souporcell
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wheaton5
Download souporcell.sif error
When I downloaded the souporcell.sif file with the link you provided,I got the 404 error.Is this download line invalid?
I just tested it and it worked for me. In my experience wget from google drive can be wonky and I have sometimes gotten 404 errors. Sometimes retrying immediately has worked and other times there was some period of time it wasn't working an an hour or two later it worked. I should look for a more reliable service (google drive is reliable, but somehow wget has essentially no support and we have to basically hack a solution to get wget to work). Let me know if it continues to be a problem.
But at the same time, I have deleted old versions, so if you post the command you are using, I can check if it is currently still in my google drive. I haven't updated the readme for at least 2 weeks and the link provided there is currently working.
Thanks!I will try again.But I think uploading this file to github as a package is a nice idea,haha!
It's 3Gb so can't upload it to github. There are other services that might be better options than google drive.
I can not still download the souporcell.sif file with the link you provided,I got the 404 error again and again.Can you check it,thanks!
It works for me, but if wget isn't working a directly link is more google drive friendly. Problem with that is that you can't easily download it directly to a server (unless you have a text browser or x forwarding which is possible, just not 100% standard). So in this case you will download it to your computer then scp it to your server assuming you are working on a cluster of some sort.
https://drive.google.com/file/d/124sRtZoDlKt-jJYS6BbWGC1-CY01aAGT/view?usp=sharing
That file only appears to be 990MB to me. I'm also attempting to do a little trial balloon with this - any thoughts of just putting it in AWS S3 or something? Or throw the equivalent docker container up into docker hub for free?
I download it(souporcell.sif) for a few times，and the size of file was 1009541120 b(963M). What is more, it did not work with errors, my cmd is:
wget --load-cookies /tmp/cookies.txt "https://docs.google.com/uc?export=download&confirm=$(wget --quiet --save-cookies /tmp/cookies.txt --keep-session-cookies --no-check-certificate 'https://docs.google.com/uc?export=download&id=1tj2j8QZuGz8sylHgWbnejWyUn8n6m0Y8' -O- | sed -rn 's/.*confirm=([0-9A-Za-z_]+).*/\1\n/p')&id=1tj2j8QZuGz8sylHgWbnejWyUn8n6m0Y8" -O souporcell.sif && rm -rf /tmp/cookies.txt
and run cmd as follows：
singularity exec souporcell.sif souporcell_pipeline.py -h
Got errors 'ERROR : Failed invoking the NEWUSER namespace runtime: Invalid argument
ABORT : Retval = 255'
Best wishes
What is the size of the singularity image (ls -lah souporcell.sif) Also what version of singularity do you have? singularity --version
Best, Haynes
What is the size of the singularity image (ls -lah souporcell.sif) Also what version of singularity do you have? singularity --version
Best, Haynes
Thank you for your reply. The size of the singularity image (ls -lah souporcell.sif) 963M
ls -lah ../souporcell.sif
#-rw-r--r-- 1 yaomengcheng bioinfo 963M Oct 26 09:22 ../souporcell.sif
when I updata singularity (3.6.4), it worked with root user, not for other user. Is this necessary?
Best