Opened 2 years ago

Closed 2 years ago

#1051 closed enhancement (fixed)

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

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v4.18
Component: net.sf.basedb.reggie Keywords:
Cc:

Description (last modified by 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

Change History (2)

comment:1 Changed 2 years ago by Nicklas Nordborg

Description: modified (diff)
Summary: The Release exporter plug-in should create a script that always copy some data filesThe Release exporter plug-in should assist when creating zip files with expression data

comment:2 Changed 2 years ago by Nicklas Nordborg

Resolution: fixed
Status: newclosed

(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.

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