Opened 6 years ago
Closed 6 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 )
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 by , 6 years ago
Description: | modified (diff) |
---|---|
Summary: | The Release exporter plug-in should create a script that always copy some data files → The Release exporter plug-in should assist when creating zip files with expression data |
comment:2 by , 6 years ago
Resolution: | → fixed |
---|---|
Status: | new → closed |
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(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.