Modify Read-only file in terminal
Posted in TCGA data on the CGC by Yiyun Rao Tue Feb 04 2020 22:55:06 GMT+0000 (Coordinated Universal Time)·1·Viewed 390 times
Hi!
I am analyzing the TCGA MAF files using terminal in Data cruncher. Some MAF files are .gz format and I have to unzip them. But it's a read-only file system. Would you please help find a solution? Thank you!
Best,
Yiyun
Hi Yiyun,
Here's a suggestion from our Data Cruncher engineering team:
The folder in which the project files are mounted is read-only to prevent unwated changes to the files located on the platform. So you will not be able to use that folder to create or modify files there.
It depends on what your approach is to decompressing (using the terminal or through python) but all of the options should allow you to specify in some way the output directory in which the decompressed file will be. For instance, if using the terminal, it can be done though piping, for instance
cat /sbgenomics/project-files/<filename>.ext.gz | gzip -d > /sbgenomics/workspace/<filename>.ext
Or through python by using the
gzip
module. Usingshutil
will allow decompression of large files in chunks without running out of memory:Hope this helps.