Install STRetch with bioconda

[wdecoster]

Hi,

I'm eager to try this tool, but I'm a bit unpleasantly surprised by the installation instructions. I already have anaconda installed - but it seems that it's required to install miniconda again specifically for STRetch (except when I start to hack the install.sh script).

Could STRetch be added to bioconda directly, to solve dependencies? I installed bwa - samtools - picard - bazam using bioconda but the install.sh script is now installing those again...

I recognize this might be the easiest way to make things portable/reproducible, but it's not particularly efficient.

Cheers, Wouter

[hdashnow]

Hi Wouter,

I agree, getting STRetch on bioconda would be a great idea. As you say the current install is wasteful, but designed to make sure the user has an isolated ecosystem of dependancies so there are no nasty surprises from different versions. I think I may have to change the command line interface to match the bioconda requirements though, so it may not be straightforward. I'll look into it for the next release version. If you have any experience with this, I welcome a pull request!

In the meantime, if you want to install dependancies individually (without running the install script), you can certainly do so, then just point to the specific tools in STRetch/pipelines/pipeline_config.groovy (see pipeline_config_template.groovy for the format required). My guess is doing all that will ultimately take longer than just letting the install script run though (it takes about 15-20 minutes depending on your internet speed, including downloading genome references).

Warm regards, Harriet

[wdecoster]

Hi Harriet,

I agree it's not too bad - hit install and grab a coffee. Probably very convenient for new users, too. But uses 19Gbytes now. I have some experience with adding simple executables to bioconda, put a pipeline like this is maybe quite different. Haven't looked into your command line interface and I don't feel confident making suggestions there. One system that interfaces nicely with bioconda is snakemake...

And now is it running and I'm eagerly waiting for the results ;-)

Cheers, Wouter

[hdashnow]

Another bpipe-based tool is working on a bioconda install. I'll see how they manage it and hopefully copy their approach. https://github.com/Oshlack/Clinker/issues/8#issuecomment-438540622