GALA

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I have assembled multiple versions of contig genomes, and I would like to use the gala software. Do these genomes require chromosome scaffolding before I input them into the gala...

YouxinZhao

Can it be installed through Conda

1

This software has many dependencies, can it be installed through Conda?

ZKYthli

Hi, when running GALA on two draft assemblies, i found that both .paf, scaffolding and gathering files of one of the draft is empty, is this normal or does it...

WeiCSong

minimap commands in the auto-generated draft_comp.sh file resulting in usage errors

3

Hi, Thanks for the interesting tool. The very first Minimap2 step in the Gala pipeline is throwing usage errors. This is what my drafts file essentially looks like (paths shortened...

JohnUrban

how to deal with the ccm results

2

I am currently trying to split the raw reads by chromosome, and I have a few draft assemblies based on Canu, Nextdenovo, Flye, and Necat. However, the scaffold numbers ended...

lilinzhou

Hi, thank you for the nice pipeline GALA. The main problem i met these days is that the process 'bwa mem -x ont2d' is too slow. It takes me two...

caixu0518

Hello, I was working with GALA back in October 2022. Many thanks for the creative tool. Back in Oct 2022, I forked it and improved various aspects of it as...

JohnUrban

TabError: inconsistent use of tabs and spaces in indentation

1

Hi, Thanks for the cool program. I am giving it a try. First thing that pops up is this error: ``` Traceback (most recent call last): File "/central/groups/carnegie_poc/jurban/software/gala/GALA/gala", line 19,...

JohnUrban

Hi, I am trying to use GALA in a single command on the cluster using the sun grid engine. But it is very slow due to the unavailability of multithreading...

arslan9732

Syntax confusion regarding sequencing_platform

2

Hi, Thanks for the cool tool. I hope to get it running. I have been trying to get it run with the following command syntax: ``` ${GALA} ${DRAFTS} -a canu...

JohnUrban