Simon Ye

Rename executables to avoid conflict with kraken

1

When installing both `krakenuniq` and `kraken` (or `kraken2`) using conda, they both contain same-named executables such as `classify` and `db_sort`. Conda isn't aware of this conflict and overwrites these executables...

Fix krakenhll-download to use versioned accession ids during sorted taxid map creation because there's no stripping of accession versions in the classifier.

Add --db-index, --db-file, --taxonomy, --db-pipe for piped db files

8

This allows loading the database from a pipe instead of a file. This is useful in cloud platforms like AWS/GCP to load the database from an object store download and...

Make build db compatible for OS X

1

Make build db scripts OS X compatible.

Only symlink the binaries that users are supposed to call. This approach (from `homebrew-science`) reduces the number of binaries on `$PATH`

Support zst compressed fastq

1

Feature request to support zstandard compressed fastq e.g. `.fastq.zst`. Its compression performance is much better than gzip.

Simplify debugging recipe builds via `bioconda-utils build-debug`

2

Since `bioconda-utils build` invokes `conda build` in a subprocess, this is mainly feature tracking https://github.com/conda/conda-build/issues/1751. The change here would be simple when it is supported in `conda-build`.

Since the last release of AMOS was in 2011 on sourceforge https://sourceforge.net/projects/amos/, I was wondering if this can be considered "official-enough" seeing as how it was updated much more recently.