There is the help page for accessing SeqWare LIMS system.

For postgresql, the query language is slightly different from other sql language.

To clean up SeqWareLIMS event, follow the following steps:

1. To to SeqWareLIMS and find run with either running or errors. Currently, Brian will need to fix the bug in the deleting scripts, also he will take care errors associated with Illumina2srf workflow.

2. Leave Illumina2srf untouched (Brian will take care of it)
3. Doing this from the most recent finished run
4. Drill down to deeper hiearchy and file the access number
5. Log into swmaster and go into ~/svnroot/*/seqware-pipeline/
6. Issue the following command:

perl perl/bin/sw_util_delete_processing_events.pl –username seqware
–password seqware –dbhost swmaster.bioinf.unc.edu –db
seqware_meta_db –accession

7. This will delete the LIMS event as a result, leave output files on the file systems as orphan
8. Further actions are needed and maybe new run will be executed, which will overwrite those output files.
9. In the mean time, if the researchers want the data, we can still get them through the file system.

Query for samples done with pipeline process (little report)

A script (sw_reports_find_files.pl) is written by Brian located at /home/jyli/svnroot/seqware-complete/trunk/seqware-pipeline/perl/bin/site-specific/unc/sw_reports_find_files.pl

1. log into swmaster
2. run the script as ” perl /home/jyli/svnroot/seqware-complete/trunk/seqware-pipeline/perl/bin/site-specific/unc/sw_reports_find_files.pl –username seqware –password seqware –dbhost swmaster.bioinf.unc.edu –db seqware_meta_db –workflow-accession 23324 > temp.txt ”
3. Keep in mind that we need “amdin” log in “seqware seqware”
4. To get –workflow-accession number:
a. Log into seqware_meta_db as “seqware seqware”
b. Issue query “select * from workflow where name = ‘RNASeqAlignmentBWA’;”
seqware_meta_db=> select sw_accession, version, name, update_tstmp from workflow where name = ‘RNASeqAlignmentBWA’;
-[ RECORD 1 ]+—————————
sw_accession | 7535
version | 0.7.2
name | RNASeqAlignmentBWA
update_tstmp | 2010-08-13 16:23:21.069316
-[ RECORD 2 ]+—————————
sw_accession | 7603
version | 0.7.0
name | RNASeqAlignmentBWA
update_tstmp | 2010-08-14 16:42:02.141734
-[ RECORD 3 ]+—————————
sw_accession | 7604
version | 0.7.1
name | RNASeqAlignmentBWA
update_tstmp | 2010-08-14 16:43:29.010826
-[ RECORD 4 ]+—————————
sw_accession | 21544
version | 0.7.3
name | RNASeqAlignmentBWA
update_tstmp | 2010-08-28 06:28:02.482627
-[ RECORD 5 ]+—————————
sw_accession | 23324
version | 0.7.4
name | RNASeqAlignmentBWA
update_tstmp | 2010-08-30 00:45:13.497882

c. Look for the latest processing date.

To associate the processing event with the files stored on the system:

Email from Brian:
*******************************************************************************************
You’re querying the file table using sw_accession from the processing table. This is wrong. Use “d tablename” to see table keys and how they relate via foreign keys. Also look at the sample queries in the wiki. They will show you that you need to do a join on processing processing_files files to get the file path you need.
*******************************************************************************************
First: Understand the DB schema/layout, where? how?
Second: joined the tables processing processing_files files
Third: get the file path