- Run: Run on a specified work directory. This is meant to run manually.
- Scan: Search a directory for work directories that haven't been processed. This is meant to be run by cron job.
- Deliver: Transfer results to the end users.
Go into /home/bufferbox/XXXXX directory.
- This is set by the command line.
IF running in Scan mode: Do an `ls`, sort, and then pick the last result (tail -n 1). That is the latest directory to check. This is our "Work Directory".
Check for a file called "workflow-complete.txt". If this file exists, then skip the directory, because it's been processed. IF running in Run mode, let the user know that he/she should delete this file, and then re-run the command.
Check for "workflow-lock.txt". If it exists, then read the process ID. If the process is running, then exit, because we know that the job is being worked on. If the proces is not running, then log a message, delete the lock file, and continue.
Create the file "workflow-lock.txt", and put in the current process ID. This will serve as a lock.
Create the file "workflow-log.txt", and start writing log entries to this file. IF there is an old workflow-log.txt directory, append a .0 to it.
Wait for the file "RTAComplete.txt" to appear. This can take up to X hours.
* How long can it take for the run to complete, excluding cleanup?
* Timeout should be 2 days for NextSeq, and 5 days for MiSeq.
! Email if we run out of time.
Look for a file "RunCompletionStatus.xml".
! This file doesn't exist in the MiSeq
Within the file, look for the XML tag "CompletionStatus". If the string inside the tag is "CompletedAsPlanned", then continue. If not, then wait.
* Timeout should be 2 hours, on NextSeq only. Does not apply to MiSeq.
* File does not exist in MiSeq.
* What other values can appear in the "CompletionStatus" tag?
! Email if we end up seeing an unknown XML Tag.
Look for a file "RunParameters.xml".
Within the file, look for the XML tag "LibraryID". Capture the string inside the tag.
* This entire section doesn't apply for MiSeq.
Go into /home/bufferbox/gdrive/NS Samplesheets directory
- The gdrive folder should be configurable.
- The list of subfolders to pull should also be configurable.
Run `drive pull -no-prompt -verbose`.
If the exit code is 13, then run `drive pull -no-prompt -verbose -fix-clashes`.
If the fix-clashes exit code is 0, then re-start this section.
For any other exit codes, error.
! Email if we have an error here.
Repeat the above section for the MS Samplesheets directory.
Search all of our directories for a file matching the following qualifications:
* File name begins with the LibraryID, then a space, then "SampleSheet".
* File name ends with .csv.
If multiple files are found, then choose the newest one.
---DO VALIDATION HERE---
Copy the located file into the work directory, using the name "SampleSheet.csv".
Check to see if anything matching ${WORKDIR}/Data/Intensities/BaseCalls/Project_* exists.
If it does, prepend "old_"
Within the work directory, run the following command:
Include instructions on how to continue if things are OK. This will be a new command run.
Assuming that the results are OK, then we need to get the data to the person.
First, get the username of the person, by looking in ${WORKDIR}/Data/Intensities/BaseCalls, and looking for something called Project_XXXX. The XXXX is the username. If we have multiple Project_XXX directories, then we need to do two transfers.
Next, find their home directory. Their home directories are in /b?_?/home*/${USERNAME}.
If no home directory is found using the above, then error out with a message that the person doesn't have a home directory.
As root, create ${HOMEDIR}/${WORKDIR}
As root, copy the contents of Project_XXX to ${HOMEDIR}/${WORKDIR}
As root, do a stat of ${HOMEDIR}, and get the userID/groupID
As root, chown evertything in ${HOMRDIR}/${WORKDIR}, using the userID/groupID that we just got.
- If username is "spyros", then use /b7_1/home/spyros ${HOMEDIR}
Once the transfer is complete, say that things are done and its OK to send the email.
Be sure to provide the absolute path to where the data has been copied.
Include a reminder to mark the data as delivered in the Queue sheet.
Runs to copy for testing:
NextSeq/160726_NS500126_0547_AH3Y7YBGXY, corresponds to N253 SampleSheet.csv
