Comments (8)
Based on the MATLAB glmnet download and revision history pages, it does not seem to be maintained. That limits what we can do to fix this within the SINGE source.
Is Docker an option for you? I expect our Docker image will run in a newer Ubuntu system.
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Thank you for your response @agitter . I will try the Docker image and will follow up.
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@agitter I have installed Docker and pulled the image, but there seems to be a problem with the command in the README. When I run docker run -v $(pwd):/SINGE -w /SINGE agitter/singe:0.4.0 standalone data1/X_SCODE_data.mat data1/gene_list.mat Output default_hyperparameters.txt
, I get the error Unable to read file 'data1/gene_list.mat'. No such file or directory.
This happens even when I use the full path to gene_list.mat
.
Shall I write this up as a separate issue?
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We can discuss the Docker issue here. I don't see a way to resolve the root cause of the dependency issue without help from the MATLAB glmnet team, and they do not seem active.
When I first tried running the Docker image I ran into the same error you did. This indicates that the Docker volume mount failed. I'm currently on Windows running in the Git for Windows, so I needed to use workarounds (docker-archive/toolbox#673 (comment)) to fix the file paths. Those should not be necessay with Ubuntu. The final command that worked for me is
winpty docker run -v /$(pwd)://SINGE -w //SINGE agitter/singe:0.5.1 standalone data1/X_SCODE_data.mat data1/gene_list.mat Output default_hyperparameters.txt
The next thing to try would be running the container interactively with -it
to see if the volume mounting worked. For me I ran
winpty docker run -it -v /$(pwd)://SINGE -w //SINGE --entrypoint "//bin/bash" agitter/singe:0.5.1
but on Ubuntu you should not need the winpty
or the //
to escape absolute paths. If that doesn't work, we can see what might be going wrong on your system.
Note that I'm also using the latest version of the Docker image, 0.5.1.
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The first command did not work for me even after upgrading to 0.5.1, but the second command (running the container iteratively) appears to have worked:
(base) root@a44f5f7ea678:/SINGE#
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If the second interactive command works, that suggests the image works correctly but path mounting is the problem. After you launch the container interactively can you see any mounted files? I see
(base) root@ef1d6d7c09fc:/SINGE# ls
LICENSE TempMat_35.mat data1 glmnet_matlab.zip run_SINGE_GLG_Test.sh
NEWS.md TempMat_55.mat data2 readme_SINGE_Aggregate.txt run_SINGE_GLG_Test_mac.sh
Output TempMat_64.mat data3 readme_SINGE_Aggregate_mac.txt scripts
README.md USAGE.md data_bifurcated readme_SINGE_GLG_Test.txt tests
SINGE.sh code default_hyperparameters.txt readme_SINGE_GLG_Test_mac.txt winpty.exe.stackdump
SINGE_Example.m compile_SINGE.sh docker run_SINGE_Aggregate.sh
TempMat_15.mat compile_SINGE_mac.sh glmnet_matlab run_SINGE_Aggregate_mac.sh
(base) root@ef1d6d7c09fc:/SINGE# ls data1/
README.md X_BranchTest.mat X_SCODE_data.mat X_regix_test.mat gene_list.mat
Are you running the command from the root of this GitHub repository, the SINGE
directory? The command expects that data1/
is a subdirectory of the working directory where you run the command from.
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Thank you for your help! It looks like it was just an issue with the working directory. After changing the working directory, I was able to see the mounted files and to run the command without any errors.
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Excellent, I'm glad that is working. Let us know if you have problems running the Docker container with your own data.
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Related Issues (20)
- Add user guidelines to the readme and manuscript HOT 1
- Glmnet mex errors for large datasets HOT 1
- Automatically match compiled binary to versions of the MATLAB files HOT 2
- Additional documentation for standalone script
- Consistent argument ordering HOT 1
- Docker build error HOT 2
- Switch to standard YYYY-MM-DD dates
- Automating SINGE for branching trajectories HOT 2
- libgfortran issue on macOS HOT 1
- Allowing file separators in outdir parameter
- Support input mat files from Octave HOT 1
- Delete Temporary mat files at the end of run_SINGE_GLG_test.sh HOT 4
- Exit if hyperparameters file does not exist
- Reference GRN for ESC to endoderm differentiation HOT 5
- Error when running with a single regulator index
- Matlab crash while glmnetMex.mexmaci64 was running HOT 15
- Is it possible to have a more detailed intro for the inputs in 'mat' format ? HOT 3
- Fix Docker image build failures HOT 3
- Switch to setup-matlab action for macOS tests
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