Algorithm SINGE fails to run on Windows - Unterminated quoted string

[yutuyt01]

When running the BLRunner portion of the pipeline, the shell command to run the docker image fails to compile with the error "Unterminated quoted string".

The command being run:

docker run --rm --entrypoint /bin/sh -v C:\Users\shang\PycharmProjects\Beeline:/usr/local/SINGE/data/ grnbeeline/singe:0.4.1 -c "echo \" --lambda 0.01 --dT 15 --num-lags 5 --kernel-width 0.5 --prob-zero-removal 0 --prob-remove-samples 0.0 --family gaussian --replicate 0 --ID 0
--lambda 0.01 --dT 15 --num-lags 5 --kernel-width 0.5 --prob-zero-removal 0 --prob-remove-samples 0.0 --family gaussian --replicate 1 --ID 1
--lambda 0.01 --dT 15 --num-lags 5 --kernel-width 0.5 --prob-zero-removal 0 --prob-remove-samples 0.0 --family gaussian --replicate 2 --ID 2
--lambda 0.01 --dT 15 --num-lags 5 --kernel-width 0.5 --prob-zero-removal 0 --prob-remove-samples 0.0 --family gaussian --replicate 3 --ID 3
--lambda 0.01 --dT 15 --num-lags 5 --kernel-width 0.5 --prob-zero-removal 0 --prob-remove-samples 0.0 --family gaussian --replicate 4 --ID 4
--lambda 0.01 --dT 15 --num-lags 5 --kernel-width 0.5 --prob-zero-removal 0 --prob-remove-samples 0.0 --family gaussian --replicate 5 --ID 5 \" > data/inputs/example/GSD/SINGE/hyperparameters.txt && ln -s data/outputs/example/GSD/SINGE/0/ out0 && octave -q --eval \"CSV = csvread('data/inputs/example/GSD/SINGE/ExpressionData0.csv'); X = sparse(CSV(2:end,1:end-1).'); 
ptime = CSV(2:end,end).'; Kp2.Kp = single(ptime); Kp2.sumKp = single(ptime*X.'); fullKp(1, 75) = Kp2; save('v7','data/inputs/example/GSD/SINGE/ExpressionData0.mat', 'X', 'ptime', 'fullKp'); f = fopen('data/inputs/example/GSD/SINGE/ExpressionData0.csv'); gene_list = strsplit(fgetl(f), ',')(1:end-1).'; fclose(f); save('v7','data/inputs/example/GSD/SINGE/GeneList0.mat', 'gene_list')\" && time -v -o data/outputs/example/GSD/SINGE/time0.txt /usr/local/SINGE/SINGE.sh /usr/local/MATLAB/MATLAB_Runtime/v94 standalone data/inputs/example/GSD/SINGE/ExpressionData0.mat data/inputs/example/GSD/SINGE/GeneList0.mat out0 data/inputs/example/GSD/SINGE/hyperparameters.txt "

It is not immediately apparent where the quoted string error is.

Call stack:

Traceback (most recent call last):
  File "BLRunner.py", line 77, in <module>
    main()
  File "BLRunner.py", line 68, in main
    evaluation.runners[idx].run()
  File "C:\Users\shang\PycharmProjects\Beeline\BLRun\runner.py", line 87, in run
    AlgorithmMapper[self.name](self)
  File "C:\Users\shang\PycharmProjects\Beeline\BLRun\singeRunner.py", line 120, in run
    subprocess.check_call(cmdToRun, shell=True)
  File "C:\Users\shang\anaconda3\envs\Beeline37\lib\subprocess.py", line 341, in check_call
    raise CalledProcessError(retcode, cmd)

[yutuyt01]

Fixed in #110