PaulBrack / Yamato

SWATH-QC metrics
Apache License 2.0
1 stars 1 forks source link

Not working on any non-bash shell #109

Closed mwalzer closed 4 years ago

mwalzer commented 4 years ago
Yamato.Console: line 1: can't create ??@@: Read-only file system
Yamato.Console: line 1: ELF: not found
Yamato.Console: line 2: syntax error: unexpected word (expecting ")")
mwalzer commented 4 years ago

tested alpine's ash so far only

PaulBrack commented 4 years ago

This seems like an environment issue - not sure I know how to resolve this

mwalzer commented 4 years ago

@Ozzard any experience with non-bash .dotnet? Would be a shame if the standalone would be limited to some distros only. Worse if root cause is in the env, because that would mean that in other bash based OS it could not work as well. I can't help more as I know too little about the build process of yamato. (: limited as in not without serious efforts to install )

Ozzard commented 4 years ago

@mwalzer Could you send me your Dockerfile (or point to it on here if it's committed) and I'll take a look? Could you also send me the command line that you're giving to ash? Alpine is a supported platform for .Net Core 2.1+ (Yamato is on 2.2) and there are base containers with the .Net Core prereqs installed available from Microsoft, so I suspect all of our experimentation so far hasn't quite worked!

mwalzer commented 4 years ago

Sure @Ozzard here you go: yamato.Dockerfile.txt yamato.sdef.txt yamato_alpine.Dockerfile.txt yamato_alpine.sdef.txt

I added both the Ubuntu version as well as the Alpine version and both also as singularity container definitions in case that might be of any interest (IMO singularity is superior). You might need to remove the '.txt' suffix. I had to add that otherwise GitHub would not have let me attach them to the issue.

Ozzard commented 4 years ago

I believe this is addressed by #119. This uses Microsoft's dependency base image (based on Debian) and builds it up. Note that the Alpine image could not work with the standard Linux build - see https://github.com/dotnet/core/issues/1689 for the gory details. We should work on getting a non-standard standalone build made for Alpine, as it's a much smaller image.

Built versions of v1.0.0-b available at https://hub.docker.com/r/ozzard/yamato - please test

mwalzer commented 4 years ago

the container seems to have a blank entry point (Yamato.Console w/o parameters). I had to override it with --entrypoint=/bin/bash otherwise I wouldn't know how to convey my input parameter values