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_22.214.171.124_linux.tar.gz tar zxvf ibm-aspera-connect_126.96.36.199_linux.tar.gz bash ibm-aspera-connect_188.8.131.52_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_184.108.40.206_macOS_x86_64.dmg
For Linux that creates the binary and openssh key in these locations:
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 email@example.com:vol1/fastq/SRR144/004/SRR1448774/SRR1448774.fastq.gz .
Let me know if this needs and changes.
Worked perfectly. Thank you!
You're very welcome :)
Hopefully this is just a glitch with new version installer and may be fixed by IBM.
I have installed it, I have all the files that you mention but the terminal does not recognized "ascp" command!
I am trying to run:
Do you know what is happening?
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):
Does that work for you?
Thank you very much! it worked!!
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!
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.
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)