pipeline-stitching

computational pipeline that creates yml file that will be consumed by the render

1. Create a folder and clone the repo

cd pipe
clone https://github.com/erhanbas/pipeline-stitching.git 

2. run main.m in matlab

main(brain,[inputfolder,pipelineoutputfolder])

inputs/outputs

brain : sample name, e.g. '2018-06-14';
inputfolder [OPTIONAL]: acqusition folder, e.g. sprintf('/groups/mousebrainmicro/mousebrainmicro/data/acquisition/%s',brain);
pipelineoutputfolder [OPTIONAL]: outputfolder e.g. sprintf('/nrs/mouselight/cluster/sandbox2/%s',brain)

sample usage

main('2018-06-14')
This will create tilebase.cache.yml file in the '/nrs/mouselight/cluster/classifierOutputs/'2018-06-14' folder 
Then run the render

sample render usage

copy a sample parameter file next to yml file, e.g. 
copy /nrs/mouselight/cluster/classifierOutputs/2018-07-02/set_parameters_raw.jl /nrs/mouselight/cluster/classifierOutputs/'2018-06-14/parameters_raw.jl

then modify the paths in parameters_raw.jl as follows
const user="mluser"
const input="2018-06-14"
const output="2018-06-14-raw"

then run
/groups/mousebrainmicro/mousebrainmicro/Software/barycentric4/src/render/src/render parameters_raw.jl

with default settings, this will create output render in /nrs/mouselight/Users/mluser/2018-06-14