gitter-lab / SINGE

Gene regulatory network reconstruction from pseudotemporal single-cell gene expression data
MIT License
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Exit if hyperparameters file does not exist #62

Open agitter opened 3 years ago

agitter commented 3 years ago

I was testing SINGE in the Docker image and provided a hyperparameters files that did not exist. However, SINGE continued running with default hyperparameters. SINGE.sh and SINGE.m should exit with an error in this case.

Here is the start of the output:

SINGE operating in standalone mode
standalone mode running GLG tests
grep: input/default_hyperparameters.txt: No such file or directory
hypenum: 1
arg:
sed: can't read input/default_hyperparameters.txt: No such file or directory
------------------------------------------
Setting up environment variables
---
LD_LIBRARY_PATH is .:/usr/local/MATLAB/MATLAB_Runtime/v94/runtime/glnxa64:/usr/l
ocal/MATLAB/MATLAB_Runtime/v94/bin/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v94/
sys/os/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v94/sys/opengl/lib/glnxa64
Creating MATLAB Runtime Cache at location: /tmp/.mcrCache9.4
.max_size not found.  Using default size of 33554432 bytes.
MATLAB Runtime cache extracting component: SINGE_GLG_Te_DE1F291F7B6F70644FA3E2EA
0D86137D
Acquiring MATLAB Runtime cache root-level directory lock... acquire succeeded.
Reading cache index file...
File open failed for /tmp/.mcrCache9.4/.mcr_cache_index
MATLAB Runtime cache: extractDir is /tmp/.mcrCache9.4/SINGE_0

Adding component SINGE_GLG_Te_DE1F291F7B6F70644FA3E2EA0D86137D to the cache.
MATLAB Runtime Cache: performing maintenance...
Processing cached components...
Done with cache maintenance.
Creating component directory: /tmp/.mcrCache9.4/SINGE_0
Acquiring component directory WRITE lock... acquire succeeded.
Extracting component... Component extracted to cache.  Writing creation timestam
p...
Timestamp successfully created.
done.
Downgrading WRITE lock to READ lock... downgrade successful.
Component SINGE_GLG_Te_DE1F291F7B6F70644FA3E2EA0D86137D has successfully been ac
cessed from the cache.
MATLAB Runtime Cache: performing maintenance...
Processing cached components...
Done with cache maintenance.
Checking whether index file /tmp/.mcrCache9.4/.mcr_cache_index needs to be writt
en...
Write is needed.
Writing cache index file: /tmp/.mcrCache9.4/.mcr_cache_index
Writing cache index entry:
SINGE_GLG_Te_DE1F291F7B6F70644FA3E2EA0D86137D
SINGE_0
2519071
2021-Jan-23 21:43:46.477392

params =

  struct with fields:

                   Data: 'input/X_SCODE_data.mat'
                   date: '23-Jan-2021'
                     dT: 1
                 family: 'gaussian'
                     ID: 0
           kernel_width: 2
                 lambda: 0.0100
               num_lags: 15
                 outdir: 'output'
    prob_remove_samples: 0.2000
      prob_zero_removal: 0
              replicate: 0
                     p1: 15
             DateNumber: 738179