Shaun Jackman
Shaun Jackman
Just a long shot question, should the `.travis.yml` variable perhaps be `addons.artifacts.s3_region` rather than `addons.s3_region` as the documentation indicates?
> Put stuff into the /: prefix... I'm seeing this as well. See #67
No. I just looked for the artifacts in the directory named `:`.
Thanks, Leo. I ended up moving to Circle CI, because it's not possible (as far as I know) to upload artifacts to S3 from a fork pull request with Travis...
assemblerflow.py assembles Nextflow pipelines of modular tools for genome assembly. https://github.com/ODiogoSilva/assemblerflow#readme For example ```sh assemblerflow.py build -t "trimmomatic fastqc skesa pilon" -o my_pipeline.nf nextflow run my_pipeline.nf --fastq path/reads.fastq ```
Shovill is a good example of an assembly pipeline. https://github.com/tseemann/shovill#main-steps I wonder whether the subcomponents of SPAdes could be separated.
It's usually a matter of using `$srcdir`, `$builddir`, `$top_srcdir`, and `$top_builddir` as appropriate in the `Makefile.am`.
`walaj/htslib` doesn't use `automake`. There's no `Makefile.am` nor `Makefile.in` file, just a bare `Makefile`. It may be possible to hack it up to get it working, but it may not...
Any thoughts on this feature request? My motivation is that `longranger wgs` takes ~3 days to run (for this particular data set), and `bwa mem` takes ~1.5 hours to run...
No apologies needed. Thanks for your response, Jeremiah. Yep, that's what I'm thinking. It should work on a BAM file sorted by target position. It can keep a priority queue...