Batch version ?

[zimoun]

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]

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]

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]

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 ***@***.***> 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 <6a3d530> and there is no file named X-shift_standalone_README.txt. Have you pushed it ? All the best — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#11 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADacLxBPA4fSbjlzaBJATC_xlMV-p1c3ks5tjNfwgaJpZM4Q60lT> .

-- Nikolay

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[zimoun]

Download from where ?

[nsamusik]

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

On Mon, Apr 9, 2018 at 1:58 AM zimoun ***@***.***> wrote: Download from where ? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#11 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADacL3sHg85MdmHjd3xmPFZdm2XABxhqks5tmyK4gaJpZM4Q60lT> .

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