Just going to put it this out here in case you feel like getting involved and/or just practice your PR's in open source project :)
Basically I have quick_install.bash script that I'm using to quick install RNAsik pipeline with conda.
It would be nice if this script had a couple of options e.g install to conda install RNAsik and test to run a testing run of RNAsik. That would full run on a small ish data set.
The sample data to run is the one that is available in the main README
Of course you'd need to do some checking there, for example if RNAsik not available in the environment then one will need to install it first obviously. And so ideally I can use that script with travisCI to both install and test the pipeline.
Just remember that STAR aligner takes fair bit of memory and travisCI does out of memory kill, as expected (don't actually know how big travis machines are). And so perhaps for testing purposes one can use any other aligners e.g hisat2?
Hi world,
Just going to put it this out here in case you feel like getting involved and/or just practice your PR's in open source project :)
Basically I have quick_install.bash script that I'm using to quick install
RNAsikpipeline with conda.It would be nice if this script had a couple of options e.g
installtoconda install RNAsikandtestto run a testing run ofRNAsik. That would full run on a small ish data set.The sample data to run is the one that is available in the main README
Of course you'd need to do some checking there, for example if
RNAsiknot available in the environment then one will need to install it first obviously. And so ideally I can use that script with travisCI to both install and test the pipeline.Just remember that STAR aligner takes fair bit of memory and travisCI does out of memory kill, as expected (don't actually know how big travis machines are). And so perhaps for testing purposes one can use any other aligners e.g hisat2?
Anyway this would be a massive help !
Looking forward to your PR!
Cheers