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A. Karl Kornel <a****l@s****u>
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about 10 years ago
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89b2972c
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speling
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A. Karl Kornel <a****l@s****u>
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about 10 years ago
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eaab1a83
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Misc. cleanup
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A. Karl Kornel <a****l@s****u>
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about 10 years ago
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84b2922c
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Work out the laneBarcode.html path
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A. Karl Kornel <a****l@s****u>
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about 10 years ago
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62e34ffb
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Use correct runfolder variable
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A. Karl Kornel <a****l@s****u>
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about 10 years ago
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7698e9cc
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Create workflow-complete.txt file
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A. Karl Kornel <a****l@s****u>
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about 10 years ago
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0a058e95
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Add code to send the analysis email.
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Karl Kornel <a****l@s****u>
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about 10 years ago
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e8d90ca0
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Karl's workflow notes
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Karl Kornel <a****l@s****u>
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about 10 years ago
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53843db5
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More email cleanup
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Karl Kornel <a****l@s****u>
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about 10 years ago
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0ee1f288
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A little more cleanup
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Karl Kornel <a****l@s****u>
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about 10 years ago
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fd3be5f5
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Use autoflush on the log file
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Karl Kornel <a****l@s****u>
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about 10 years ago
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dfa04fb2
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Use smtp-unencrypted instead of smtp, to avoid needing SSL/STARTTLS
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Karl Kornel <a****l@s****u>
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about 10 years ago
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988d507c
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Trying using SMTP instead of sendmail
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Karl Kornel <a****l@s****u>
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about 10 years ago
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8fed11e9
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Try a regexp that doesn't match whitespace
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Karl Kornel <a****l@s****u>
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about 10 years ago
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a9f2ef85
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Fix how we set the To header
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Karl Kornel <a****l@s****u>
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about 10 years ago
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82e828a1
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Try a different match to clean up email address from the config file
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Karl Kornel <a****l@s****u>
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about 10 years ago
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ff77026d
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Clean up our failure email
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Karl Kornel <a****l@s****u>
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about 10 years ago
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b980ae56
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Log sending email, and fix mailer name
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Karl Kornel <a****l@s****u>
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about 10 years ago
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81a4c043
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Stupid comma
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Karl Kornel <a****l@s****u>
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about 10 years ago
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c741f995
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Send a few failure emails
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Karl Kornel <a****l@s****u>
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about 10 years ago
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fb261ad7
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Start our email-sending code
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Karl Kornel <a****l@s****u>
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about 10 years ago
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04ba9d22
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Stupid @ symbol
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Karl Kornel <a****l@s****u>
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about 10 years ago
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9b62e8dc
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Create the email settings file
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Karl Kornel <a****l@s****u>
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about 10 years ago
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8583e383
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Reduce forked process read down to 10 bytes at a time.
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Karl Kornel <a****l@s****u>
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about 10 years ago
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13cf4a39
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Text fix
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Karl Kornel <a****l@s****u>
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about 10 years ago
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4ab0f9e6
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Add check for existing Project_ directories
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Karl Kornel <a****l@s****u>
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about 10 years ago
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850f4fa1
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Revert "Use INFO log level for the analysis command"
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Karl Kornel <a****l@s****u>
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about 10 years ago
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12f3954b
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Only release lock if we have a valid handle
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Karl Kornel <a****l@s****u>
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about 10 years ago
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a23a94f1
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Use INFO log level for the analysis command
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Karl Kornel <a****l@s****u>
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about 10 years ago
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e0d31e31
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Finish fixing up our use of open3
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Karl Kornel <a****l@s****u>
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about 10 years ago
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6b0edfec
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Stop adding extra newlines to STDOUT
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Karl Kornel <a****l@s****u>
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about 10 years ago
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d58f1676
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Stop closing a non-file handle
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Karl Kornel <a****l@s****u>
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about 10 years ago
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59dde1cd
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Use a temporary buffer for analysis output
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Karl Kornel <a****l@s****u>
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about 10 years ago
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