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.
(In [3600]) References #785: Separate project archive folder for external samples
Added
<external-archive>setting toreggie-config.xml. A newFileServeritem 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:
<project-archive>to<external-archive>./home/SCANB/SecondaryAnalysisto/home/External/SecondaryAnalysis.FileServerproperty for external file items must be changed fromProjectArchivetoExternalArchive.