Nathan Sheffield

Instead of collections, loading a LOLA PEP should allow a sample attribute value filter. it's more flexible because it can filter out files from multiple collections.

PEP file read caching

2

We should make sure the PEP loading function has the same caching capability the current loadRegionDB function has: https://github.com/joseverdezoto/LOLA/blob/127efbb6b273a526d64dd10a3a71460012288653/R/loadRegionDB.R#L288-L299

Suggestion: move description column further to the left, since this is sometimes the only information about the comparison.

reading zipped bed files

1

Christoph made a suggestion that LOLA could understand a zipped archive of bed files, in addition to the current custom database parsing.

The checkUniverseAppropriateness is a bit confusing, with no real recommendations. I need to clean it up a little bit to make it more universal and useful, and formalize some of...

sra-tools repository is missing curl dependency

1

fastq-dump requires curl, but the sra-tools container doesn't contain it, so fastq-dump can't run: The container I'm using is: quay.io/biocontainers/sra-tools:2.10.0--pl526he1b5a44_0 Here's what you get: ``` docker run --rm --init \...

bigwigcat container is missing dependency

3

The latest ucsc-bigwigcat container is missing a shared object: ```docker run --rm \ > quay.io/biocontainers/ucsc-bigwigcat:377--h199ee4e_0 bigWigCat bigWigCat: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such...

Thanks for clustermq, I haven't used it yet but it looks very useful. I have written a package with similar goals in python called [divvy](http://divvy.databio.org). It strikes me that it...

Restrict search to certain table columns

1

I have a table with a few invariant columns holding action buttons. I'd like the search to ignore these columns, because they don't provide any row specificity. Is it possible...

I'm wondering if there's a way to do something like the `--max-depth` option but with the `duc xml` command. The use case is that I'd like to see an xml...