Opened 2 years ago

Closed 23 months ago

Last modified 21 months ago

#785 closed enhancement (fixed)

Separate project archive folder for external samples

Reported by: nicklas Owned by: nicklas
Priority: critical Milestone: Reggie v4.0
Component: net.sf.basedb.reggie Keywords:
Cc:

Description (last modified by nicklas)

The library preparation/sequencing wizards have support for processing external samples (RNA). In the end data files from the sequencing (FASTQ, etc) end up in the 'scanb' project archive folder. This is currently configured in the <project-archive> setting in the reggie-config.xml file and in the ProjectArchive fileserver item in BASE.

Since we are already generating different subfolder structures for regular and external samples it should not be too difficult to add settings for an 'external project archive'. Basically we need another configuration setting in the XML file (<external-project-archive>) and one more fileserver item (ExternalProjectArchive).

For external samples with an underscore in the name the characters before the underscore should be used as the name of the top-most folder inside the external project archive. External samples without an underscore doesn't have the extra folder. For example:

  • AA_FOO is stored in <external-archive>/AA/FOO
  • AA_BAR is stored in <external-archive>/AA/BAR
  • BB_XYZ is stored in <external-archive>/BB/XYZ
  • MYSAMPLE is stored in <external-archive>/MYSAMPLE

The folder structure is repeated in the BASE server file structure, but instead of using /home/SCANB/SecondaryAnalysis as the main directory, /home/External/SecondaryAnalysis should be used.

Already existing information have to be fixed so that it is compatible with the new scheme. Some things may be possible to do with batch importers, some things may have to be done manually. The details about this are documented in a special update notes wiki page. Note that the update procedure will not create the extra folder for samples with an underscore in the name.

Change History (11)

comment:1 Changed 23 months ago by nicklas

  • Description modified (diff)
  • Milestone changed from Reggie v3.x to Reggie v4.0
  • Priority changed from minor to major

comment:2 Changed 23 months ago by nicklas

  • Priority changed from major to critical

comment:3 Changed 23 months ago by nicklas

  • Status changed from new to assigned

comment:4 Changed 23 months ago by nicklas

  • Description modified (diff)

comment:5 Changed 23 months ago by nicklas

(In [3600]) References #785: Separate project archive folder for external samples

Added <external-archive> setting to reggie-config.xml. A new FileServer item is needed to represent this path in BASE. The installation wizard will create the new item, but it must be manually configured with login information, SSH fingerprint and with the same root path as specified in <external-archive>.

The demux servlet now generates a script that save external files to the path specified in <external-archive>. Downstream analysis steps are not yet aware of this and will fail.

Already existing files that belong to external samples must be updated manually. Details need to be specified in a special update notes document on the wiki. In short:

  • Files on the file server must be moved from <project-archive> to <external-archive>.
  • File items in BASE must be moved from /home/SCANB/SecondaryAnalysis to /home/External/SecondaryAnalysis.
  • The FileServer property for external file items must be changed from ProjectArchive to ExternalArchive.

comment:6 Changed 23 months ago by nicklas

(In [3601]) References #785: Separate project archive folder for external samples

The alignment wizard has been updated to handle <external-archive>.

comment:7 Changed 23 months ago by nicklas

(In [3605]) References #785: Separate project archive folder for external samples

Viewing and downloading of remote files from the "Confirm..." wizards should now support using different archive roots.

comment:8 Changed 23 months ago by nicklas

(In [3606]) References #785: Separate project archive folder for external samples

The cufflinks wizard has been updated to handle <external-archive>.

comment:9 Changed 23 months ago by nicklas

(In [3607]) References #785: Separate project archive folder for external samples

The gene report plug-in has been updated to handle <external-archive>.

comment:10 Changed 23 months ago by nicklas

  • Resolution set to fixed
  • Status changed from assigned to closed

comment:11 Changed 21 months ago by nicklas

  • Description modified (diff)
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