1. Introduction to SeqWare
  2. Installation
  3. Getting Started
  4. SeqWare Pipeline
  5. SeqWare MetaDB
  6. SeqWare Portal
  7. SeqWare Web Service
  8. SeqWare Query Engine
  9. Glossary
  10. Frequently Asked Questions
  11. APIs
  12. Source Code
  13. Plugins
  14. Modules
  15. Advanced Topics

File Linker

The FileLinker plugin was designed to import files from the LIMS into the SeqWare MetaDB for processing, but can be used to attach any file paths to any IUS or Lane.

Add the Workflow

The “FileImport” workflow is already added into the MetadataDB, but this method can be used to create new workflows to link to.

java -jar ~/.seqware/self-installs/seqware-distribution-1.1.0-full.jar  -p net.sourceforge.seqwe.pipeline.plugins.Metadata -- --create --table workflow --field name::FileImport --field version::1.0 --field description::'Imports files into the database, links them to IUSs or Lanes and creates intermediate Processings. Initially used to import files from the LIMS and attach them to IUSes'

Command line parameters

See Plugins

Get the linking file

In one of the following formats, whitespace-separated. The first three columns are not parsed by the FileLinker, but this was the format of the file provided for mass import. The only columns that are used are ius_sw_accession, mime_type (if it exists) and file. The header is required, but all other columns can be empty and separated by tabs.

Mime-type (preferred):

sequencer_run    sample    lane    ius_sw_accession    file_status    mime_type    file
.                .         .       7937                .              txt          /absolute/file/path/myfile.txt

No mime-type:

sequencer_run    sample    lane    ius_sw_accession    file_status    file
.                .         .       7937                .              /absolute/file/path/myfile.txt

Input File Alternatives

The files above are tab delimited, but any single character delimiter may be used. Here comma is used as a delimiter.


The fields ‘’’size’’’ and ‘’’md5sum’’’ are optional, but if include the information will be saved into the SeqWare database.

Run the tool

You can get the workflow accession using the –list-install option in BundleManager.

java -jar seqware-distribution-1.1.0-SNAPSHOT-full.jar --plugin net.sourceforge.seqware.pipeline.plugins.FileLinker -- \
     --file-list-file /home/mtaschuk/Downloads/link_files_report.txt --workflow-accession 375894 --csv-separator ,

By default error messages will be written to standard out. To see more information, such as successfully linked entries create a ‘’’log4j.properties’’’ file similar to the one below.

log4j.logger.net.sourceforge.seqware.pipeline.plugins=DEBUG, console

log4j.appender.console.layout.ConversionPattern=%p %t %c - %m%n

Use ‘’‘-Dlog4j.configuration=file:./log4j.properties’’’ to specify the properties file when running the FileLinker command.

java -Dlog4j.configuration=file:./log4j.properties -jar -jar seqware-distribution-1.1.0-SNAPSHOT-full.jar \
     --plugin net.sourceforge.seqware.pipeline.plugins.FileLinker -- \
     --file-list-file /home/mtaschuk/Downloads/link_files_report.txt --workflow-accession 375894 --csv-separator ,