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graph-genome / pipeline

odgi - component_segmentation - Schematize
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Cloning Schematize is run everytime I change the binning size #3

Closed subwaystation closed 4 years ago

subwaystation commented 4 years ago 
ubuntu@pantograph2:~/sh/test_pipeline/pipeline$ docker run -ti --rm --publish=3000:3000 --volume=`pwd`:/usr/src/app/data pipeline data/run1.B1phi1.i1.seqwish.gfa 10
### odgi build
### odgi sort
### odgi bin
### component segmentation
mkdir: cannot create directory ‘data/run1.B1phi1.i1.seqwish.seg’: File exists
fatal: destination path 'component_segmentation' already exists and is not an empty directory.

Can we prevent that?

6br commented 4 years ago

YES.

6br commented 4 years ago

Fixed!

subwaystation commented 4 years ago

Sorry, but Schematize is still cloned everytime I run

docker run -ti --rm --publish=3000:3000 --volume=`pwd`:/usr/src/app/data pipeline data/run1.B1phi1.i1.seqwish.gfa 100

This is not a major thing, but if I run the container with different bin sizes, I don't want to wait until the whole thing has been cloned and all packages installed every time.

6br commented 4 years ago

I'll check it again.

6br commented 4 years ago

I think in the master HEAD is fixed this issue.

subwaystation commented 4 years ago

No I get 

Failed to compile.

./src/PangenomeSchematic.js
Module not found: Can't resolve './data/data/run1.B1phi1.i1.seqwish.w1000.schematic.json' in '/usr/src/app/Schematize/src'

I guess one data too much in the code.