Changes between Version 1 and Version 2 of net.sf.basedb.reggie/notes216


Ignore:
Timestamp:
Aug 18, 2014, 11:09:39 AM (10 years ago)
Author:
Nicklas Nordborg
Comment:

More update notes for Reggie 2.16

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  • net.sf.basedb.reggie/notes216

    v1 v2  
    11= Updating to Reggie 2.16 =
     2
     3== 1. Serial number of sequencer items ==
     4
     5It is recommended that serial numbers are added to sequencer hardware items. Go to the '''Administrate->Hardware''' page and
     6add '''!SerialNumber''' annotation to the '''Sequencer''' items currently in use. See also ticket #579.
     7
     8
     9== 2. Set embedding date on histology work lists ==
     10
     11The histology section now uses the '''!EmbedDate''' to keep track of progress. Existing work lists that have been
     12completed should be updated.
     13
     14 * Go to '''Biomaterial LIMS->Biomaterial lists''' and find all lists with '''External ID=net.sf.basedb.reggie.histology.work-list-complete'''.
     15 * 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.
     16 * Change the '''External ID''' to '''net.sf.basedb.reggie.histology.work-list''' (eg. remove `-complete`)
     17
     18See also ticket #560.
     19
     20
     21== 3. Secondary analysis ==
    222
    323Reggie 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.
    424
     25=== User permissions ===
    526
    6 == Open Grid Scheduler ==
     27All 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.
     28
     29=== Project archive ===
     30
     31The 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:
     32
     33 * Host: The host name of the file server
     34 * !Username/Password: Login information to the file server
     35 * Root path: The path to root directory of the project files (eg. `/casa4/project_archive/scanb`)
     36 * SSH fingerprint: The MD5 fingerprint for the file server
     37
     38Note that [wiki:net.sf.basedb.xfiles External files support package] (version 1.1 or higher) must be installed for this to work.
     39
     40=== Open Grid Scheduler ===
    741
    842To 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.
    943
    10 == Programs that must be installed on the cluster ==
     44=== Programs that must be installed on the cluster ===
    1145
    1246 * Picard: Customized version currently found at: https://github.com/nnordborg/picard/tree/lorry
    … …  
    2559
    2660
    27 == Configuration ==
     61=== Configuration ===
    2862
    29 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 public key to be able to connect to the cluster.
     63Before 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.
    3064
    3165In 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.
    3266
    33 In the configuration you can also specify parameters for some of the above mentioned programs (picard and trimmomatic).
    34 
    35 For some of the programs the parameters are coded directly into the pipeline scripts (bowtie and tophat).
     67In the configuration you can also specify parameters for most of the above mentioned programs.
    3668
    3769