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-   -   Download BaseSpace runs from an Ubuntu (Linux) box (http://seqanswers.com/forums/showthread.php?t=57937)

cement_head 04-24-2015 03:22 AM

Download BaseSpace runs from an Ubuntu (Linux) box
 
Hello,

Am I correct in assuming that in order to download data files (FastQ) from BaseSpace, I have to manually run the python downloader script using my run ID and a token????????

In other words, you'd have to be running WinBlows to have this downloaded automagically?

- Andor

GenoMax 04-24-2015 03:33 AM

http://seqanswers.com/forums/showthread.php?t=47633

Companies do not have an obligation to support all OS's. Illumina seems to have concentrated their user facing development on Windows.

cement_head 04-24-2015 03:46 AM

Quote:

Originally Posted by GenoMax (Post 170931)
http://seqanswers.com/forums/showthread.php?t=47633

Companies do not have an obligation to support all OS's. Illumina seems to have concentrated their user facing development on Windows.

I don't think this a matter of "supporting all OS's". When the overwhelming amount of software for bioinformatics is Linux based, that should be the primarily supported OS, not other operating systems. Many companies provide the ability to download a file securely regardless of OS. In other words, without having to install an OS (*.exe) specific downloader. For example, the downloader could have been JAVA based.

GenoMax 04-24-2015 04:33 AM

I don't use basespace so I don't know about the "automagical download" you are referring to (is that a separate application?). Looking at this link from the thread posted above Illumina seems to be treating Windows/OS X/Linux equally: https://support.basespace.illumina.c...run-downloader

cliffbeall 04-24-2015 06:51 AM

Apparently this is a new thing? It seemed to work direct through the browser on Linux about 6 months ago.

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.

There is a blog post from April 11th talking about "New Download Experience" and asking for feedback so I left a comment asking for a Linux port. Maybe if enough other people do the same?

cement_head 04-24-2015 07:54 AM

Quote:

Originally Posted by cliffbeall (Post 170984)
Apparently this is a new thing? It seemed to work direct through the browser on Linux about 6 months ago.

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.

There is a blog post from April 11th talking about "New Download Experience" and asking for feedback so I left a comment asking for a Linux port. Maybe if enough other people do the same?

Yes, you are correct - it used to work on Linux from within the browser. I can't login to their stupid website

cement_head 04-24-2015 08:03 AM

Quote:

Originally Posted by GenoMax (Post 170941)
I don't use basespace so I don't know about the "automagical download" you are referring to (is that a separate application?). Looking at this link from the thread posted above Illumina seems to be treating Windows/OS X/Linux equally: https://support.basespace.illumina.c...run-downloader

Yeah, problem is, that downloads EVERYTHING - image files, everything! :eek:

GenoMax 04-24-2015 08:08 AM

If you only need the fastq files why aren't you grabbing them directly from the MiSeq (if you have direct access to MiSeq of course)?

They should be in the D:\Illumina\MiSeq Analysis\Flowcell ID\Data\Intensities\BaseCalls directory (if I am remembering path right). Apologies in advance, if use of BaseSpace somehow turns local analysis off.

kcchan 04-24-2015 05:38 PM

It's still possible to download files without their download program. You will need to go into each file and download them one by one.

cement_head 04-26-2015 12:31 PM

Quote:

Originally Posted by GenoMax (Post 170995)
If you only need the fastq files why aren't you grabbing them directly from the MiSeq (if you have direct access to MiSeq of course)?

They should be in the D:\Illumina\MiSeq Analysis\Flowcell ID\Data\Intensities\BaseCalls directory (if I am remembering path right). Apologies in advance, if use of BaseSpace somehow turns local analysis off.

No, you're right - but some of my collaborators are 800 miles away :(

cement_head 04-26-2015 12:36 PM

Quote:

Originally Posted by kcchan (Post 171009)
It's still possible to download files without their download program. You will need to go into each file and download them one by one.

So, I tried the python script and it started downloading EVERYTHING (all images files, etc). Is there a way to get the python script to pull only the FASTQ files?

kcchan 04-26-2015 10:17 PM

You have to go into the Sample section (tube icon on the left sidebar) and click on the file name for each file (and not the checkbox). It will give you the error message "File is either not text-based or too large for viewing, please download the raw file." but also contain a download button to get the file via a normal download. It'll get pretty tedious if you have a lot of samples.

cliffbeall 04-27-2015 07:45 AM

This appeared on the Illumina blog post I linked to earlier, with a video of their upcoming tool:
Update (04/24/2015): We have received feedback regarding the inability of using the new downloader on Linux machines. At the BaseSpace WWDC today at the Broad Institute we announced that a new feature called BaseMount will be released soon. BaseMount enables you to mount your BaseSpace data as an Linux read-only FUSE-based virtual file system. You can do normal file system operations and can download files from a command line. We have a detailed demo below.
Hopefully this will solve peoples's issues.

eco32i 05-08-2015 11:51 AM

An ugly workaround we use for this (with NextSeq) is to mount a target directory on a linux box as a Samba share on NextSeq and use the Windows download tool from NextSeq to save .fastq files to that share.

But yes, it is annoying.

greghroberts 07-23-2015 08:01 PM

BaseMount is now available
 
BaseSpace team just released early access to BaseMount. It allows you to mount your entire account as a filesystem.

More info at:
https://basemount.basespace.illumina.com

eco32i 07-24-2015 06:01 AM

That's great news.
From my (very brief) test it works fine.

jdv 08-04-2015 10:57 AM

Another cross-platform command-line alternative is my bsclient software:

http://sourceforge.net/projects/bsfetch/

It was written prior to the existence of BaseMount when I wanted an interactive tool for headless server downloads, a niche which BaseMount also fills. One advantage is that not all users will have mount permissions on the server they're using - a requirement for BaseMount but not for bsclient.

cement_head 08-06-2015 12:23 PM

BaseMount is now regular access:

http://blog.basespace.illumina.com/2...for-basespace/

hr3y 05-29-2017 10:01 AM

basemount is weird.
 
Hi everyone, I was wondering if anyone has experience with mounting their BaseSpace account and regularly using it (reading, copying from it, etc). I was just trying to change the permissions of the directory where I mounted it and I can't.... even though I am the server's admin. :confused: :confused:

thermophile 05-30-2017 06:41 AM

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).


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