Updating to Reggie 2.16

1. Serial number of sequencer items

It is recommended that serial numbers are added to sequencer hardware items. Go to the Administrate->Hardware page and add SerialNumber annotation to the Sequencer items currently in use. See also ticket #579.

2. Set embedding date on histology work lists

The histology section now uses the EmbedDate to keep track of progress. Existing work lists that have been completed should be updated.

• Go to Biomaterial LIMS->Biomaterial lists and find all lists with External ID=net.sf.basedb.reggie.histology.work-list-complete.
• For each list set the EmbedDate annotation to the date the blocks in the list were embedded. This is the same date as the creation date for the paraffin blocks.
• Change the External ID to net.sf.basedb.reggie.histology.work-list (eg. remove -complete)

See also ticket #560.

3. Secondary analysis

Reggie 2.16 contains several new wizards in the "Secondary analysis" section. Those wizards are not plug-and-play, but require that a lot of other infrastructure has been setup and configured in a compatible manner. In this document I'll try to collect as much information as possible about the required infrastructure, but it may take some time until the information is 100% complete and up to date.

User permissions

All users with the SecondayAnalysis ROLE should be moved to the SecondaryAnalysis GROUP. The role item can then be deleted since it is no longer user.

Project archive

The installation wizard creates the ProjectArchive FILESERVER item which is used to access FASTQ and other data files produced in the secondary analysis. This server is accessed with SSH/SFTP protocol and must be configured with:

• Host: The host name of the file server
• Username/Password: Login information to the file server
• Root path: The path to root directory of the project files (eg. /casa4/project_archive/scanb)
• SSH fingerprint: The MD5 fingerprint for the file server

Note that External files support package (version 1.1 or higher) must be installed for this to work.

Open Grid Scheduler

To run the analysis jobs, an Open Grid Scheduler cluster is required (​http://gridscheduler.sourceforge.net/). Reggie will connect to the cluster via SSH and auto-generate scripts that interact with the cluster and add jobs to the queuing system. Information about how to setup a cluster is beyond the scope of this document and must be sought elsewhere.

Programs that must be installed on the cluster

• Picard: Customized version currently found at: ​http://dev.thep.lu.se/basehacks/wiki/Picard

• Trimmomatic: ​http://www.usadellab.org/cms/?page=trimmomatic

• Bowtie2: ​http://bowtie-bio.sourceforge.net/bowtie2/index.shtml

• Tophat: ​http://ccb.jhu.edu/software/tophat/index.shtml

• Samtools: ​http://samtools.sourceforge.net/

• Custom scripts: Some bash scripts for our custom analysis pipeline found at: ​http://baseplugins.thep.lu.se/browser/other/pipeline/trunk At the moment, use the 'trunk' version. In the future, more formalized release procedure is expected.

Configuration

Before all of this can work, everything must be configured. The reggie distribution include reggie-ogs-hosts.xml which should be placed in the WEB-INF\classes directory (same as base.config). In this xml file, it is possible to configure connection information for the Open Grid cluster. You'll need the address, username and password and the SSH fingerprint to be able to connect to the cluster.

In the configuration file, you'll also set up various paths on the cluster. Some paths must be globally accessible from all nodes on the cluster and some can be internal for each node. You'll also need to configure paths where data (eg. from the HiSeq) can be found and where the analyzed data should be stored.

In the configuration you can also specify parameters for most of the above mentioned programs.