Pat Schloss

Any interest in changing scripts from python to bash?

9

Admittedly, I'm not a pythonista, but I wonder whether there would be value in using bash versions of the three python scripts. For whatever reason, I'm running into problems with...

The files in the `data` repository have `\r` line endings. This pull request replaces those with `\n` line endings. Addresses issue #284

I've been using the data from your [comma survey](https://raw.githubusercontent.com/fivethirtyeight/data/master/comma-survey/comma-survey.csv) for teaching R and some recent changes to the [R packages we use](https://github.com/r-lib/vroom/issues/360) make the line endings in your file problematic....

Is code highlighting possible?

1

Is it possible to get code highlighting applied by default to output from `blastula`? If I do something like this... ``` --- title: test output: blastula::blastula_email highlight: pygments --- ```{r}...

fastq_pctid option for fastq_mergepairs

1

I'm trying to replicate read pair assembly that I've tested with `usearch` and want to replicate with `vsearch`. In the [`usearch`](https://www.drive5.com/usearch/manual/merge_options.html) documentation, it suggests raising `fastq_pctid` and `fastq_maxdiffs` from the...

This PR addresses issue #78 where `lib_path` is empty when building in conda because `.Platform$dynlib.ext` is `.dylib` rather than `.so`. Not sure how to have `lib_path` fall back to `libconnection.dylib`...

Blank lib_path in R/zzz.R in Mac OS X conda environment

1

I've been trying to create a conda recipe to build `archive`. After much sleuthing, I tracked down an issue with Lines [2](https://github.com/r-lib/archive/blob/30eb4d6c649aed8df89167c9b773865645e339d7/R/zzz.R#L2) and [9](https://github.com/r-lib/archive/blob/30eb4d6c649aed8df89167c9b773865645e339d7/R/zzz.R#L9) in `R/zzz.R` ``` lib_path 4.1) inside...

I'm trying to read the contents of an archive (~3GB) with many little files in it (~100k) without decompressing the archive. I don't have the ability to reconfigure what the...

Adding r-archive R package

11

Checklist - [x] Title of this PR is meaningful: e.g. "Adding my_nifty_package", not "updated meta.yaml". - [x] License file is packaged (see [here](https://github.com/conda-forge/staged-recipes/blob/5eddbd7fc9d1502169089da06c3688d9759be978/recipes/example/meta.yaml#L64-L73) for an example). - [x] Source is...

Sample IDs in fastq data

2

I just took a quick look at your fastq files in the `fastq-spragueuBiomeJan2015` folder. A couple things jump out at me... 1. Do you know which body sites these are...