File Transfer Methods¶

SFTP Clients¶

Cyberduck¶

CyberDuck is a popular open source SFTP client for Windows and Mac. Download and install Cyberduck. Open the Cyberduck application. Click the "Open Connection" button on the toolbar.

Select SFTP (SSH File Transfer Protocol) from the drop-down.
Enter htc.crc.pitt.edu in the Server box.
Enter your Pitt username and password, and click Connect.

Your files on the server will appear in the CyberDuck window. You can now drag-and-drop files to and from the window to upload/download files.

FileZilla¶

FileZilla is cross-platform FTP application available for Windows, Linux, and macOS. Download and install FileZilla. Open the FileZilla application.

Enter sftp://htc.crc.pitt.edu in the Host box.
Enter your Pitt username and password, and click QuickConnect.

Your files on the server will appear in the FileZilla window.

The Open OnDemand File App¶

!!! warning The Open OnDemand is not suitable for larger files ( > 1 GB ) due to a limited cache size.

Log on to ondemand.htc.crc.pitt.edu
Click Files -> Home Directory
Click Upload and choose File(s) from your computer.

For large data sets, consider using Globus.

An institutional endpoint is not required to use Globus; You can set up a personal endpoint on your computer if you need to transfer large amounts of data.

Command Line Tools¶

rsync¶

You can use rsync from a terminal/shell on your local computer.

Copy to the cluster: rsync -aP {files} fangping@htc.crc.pitt.edu:/bgfs/sam/fangping/

Where {files} is a local directory on your computer. This makes a recursive copy of the local files to a folder on the cluster.

Copy from the cluster: rsync -aP fangping@htc.crc.pitt.edu:/bgfs/sam/fangping/files/ .

This copies the /bgfs/sam/fangping/files folder on the cluster to the working directory on the local machine.

scp¶

scp is similar to rsync in that it runs in a terminal on your local machine.

scp -r files fangping@htc.crc.pitt.edu:/bgfs/sam/fangping/

This copies the folder files in the current directory on the computer you issued the command on to a folder on the cluster.

scp -r fangping@htc.crc.pitt.edu:/bgfs/sam/fangping/files/ .

This copies the /bgfs/sam/fangping/files folder on the cluster to the current directory on the computer you issued the command from.

aspera¶

Aspera is IBM's high-performance file transfer software which allows for the transfer large files and data sets with predictable, reliable and secure delivery regardless of file size or transfer distance from a location that has the aspera transfer server running. The NCBI recommend the use of aspera for transfer of data sets from their site.

Download aspera from to your home directory on HTC cluster.

Download link: https://download.asperasoft.com/download/sw/connect/3.9.1/ibm-aspera-connect-3.9.1.171801-linux-g2.12-64.tar.gz

tar xzvf ibm-aspera-connect-3.9.1.171801-linux-g2.12-64.tar.gz

You will find file ibm-aspera-connect-3.9.1.171801-linux-g2.12-64.sh:

./ibm-aspera-connect-3.9.1.171801-linux-g2.12-64.sh

aspera is installed to ~/.aspera

You can then use aspera to download files. The aspera binary is at ~/.aspera/connect/bin/ascp and the key is at ~/.aspera/connect/etc/asperaweb_id_dsa.openssh

[fangping@login0b aspera]$ ~/.aspera/connect/bin/ascp -QT -l 300m -P33001 -i ~/.aspera/connect/etc/asperaweb_id_dsa.openssh era-fasp@fasp.sra.ebi.ac.uk:/vol1/fastq/SRR949/SRR949627/SRR949627_1.fastq.gz .

Using wget or curl to Download Files¶

wget is a networking command-line tool that lets you download files. It supports the HTTP,HTTPS, FTP, and FTPS internet protocols.

In order to download a file using Wget, type wget followed by the URL of the file that you wish to download. Wget will download the file in the given URL and save it in the current directory.

wget https://domain.com/file

The equivalent curl command is:

curl https://domain.com/file

The file will keep the name embedded in the url. You can specify a destination name.

curl -o newname https://what.ever

wget -O newname https://domain.com/file.

If your url includes specific characters, such as ?, you can put the full url in single quotes to prevent the shell from mangling these characters.

wget -O newname 'https://domain.com/file?userId=id&Credential=password’

curl -o newname 'https://domain.com/file?userId=id&Credential=password’

Cloud Tools¶

Pitt OneDrive¶

You can transfer data between Pitt OneDrive and the cluster. See this page for details.

Pitt Box¶

You can transfer data from and to Pitt box from the cluster. Follow these steps.

AWS S3¶

awscli has been installed as a module in Lmod. You can transfer data from the cluster to AWS S3.

module load awscli/1.16.135

aws s3 sync /bgfs/sam/fangping/DataUpload s3://my-s3-bucket/data_from_htc

This will transfer /bgfs/sam/fangping/DataUpload folder to s3://my-s3-bucket/data_from_htc

You can submit this command as a job on HTC computational node.

google bucket¶

You can install and configure gsutil to transfer data from/to gs bucket.

module load gsutil/5.16

gsutil config

gsutil cp -r gs://gs-bucket-name/ .

This will recursively transfer gs://gs-bucket-name/ folder to the current folder.

Azure Storage¶

AzCopy is a command-line tool that moves data into and out of Azure Storage. azcopy has been installed as a module.

module load azcopy/10.11.0 azcopy --help

azcopy copy "/bgfs/your/folder/" "https://account.blob.core.windows.net/mycontainer1/?sv=2018-03-28&ss=bjqt&srt=sco&sp=rwddgcup&se=2019-05-01T05:01:17Z&st=2019-04-30T21:01:17Z&spr=https&sig=MGCXiyEzbtttkr3ewJIh2AR8KrghSy1DGM9ovN734bQF4%3D" --recursive=true

This example command recursively copies data from a local directory to a blob container. A fictitious SAS token is appended to the end of the container URL.