The Release exporter plug-in should assist when creating zip files with expression data

[Nicklas Nordborg]

Some of the data files that belong to Cufflinks and StringTie raw bioassays need to be packaged as zip files for releasing to external partners. The ReleaseArchive is not suitable since it contains other files and it is difficult to select the exact files that are needed:

• Cufflinks
  • genes.fpkm_tracking
  • isoforms.fpkm_tracking
  • skipped.gtf
  • transcripts.gtf
• StringTie
  • e2t.ctab
  • e_data.ctab
  • gene.tsv
  • i2t.ctab
  • i_data.ctab
  • t_data.ctab
  • transcript.gtf
  • transcript_covered.gtf

A simple solution is to create "list" files that list all files that are part of the data set. For example, cufflinks.lst:

./S000084/l.r.m.c.lib.g/k.a/t/genes.fpkm_tracking
./S000084/l.r.m.c.lib.g/k.a/t/isoforms.fpkm_tracking
./S000084/l.r.m.c.lib.g/k.a/t/skipped.gtf
./S000084/l.r.m.c.lib.g/k.a/t/transcripts.gtf
...

The zip command can then be used to create cufflinks.zip with all Cufflinks data:

zip -@ cufflinks.zip < cufflinks.lst

[Nicklas Nordborg]

(In [4814]) Fixes #1051: The Release exporter plug-in should assist when creating zip files with expression data

The release exporter now create file lists for StringTie and Cufflinks. A README file was also added to help as a reminder about the commands to use.