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sheynkman-lab / Long-Read-Proteogenomics

A workflow for enhanced protein isoform detection through integration of long-read RNA-seq and mass spectrometry-based proteomics.
MIT License
38 stars 16 forks source link

Nextflow MetaMorpheus #126

Closed bj8th closed 3 years ago

bj8th commented 3 years ago

An error arises when trying to implement the MetaMorpheus. This error was seen both in the latest and proteogenomic tags of the MetaMorpheus dockerfile. When running dockerfile as described in issue 94 the image runs as expected. Issue found even when script is empty, pointing to issue coming from when nextflow tries to connect to image.

Error code :

Error executing process > 'metamorpheus'

Caused by: Process metamorpheus terminated with an error exit status (127)

Command executed:

Command exit status: 127

Command output: (empty)

Command error: docker: Error response from daemon: OCI runtime create failed: container_linux.go:349: starting container process caused "exec: \"/bin/bash\": stat /bin/bash: no such file or directory": unknown.

cgpu commented 3 years ago

We can modify the MetaMorpheous Dockerfile a bit to copy the executable in a predictable path in the container.

.
.
.
dotnet /metamorpheus/CMD.dll
COPY metamorpheus/  /

@rmillikin added this info for building from source https://ci.appveyor.com/project/smith-chem-wisc/metamorpheus/builds/37176430.

We can use this and build-push the container to gsheynkman DockerHub.