add continuous integration with travis

sanjaynagi / rna-seq-pop

Snakemake workflow for Illumina RNA-sequencing experiments - extract population genomic signals from RNA-Seq data

https://sanjaynagi.github.io/rna-seq-pop/

MIT License

18 stars 7 forks source link

add continuous integration with travis #10

Closed sanjaynagi closed 3 years ago

sanjaynagi commented 3 years ago

Need to specify a .travis.yaml which runs snakemake on .test/
Build set of test data in .test/

sanjaynagi commented 3 years ago

test set built. Only problem now is that running snakemake in the .test folder means scripts not provided through the "script:" directive are no longer relative to the working directory. this is important for snpEff, which is not yet done through conda due to a db error with current conda version 4.3.1. also with baseParser, a separate rule could be made for this so it can be used as a 'script'

sanjaynagi commented 3 years ago

DONE. test data was made by using the X chrom only, and subsampling the bam files. data is stored in .test/