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Description
Hi, I have met a problem in msconvet with singularity in linux,here are my processing:
Fisrt i pull a docker from docker hub and convert to singularity:
singularity pull docker://chambm/pwiz-skyline-i-agree-to-the-vendor-licenses
Then i used this singularity file to convert my ms data, the data formart is .raw(also i try another ms format file: .wiff, .wiff2, .d):
singularity exec --cleanenv -S /mywineprefix/ --writable-tmpfs -B /mydata/input:/data -B /mydata/output:/output /singularity/pwiz-skyline-i-agree-to-the-vendor-licenses_latest.sif mywine msconvert --mgf --zlib --64 --filter "peakPicking true 1-" "zeroSamples removeExtra" /data/*.raw -o /output
(also i try this code: singularity exec --cleanenv -B ~:/mywineprefix -B /mydata/input:/data -B /mydata/output:/output /singularity/pwiz-skyline-i-agree-to-the-vendor-licenses_latest.sif mywine msconvert --mgf --zlib --64 --filter "peakPicking true 1-" "zeroSamples removeExtra" /data/*.raw -o /output)
But it's error:[RawFileImpl::getInstrumentMethods()] Access to the path 'C:\users\root\Temp\tmp1e7.tmp' is denied.
I have try many ways to make it run,but it failed; Any one can help me with this?
and i can't use root in my linux
I used a old protoewizard of docker version in 2020, and in same linux ,it's worked before,but this year, i found its error,and i download the latest version, also error above ,the msconvert.sif is named by myself:
my old code: singularity exec -S /mywineprefix/ -B /mydata/input:/data -B /mydata/output:/output /singularity/msconvert.sif mywine msconvert --mgf --zlib --64 --filter "peakPicking true 1-"
My linux information:
- CentOS 7
- singularity version 3.8.7(3.1.0, 3.7.3)