###Plan

:: RunIssue -> (SamleList, RunName)

• Grab the sample list
• Also fetch the RunName
• Validate the sample names: Should not have /,etc. (filepath restrictions). If fail, ERROR with suggested new sample list.
• If the sample list names do not match the file names, ERROR.

:: RunIssue -> SampleList -> (Map SampleName IssueId)

• Within the context of some run issue
• Search the Samples project for issues with the subject name equal to the sample name (from the sample list). (NOTE: how to do this search?)
• If there's a match:
  • link the sample issue to the run
• If there is no match:
  • Create a new issue for the sample
  • link that sample issue to the run
• return a map of issue id to sample name

:: (Map SampleName IssueId, RunName) -> NGSDataPath -> ()

1. Copy TMPDIR/RunName to RawData, renaming via SampleName->IssueId
2. create a RunName directory in ReadData
   • extract the gz files into this directory
3. create a directory in ReadsBySample for each sample
   • symlink each readpair into its directory

:: RunIssue -> ()

1. Update the run issue to completed
2. Maybe log info there like where the files are and stuff.

(what do with undetermined data)? (run miseqreport at some point)

#Algebra

##Data:

TODO

##Operations:

###Redmine

• create an issue (need to use result)
• search for sample name (need to use results)
• link two issues
• read a sample list
• Construct a SampleIssue

###FileSystem

• SymLink
• Copy
• ReadFile (SampleSheet) (?), no, just read the sample list

###More Stuff

Tech pastes sample list into issue tech pastes sample list into miseq machine tech runs machine; tech transfers data to TMPDIR

We run sync_latest_miseq.pbs: ngs_mapper.miseq_sync (via qsub) the runpath is determined by the directory containing the most recently touched samlpesheet. we run miseqreport.py on the runpath, outputs tothe syncpath syncpath=/media/VD_Research/NGSData/RawData/MiSeq/${runname}

(miseq_sync.py copies a bunch of stuff and we get the samplenames as directories in ReadsBySample)

remove watchers etc, use apikey, run syncsample.py, select correct issue add watchers & author back

extract sample name/id from samplesheet; look up the issue IDs by sample name; (get_issue_id.py) run rename_sample with each samplename and issue id.

1. Copies .gz files to RawData/$runpath/Data/Intensities/BaseCalls
2. extracts .fastq files to ReadData/$runpath, but with run date in the name (before .fastq)
3. creates ReadsBySample/ for each samplename, and links to the fastq files in REadData (name stays the same) (the is the field before the first unerscore)

in redsample/bin sr = SequenceRequest( args.url, args.key ) sr.DRY = args.dry # dry is dry-run sr.sync_requests()

in redsample/bin

rename_sample.py:main

#TODO

• Drop any existing support for non-miseq data
• Ensure correct permissions after syncing
• ensure have permissions before syncing
• It's no longer necessary to rsync, seeing as the data is already local in TMPDIR
• samplesheet parsing is repeated code
• should just fetch the IDs when running syncsample.py instead of using get_issue_id.py
• rename_sample.py contains a bunch of non-MiSeq support why copy sample dirs into ReadsBySample?
• do validation immediately on the sample names

15:02

Sync issue to vdbpm creating issue id's for all samples
Rename fastq.gz
miseq_sync