Download BaseSpace runs from an Ubuntu (Linux) box - Page 2

GenoMax · 05-30-2017, 07:49 AM

Following is logical speculation.

It is possible that Illumina provides "read-only" mounts of your basespace account (to prevent inadvertent mistakes).

thermophile · 05-30-2017, 08:04 AM

That makes sense to me and is a good idea but I thought that basemount was supposed to enable uploading projects as well as downloading (i.e. if you don't want to use standard demultiplexing).

My biggest issue with the permissions problem (again, not sure if it was basemount or fusemount) was that I couldn't unmount which meant that I couldn't get new data

hr3y · 05-30-2017, 01:12 PM

Quote:

Originally Posted by thermophile

I have yet to figure out how to mount basemount so it's writable but am not sure if that's related to the server that I'm mounting on rather than basemount itself. The server I"m using uses fusermount which seems to do very strange things to basemount (ie. to unmount basemount, I have to chmod my entire home directory to 775 not just the folder containing the mountpoint).

Yes... I guess we would have to take a look at the code to figure out wth with the permissions. I did something lazy which is just an importer that hard links to the files and changes permissions in the destination directory then the fastq files can be used automatically in my pipeline.

ps. Thanks a million for replying! I'm kinda new here, it's nice to receive the email saying someone interacted with you

cement_head · 04-24-2020, 12:48 PM

Still have absolutely no idea how to do this.

krankins · 06-17-2020, 12:31 AM

There is an OSX downloader but it wasn't Snow Leopard compatible which left out my slightly older Mac Pro. At that point I looked at the python thing but decided it looked too complicated and it was easier to find a different machine. get-mobdro.com tubemate

samd · 06-19-2020, 01:56 PM

I actually made a markdown tutorial of how to download basespace files through your terminal. Should work on LINUX.
Let me know if it works! : https://github.com/samd1993/bioinfor...20Basespace.md

cement_head · 09-23-2020, 10:47 AM

Quote:

Originally Posted by samd

I actually made a markdown tutorial of how to download basespace files through your terminal. Should work on LINUX.
Let me know if it works! : https://github.com/samd1993/bioinfor...20Basespace.md

Thanks! 10 caharacters

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05-30-2017, 08:04 AM	#22
thermophile Senior Member Location: CT Join Date: Apr 2015 Posts: 243	That makes sense to me and is a good idea but I thought that basemount was supposed to enable uploading projects as well as downloading (i.e. if you don't want to use standard demultiplexing). My biggest issue with the permissions problem (again, not sure if it was basemount or fusemount) was that I couldn't unmount which meant that I couldn't get new data __________________ Microbial ecologist, running a sequencing core. I have lots of strong opinions on how to survey communities, pretty sure some are even correct.

06-17-2020, 12:31 AM	#25
krankins Junior Member Location: TEXAS Join Date: Jun 2020 Posts: 1	There is an OSX downloader but it wasn't Snow Leopard compatible which left out my slightly older Mac Pro. At that point I looked at the python thing but decided it looked too complicated and it was easier to find a different machine. get-mobdro.com tubemate Last edited by krankins; 07-27-2020 at 03:55 AM.

05-30-2017, 07:49 AM	#21
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,080	Following is logical speculation. It is possible that Illumina provides "read-only" mounts of your basespace account (to prevent inadvertent mistakes).

04-24-2020, 12:48 PM	#24
cement_head Senior Member Location: Oxford, Ohio Join Date: Mar 2012 Posts: 253	Still have absolutely no idea how to do this.

06-19-2020, 01:56 PM	#26
samd Member Location: California Join Date: Nov 2019 Posts: 20	I actually made a markdown tutorial of how to download basespace files through your terminal. Should work on LINUX. Let me know if it works! : https://github.com/samd1993/bioinfor...20Basespace.md