Question: How to upload fasta file to SSH Supercomputer
0
gravatar for wkmustahs21
3.1 years ago by
wkmustahs2130
wkmustahs2130 wrote:

Hi

I would like to know how to upload a fasta file on the the supercomputer (Unix/Linux etc). I have downloaded the whole genome reference of Nipponbare from Rap-DB. I would like to upload to Unix Linux so that I can do my Tuxedo pipeline using Unix/Linux. Can you please me commands or information on how to upload my Nipponbare Ref Genome fast file onto Linux UNIX?

rna-seq • 1.9k views
ADD COMMENTlink modified 7 months ago by Biostar ♦♦ 20 • written 3.1 years ago by wkmustahs2130
3
gravatar for ATpoint
3.1 years ago by
ATpoint40k
Germany
ATpoint40k wrote:

Use rsync, with parameters for maximum speed:

rsync -axv --numeric-ids --delete --progress -e "ssh -T -o Compression=no -x"

It outperforms scp in many regards.

ADD COMMENTlink modified 7 months ago • written 3.1 years ago by ATpoint40k
1
gravatar for Dan D
3.1 years ago by
Dan D7.1k
Tennessee
Dan D7.1k wrote:

You can use SFTP through an FTP client like filezilla. There are command line clients as well but I'm not sure if you prefer command line or not. Use port 22 on the destination host.

If you want to transfer over SSH, the scp command is what you want.

For example, if you're on the host with the FASTA file and you want to transfer it to your destination host:

scp /path/to/my.fasta username@my.remote.host:/destination/path/

This will copy my.fasta to the directory /destination/path/ on the remote host.

ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by Dan D7.1k
0
gravatar for ac.research
3.1 years ago by
ac.research10
ac.research10 wrote:

There is a very simple command:

scp from to

Example to supercomputer:

scp /path/to/your/file username@132.343.12.3:/path/to/your/destination/on/supercomputer
scp /home/acresearch/desktop/uniprot90 acresearch@castor:/home/acresearch/databses

Example from supercomputer:

scp username@132.343.12.3:/path/from/your/supercomputer /path/to/your/computer/destination
scp acresearch@castor:/home/acresearch/databses/uniprot90 /home/acresearch/desktop

Another way:

If you understand how to SSH, then you will understand how to SFTP. It is the same concept except for file transfer. You use put to upload and get to download

ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by ac.research10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1082 users visited in the last hour