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saketkc / pysradb

Package for fetching metadata and downloading data from SRA/ENA/GEO
https://saketkc.github.io/pysradb
BSD 3-Clause "New" or "Revised" License
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directing output in external hard drive #42

Closed amitpande74 closed 4 years ago

amitpande74 commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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

saketkc commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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.