directing output in external hard drive

[amitpande74]

Hi,
I want to redirect the download to an external hard drive since I have little space left in my hard drive.
I am trying
(pysradb) usr@usr-X705UDR:~$ pysradb download --out-dir ./pysradb_downloads -p SRP165962 --db cd /media/usr/LaCie/db/ , but it is not working.
Kindly help.

[saketkc]

Hi @amitpande74, You should be able to set a custom directory for the downloads using --out-dir:

pysradb download -p SRP165962 --out-dir /path/to/xyz

Feel free to reopen if you face any issues.

[amitpande74]

Hi @saketkc
I tried the command
pysradb download -p SRP165962 --out-dir , but it only downloads the empty folders.

[saketkc]

Hi @amitpande74, I am unable to replicate this at my end.
See this notebook for an example: https://colab.research.google.com/drive/141ambHwCshyMZlZjgQgci6WCEZv6Z2KO

[amitpande74]

Hi,
I think I found out the problem.
SRP165962 SRX4896814 SRS3943426 SRR8068516 anonftp@ftp-trace.ncbi.nlm.nih.gov:/sra/sra-instant/reads/ByRun/sra/SRR/SRR806/SRR8068516/SRR8068516.sra
Whereas in the colab notebook which you shared, this link is not being shown.
and when i checked the link ftp-trace.ncbi.nlm.nih.gov:/sra/sra-instant/ it is empty.
how to avoid this ?
Is sra-tools a requirement ? 'cause I dont have this installed.

[saketkc]

The file is here: https://sra-download.ncbi.nlm.nih.gov/traces/sra67/SRR/007879/SRR8068516 (See last line on colab)
and pysradb does download it. I aborted the complete download since there is not enough space on colab to do so.

[saketkc]

Are you using SRAmetadb.sqlite? Please make sure you do not have it in your current working directory. We are moving away from SRAmetadb. The above commands are for SRAweb mode which does not require SRAmetadb.sqlite.