Gzip does not work in BioContainers Docker container (missing library)
See original GitHub issueSeems like the container is missing libMonoPosixHelper.so
❯ docker run --rm -it -v $(pwd):/workdir -w /workdir quay.io/biocontainers/thermorawfileparser:1.2.3--1 thermorawfileparser -i data/mzml/A1.raw --gzip
2020-10-28 14:19:05 INFO Started parsing data/mzml/A1.raw
2020-10-28 14:19:08 ERROR An unexpected error occured:
2020-10-28 14:19:08 ERROR System.DllNotFoundException: /usr/local/lib/../lib/libMonoPosixHelper.so
at (wrapper managed-to-native) System.IO.Compression.DeflateStreamNative.CreateZStream(System.IO.Compression.CompressionMode,bool,System.IO.Compression.DeflateStreamNative/UnmanagedReadOrWrite,intptr)
at System.IO.Compression.DeflateStreamNative.Create (System.IO.Stream compressedStream, System.IO.Compression.CompressionMode mode, System.Boolean gzip) [0x0004a] in <6e58314266ea48d58d73486babe33a96>:0
at System.IO.Compression.DeflateStream..ctor (System.IO.Stream compressedStream, System.IO.Compression.CompressionMode mode, System.Boolean leaveOpen, System.Boolean gzip) [0x0002d] in <6e58314266ea48d58d73486babe33a96>:0
at System.IO.Compression.DeflateStream..ctor (System.IO.Stream stream, System.IO.Compression.CompressionMode mode, System.Boolean leaveOpen, System.Int32 windowsBits) [0x00000] in <6e58314266ea48d58d73486babe33a96>:0
at (wrapper remoting-invoke-with-check) System.IO.Compression.DeflateStream..ctor(System.IO.Stream,System.IO.Compression.CompressionMode,bool,int)
at System.IO.Compression.GZipStream..ctor (System.IO.Stream stream, System.IO.Compression.CompressionMode mode, System.Boolean leaveOpen) [0x00006] in <6e58314266ea48d58d73486babe33a96>:0
at System.IO.Compression.GZipStream..ctor (System.IO.Stream stream, System.IO.Compression.CompressionMode mode) [0x00000] in <6e58314266ea48d58d73486babe33a96>:0
at (wrapper remoting-invoke-with-check) System.IO.Compression.GZipStream..ctor(System.IO.Stream,System.IO.Compression.CompressionMode)
at ThermoRawFileParser.Writer.SpectrumWriter.ConfigureWriter (System.String extension) [0x000ad] in <41119cf2ddce4ea78f6356000798cca0>:0
at ThermoRawFileParser.Writer.MzMlSpectrumWriter.Write (ThermoFisher.CommonCore.Data.Interfaces.IRawDataPlus rawFile, System.Int32 firstScanNumber, System.Int32 lastScanNumber) [0x00026] in <41119cf2ddce4ea78f6356000798cca0>:0
at ThermoRawFileParser.RawFileParser.ProcessFile (ThermoRawFileParser.ParseInput parseInput) [0x0016a] in <41119cf2ddce4ea78f6356000798cca0>:0
at ThermoRawFileParser.RawFileParser.Parse (ThermoRawFileParser.ParseInput parseInput) [0x00176] in <41119cf2ddce4ea78f6356000798cca0>:0
at ThermoRawFileParser.MainClass.RegularParametersParsing (System.String[] args) [0x008a0] in <41119cf2ddce4ea78f6356000798cca0>:0
Issue Analytics
- State:
- Created 3 years ago
- Comments:10 (4 by maintainers)
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… and the follow up https://github.com/bioconda/bioconda-recipes/pull/26756 which solved the issue mentioned in the first message of the thread for me.
@caetera I think the bioconda build should be fixed (and package updated) with https://github.com/bioconda/bioconda-recipes/pull/26729