Tutorial:Setting up Aspera Connect (ascp) on Linux and macOS
0
4
Entering edit mode
12 weeks ago
ATpoint 65k

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 era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR144/004/SRR1448774/SRR1448774.fastq.gz .

Let me know if this needs and changes.

aspera ascp • 1.2k views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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 subasp@upload.ncbi.nlm.nih.gov:uploads/dvr_gmail.com_gNs8nDHw

Do you know what is happening?

Thanks!

Daniela

ADD REPLY
1
Entering edit mode

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?

ADD REPLY
1
Entering edit mode

Thank you very much! it worked!!

ADD REPLY
0
Entering edit mode

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

ADD REPLY
2
Entering edit mode

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.

ADD REPLY

Login before adding your answer.

Traffic: 697 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6