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nolanlab / vortex

VorteX Clustering Environment - Java graphical tool for single-cell analysis, clustering and visualization. Latest release:
https://github.com/nolanlab/vortex/releases
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Batch version ? #11

Open zimoun opened 6 years ago

zimoun commented 6 years ago

Dear,

I am trying to run vortex on large samples and it does not fit into the memory of my "standard multicore workstation" with 23GB of RAM.

Moreover, I have access to a cluster with much more RAM. However, there is no X server, i.e., the GUI cannot be enable on some node.

What is the way to launch computations from the command-line ?

In other words, the way to feed the database without any GUI ? (then explore the data with the GUI using another machine)

Since in my case, all is mounted with NFS-like, so the storage it is not a real issue. The issue comes from the computational power available under X server (GUI).

I am not a Java programmer so I have not dived into the code.

Is it already possible ? playing around the command-line java option1 option2 options. How ? Or should it be a plan to split vortex: a Lib controlled by a Gui or a command-line parser ?

How much do you think this appears to you as amount of work ?

Thank you in advance for any point of view.

nsamusik commented 6 years ago

Hi Zimoun,

Please download the latest release and look in the file: X-shift_standalone_README.txt

There should be instructions for the headless computation of X-shift

Also if you are experiencing the problems with performance, try limiting the number of cells that get sampled from each file. Standalone X-shift will automatically upsample the files upon completing the clustering so that each cell in the source FCS files gets assigned to a cluster.

Hope this helps

zimoun commented 6 years ago

Hi,

Thank you for your pointer. However, I am not able to find the file that you mention.

My repo is updated to the commit 6a3d530 and there is no file named X-shift_standalone_README.txt. Have you pushed it ?

All the best

nsamusik commented 6 years ago

It’s not on the GitHub - Can you please download it with the latest release? On Thu, Mar 29, 2018 at 5:47 AM zimoun notifications@github.com wrote:

Hi,

Thank you for your pointer. However, I am not able to find the file that you mention.

My repo is updated to the commit 6a3d530 https://github.com/nolanlab/vortex/commit/6a3d5306dc3936641dd8e6a33a85782948f8d93c and there is no file named X-shift_standalone_README.txt. Have you pushed it ?

All the best

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zimoun commented 6 years ago

Download from where ?

nsamusik commented 6 years ago

https://github.com/nolanlab/vortex/releases

On Mon, Apr 9, 2018 at 1:58 AM zimoun notifications@github.com wrote:

Download from where ?

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