Anders Sune Pedersen

> Hi @asp8200, Thanks for the reply! I want to avoid docker/singularity so I chose conda. This seems to be a conda specific issue. I faced the same error as...

> Hi @vishramt7 and @asp8200, You're right that the conda part isn't that well tested as we've had issues getting some tools to run with conda, the SNV/INDEL caller deepvariant...

So I tried setting `params.variant_caller` to blank, but the pipeline eventually failed with: ``` Caused by: Process `NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat)` terminated with an error exit status (127) Command executed: paste

@vishramt7 : Since you got conda on your system, perhaps you can just conda-install singularity? (That seems to work on my system.)

> Thanks for going through this. I'd prefer to stick to nim < 2 for this as I haven't tested fully on nim 2.0+. And the OSX build would be...

> probably the best way is to get the binaries from here: https://github.com/nim-lang/nightlies/releases/tag/latest-version-1-6 in the recipe Tried something. From the logs from the failing osx-build: ``` BIOCONDA INFO (OUT) Downloading...

> is it getting unzipped and installed by some bioconda magic? I would think you'd need to unzip and then update the path to point to the bin directory. I'm...

Got the tests passing by installing [osx-release](https://github.com/nim-lang/nightlies/releases/download/latest-version-1-6/macosx_x64.tar.xz) of nim v1.6 in the osx-part of `build.sh`-file. Seems like a pretty hacky solution 🤔 Also, I don't understand how the linux-test can...

Just tested this on both linux and macOs by conda-installing: ``` mosdepth 0.3.8 h212548b_0 bioconda ``` and running: ``` mosdepth -n --fast-mode --by 500 sample.wgs test.paired_end.sorted.bam ``` It worked fine...

As the failing job should be running in singularity, the presence of `sed` and `cat` on your HPC should be irrelevant. I suspect that there was some glitch on your...