Tutorial:Setting up Aspera Connect (ascp) on Linux and macOS

Question

[ATpoint]

This tiny tutorial cover setting up Aspera Connect (binary is called ascp) which might be used to download sequencing data, e.g. with download links provided by sra-explorer.info, see also sra-explorer : find SRA and FastQ download URLs in a couple of clicks

Setting up Aspera Connect is simple and was covered in my now deprecated tutorial. However, Aspera Connect versions > 4.2 no longer come with a required private key (asperaweb_id_dsa.openssh) so I want to share here some links to download versions < 4.2 and some install instructions:

Get the latest version that still works with the download links from sra-explorer.info

#/ Linux
wget https://ak-delivery04-mul.dhe.ibm.com/sar/CMA/OSA/0adrj/0/ibm-aspera-connect_4.1.3.93_linux.tar.gz
tar zxvf ibm-aspera-connect_4.1.3.93_linux.tar.gz
bash ibm-aspera-connect_4.1.3.93_linux.sh

#/ macOS -- download and then run the installer (have no Mac to test right now)
wget https://ak-delivery04-mul.dhe.ibm.com/sar/CMA/OSA/0adri/0/ibm-aspera-connect_4.1.3.93_macOS_x86_64.dmg

For Linux that creates the binary and openssh key in these locations:

$HOME/.aspera/connect/bin/ascp 

$HOME/.aspera/connect/etc/asperaweb_id_dsa.openssh

For Mac, after running the installer it should be:

$HOME/Applications/Aspera\ Connect.app/Contents/Resources/ascp

$HOME/Applications/Aspera\ Connect.app/Contents/Resources/asperaweb_id_dsa.openssh

Under normal circumstances that should be all it takes. You can now run the download links from sra-explorer, e.g.

ascp -QT -l 300m -P33001 -i $HOME/.aspera/connect/etc/asperaweb_id_dsa.openssh [e-mail]:vol1/fastq/SRR144/004/SRR1448774/SRR1448774.fastq.gz .

Let me know if this needs and changes.

[thomasrsewell]

Worked perfectly. Thank you!

[ATpoint]

You're very welcome :)

[spitzer]

Thank you so much for posting this. I spent the whole afternoon trying to figure out how to get ascp working, and you solved my problems in four lines of code!

[GenoMax]

Hopefully this is just a glitch with new version installer and may be fixed by IBM.

[DVR]

I have installed it, I have all the files that you mention but the terminal does not recognized "ascp" command!

(base) Danielas-MacBook-Pro:Resources dvr$ ascp

-bash: ascp: command not found

I am trying to run:

ascp -i /Users/dvr/Downloads/aspera.openssh -QT -l100m -k1 -d /Users/dvr/all [e-mail]:uploads/dvr_gmail.com_gNs8nDHw

Do you know what is happening?

Thanks!

Daniela

[ATpoint]

Like any binary you have to put it into PATH (see e.g. here) to call it without using the full path to it or alternatively use the full path. On Mac it would be (by default):

$HOME/Applications/Aspera\ Connect.app/Contents/Resources/ascp -i $HOME/Applications/Aspera\ Connect.app/Contents/Resources/asperaweb_id_dsa.openssh (...)

Does that work for you?

[DVR]

Thank you very much! it worked!!

[DVR]

Thank you very much again. I have now another issue to solve... When I uploaded the files there was also uploaded a hidden file called ".DS_Store" along with the rest of the fastq.gz files, and the NCBI platform is detecting it as an additional file of course... So my question is, how can I remove a file in this preloaded folder? Is there a way to access to it?

Thank you very much in advance!

Best,

Daniela

[GenoMax]

If you don't have access to the folder on the server (you likely have write only access) email NCBI SRA help desk and let them know. They should be able to remove the file.

[sjlee4019]

does it still work? I tried the command with different versions but it stops saying Session Stop (Error: Server aborted session: No such file or directory)

[daniel.enriquez.v]

Hi, this is Daniel Thank you for your wonderful tutorial. Does ascp work with a text file with links?

[ATpoint]

Please give an example.

[Michael]

Thank you for the tutorial. The most important application for me is to upload data to ENA (downloading is somehow going to work ok with wget or curl), especially given the other option is lftp. With lftp, it was literally impossible to upload ten medium sized fastq files (tried with screen and nohup), which were uploaded with ascp (v3) in half an hour.

As you mention versions, users of CentOS 7 and possibly other old systems may have to fall back to v3 as the Glibc versions are not compatible. Fortunately, our CentOS time will soon be over.