bam transfer

[cmccabe]

Is there a command that might help to transfer a BAM file to a website? Thank you

[GenoMax]

What sort of transfer? Uploading a bam file to a tool/site (e.g. galaxy) or uploading it to a web location so it becomes available for others to download.

For the latter, you would need to be able to access the backend server (so you can upload the file via scp/sftp). You will need an account on the server in question.

[cmccabe]

It is the latter of the two (transfer to site to download from). Would lftp work?

3 files are put in a folder named "test" (BAM ~20GB, VCF, and coverage analysis) then zipped using:

 tar -zcf /path/to/file.tar.gz -C /Desktop/test

lftp https://something.sharefile.com/login.aspx
lftp https://something.sharefile.com/login.aspx:~> user xxxxxx
Password: xxxxxxx
lftp https://something.sharefile.com/login.aspx:~> mirror -R /home/dnascopeV/Desktop/Test

To view the transfer

 lftp https://something.sharefile.com/login.aspx:~> ls

To unzip (not sure if this will work as it might be basic HTTP and not what I need):

 wget --http-user cmccabe --http -passwd xxxx*** https://something.sharefile.com/login.aspx -O - | tar -zxf -

Thanks .

[GenoMax]

Looks like you have everything under control :-)

I would just download (reversing lftp) and then unzip locally to be safe after the transfer is complete.

[cmccabe]

can lftp be used in cygwin? Thank you .

[GenoMax]

If you can compile it then yes. Give it a try.

[cmccabe]

I am not sure what you mean by downloading (reversing lftp), can you use it in an example. I just learned lftp a few weeks ago and finding it very useful. Thank you .