Open zimoun opened 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
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
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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Download from where ?
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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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 splitvortex
: 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.