Stuck on an issue?

Lightrun Answers was designed to reduce the constant googling that comes with debugging 3rd party libraries. It collects links to all the places you might be looking at while hunting down a tough bug.

And, if you’re still stuck at the end, we’re happy to hop on a call to see how we can help out.

Gzip does not work in BioContainers Docker container (missing library)

See original GitHub issue

Seems 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)

Top GitHub Comments

1reaction

bernt-matthiascommented, Feb 12, 2021

… 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.

1reaction

martensoncommented, Feb 11, 2021

@caetera I think the bioconda build should be fixed (and package updated) with https://github.com/bioconda/bioconda-recipes/pull/26729

Top Results From Across the Web

Own Docker does not work (#461) · Issues · ezlab / busco

Hi, I try to set up my own Docker container bc/ I want to add also further dependencies. However, my default way of...

Nginx gzip compression not working despite following ...

The Issue. I'm at wits end so decided to post a query, I am attempting to set up gzip compression on an nginx...

docker load

Load an image or repository from a tar archive (even if compressed with gzip, bzip2, or xz) from a file or STDIN. It...

Singularity Containers | SCINet | USDA Scientific Computing ...

Containers are self-contained application execution environments that contain all necessary software to run an application or workflow, so you don't need to ...

Quay Container Registry

Hosted private Docker repositories. Includes full user management and history. Free for public repositories.