Torsten Seemann
Torsten Seemann
@pfaucon it would be really helpful if you could make a release at https://github.com/pfaucon/PBSIM-PacBio-Simulator/releases I am a packager for Homebrew Science.
@pfaucon annual reminder - please add a tag or make a release so we can package this software.
No i am building from the `Releases` section. This is the only way to build packages for conda and brew. Are you saying it is not possible to actually build...
I had commenced a `Homebrew` package but there was a few `Makefile` issues that made it challenging. Moving to `pkg-config` would help, or `autotools` (but painful). It's still a goal...
@johnlees yeah, @slugger70 reminded me of the old build system that Conda uses which doesn't have C++11 or C++14 support yet :(
@schultzm thanks! so the error is misleading. parser issues. i will patch my tests.
At one point I had samtools 1.5 installed, and running it without options had the message `Using htslib 1.4`. Would that have caused issues? (I've since brought them into sync)
Are you able to add a `--java` option or honour a `MTBSEQ_JAVA` environment variable? As Java 9 is now standard.
I would add in "get community to try it for a while" before JOSS.
The code is https://github.com/sanger-pathogens/seroba/blob/37a57375f59d471d75da4afd4f0e6518520f1b79/seroba/tasks/sero_run.py#L10-L12 Is this operating on the read FILENAMES or the READ IDs ? Mine are `NNNN-NNNNN_S33_R2_001.fastq.gz` and R2