User: petinho86
petinho86 • 0
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Posts by petinho86
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Answer:
A: Setup PHG with Singularity
... Hi,
I'll add the CreateHaplotypesFromGVCF log in the next days. It did work in the end. And I probably had some mismatching bed files.
The out of memory problem seems very odd. I have a 430mb genome (rice) and 4 Taxons. And I only added 1000 x 1000bp ranges. Nothing spectacular.
I found the probl ...
written 17 days ago by
petinho86 • 0
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Answer:
A: Setup PHG with Singularity
... **Update**
Hi again.
Turns out having multiple config files makes this a lot easier to grasp.
It would be probably good to show that in the description of each step, eg: makeinitialDB_config.txt
Here is the way it works for me:
**Make working directory using singularity:**
$ singularit ...
written 20 days ago by
petinho86 • 0
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Answer:
A: Setup PHG with Singularity
... Hi Zack,
Yes singularity has nothing to do with this.
It looks like it all stands and falls with a proper config file.
I hacked the config file a lot and got some steps further into the pipeline.
I replaced the #required parameters section with the part you wrote and I added the sql db config sect ...
written 28 days ago by
petinho86 • 0
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A: Setup PHG with Singularity
... Hi Zack,
Thanks a lot.
I started to fill in the gaps, but there are still plenty of spaces / UNASSIGED sections to fill.
I figured that for the initial run I mainly need to setup the required parameters:
(this is how my config.txt looks now):
########################################
#Req ...
written 4 weeks ago by
petinho86 • 0
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... Hi,
I am trying to setup PHG. I am using Singularity as I am working on a cluster.
The installation sis pretty simple as described on :
https://bitbucket.org/bucklerlab/practicalhaplotypegraph/wiki/UserInstructions/CreatePHG_step0_singularity.md
So I ran:
$ cd phg_singularity
$ module l ...
written 4 weeks ago by
petinho86 • 0
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