Migrate formulae to Homebrew/core and Brewsci/bio

[sjackman]

Popular or notable formulae can be migrated to Homebrew/core. Bioinformatics formulae can be migrated to Brewsci/bio.

Metrics of popularity (number of installations) and notariety (GitHub watchers, stars, forks)

• Bioinformatics formulae

• All formulae

• [ ] a5

• [ ] abacas

• [ ] abyss-explorer

• [ ] ace-corrector

• [x] adam

• [ ] adapterremoval

• [ ] afra

• [ ] alien-hunter

• [ ] allpaths-lg

• [ ] amos

• [ ] analysis

• [ ] andi

• [ ] anvio

• [x] aragorn

• [x] arcs

• [ ] art

• [x] artemis

• [ ] astral

• [ ] atram

• [x] augustus

• [ ] bam-readcount

• [ ] bam2wig

• [ ] bamhash

• [ ] bamm

• [ ] bamutil

• [x] barrnap

• [ ] bbtools

• [ ] bcalm

• [ ] beagle

• [ ] beast2

• [ ] beetl

• [ ] bfc

• [ ] bioawk

• [ ] biobloomtools

• [ ] biointerchange

• [ ] biomake

• [ ] biopieces

• [ ] blasr

• [ ] blast

• [ ] blat

• [ ] bless

• [ ] bowtie

• [ ] bpipe

• [ ] breseq

• [x] busco

• [x] canu

• [ ] cap3

• [ ] cd-hit

• [ ] cegma

• [ ] celera-assembler

• [ ] centrifuge

• [ ] cerulean

• [ ] circlator

• [ ] clark

• [ ] clonalframeml

• [ ] clonehd

• [x] clustal-omega

• [x] clustal-w

• [ ] corset

• [ ] cutadapt

• [ ] cytoscape

• [ ] daligner

• [ ] dazz_db

• [ ] delly

• [ ] dextractor

• [ ] dida

• [ ] discovar

• [ ] discovardenovo

• [ ] dsk

• [ ] dwgsim

• [x] e-mem

• [ ] edirect

• [ ] ensembl-tools

• [x] exonerate

• [ ] express

• [ ] fasta

• [ ] fastml

• [ ] fastq-tools

• [ ] fasttree

• [ ] fastuniq

• [ ] fastx_toolkit

• [ ] fermi

• [ ] fermi-lite

• [ ] fermi2

• [ ] fermikit

• [x] flash

• [ ] flexbar

• [ ] fqzcomp

• [ ] freebayes

• [ ] freec

• [ ] fsa

• [x] fwdpp

• [ ] gaemr

• [ ] garli

• [ ] gatb

• [x] gatk

• [ ] geneid

• [ ] genewise

• [ ] gingr

• [ ] glimmerhmm

• [ ] gmap-gsnap

• [ ] grabix

• [ ] graphlan

• [ ] gubbins

• [ ] harvest-tools

• [ ] hisat

• [ ] hisat2

• [ ] hlaminer

• [x] hmmer

• [ ] hmmer2

• [ ] htsbox

• [ ] humann2

• [ ] idba

• [ ] igvtools

• [ ] impute2

• [x] infernal

• [ ] iqtree

• [ ] iva

• [ ] jellyfish

• [ ] jellyfish-1.1

• [ ] kaiju

• [x] kat

• [x] kent-tools

• [ ] kmacs

• [x] kmc

• [ ] kmergenie

• [ ] kmerstream

• [ ] kollector

• [ ] kraken

• [ ] last

• [ ] lastz

• [ ] libbigwig

• [ ] libpll

• [x] libsequence

• [x] lighter

• [ ] links-scaffolder

• [ ] lobstr

• [ ] lrsim

• [ ] lsd

• [ ] lumpy-sv

• [ ] macse

• [ ] mafft

• [x] maker

• [ ] mapsembler2

• [ ] maq

• [x] mash

• [ ] masurca

• [ ] mcl

• [ ] megahit

• [x] meme

• [ ] meraculous

• [x] metaphlan

• [ ] methpipe

• [ ] mhap

• [x] minced

• [ ] minia

• [x] miniasm

• [ ] minimap

• [x] mir-prefer

• [ ] mira

• [ ] mitofy

• [ ] mlst

• [x] mothur

• [ ] mrbayes

• [ ] multi-worm-tracker

• [x] mummer

• [ ] muscle

• [x] nanopolish

• [ ] ncbi-c++-toolkit

• [ ] ncl

• [ ] newick-utils

• [ ] newicktools

• [ ] nextflow

• [ ] nonpareil

• [ ] novoalign

• [x] ntcard

• [ ] nxtrim

• [ ] oases

• [ ] ogdraw

• [x] oma

• [ ] orthofinder

• [x] paml

• [ ] pandaseq

• [ ] parsnp

• [ ] pathd8

• [x] pathvisio

• [ ] pbsuite

• [ ] pear

• [ ] phipack

• [ ] phlawd

• [ ] phylip

• [x] phyml

• [ ] phyutility

• [ ] phyx

• [ ] piler

• [ ] pilercr

• [x] pilon

• [ ] platypusvar

• [ ] plink

• [ ] plink2

• [ ] poa

• [ ] populations

• [ ] poretools

• [ ] prokka

• [ ] proteinortho

• [ ] psmc

• [ ] quaff

• [ ] quake

• [ ] quast

• [ ] quest

• [x] quicktree

• [ ] quorum

• [ ] r8s

• [x] racon

• [ ] rampart

• [ ] rapsearch2

• [x] raxml

• [ ] ray

• [ ] rcorrector

• [ ] readseq

• [ ] readsim

• [ ] reapr

• [ ] recon

• [x] repeatmasker

• [ ] repeatmodeler

• [ ] repeatscout

• [x] rmblast

• [ ] rna-star

• [ ] rnammer

• [ ] ropebwt2

• [ ] sailfish

• [x] salmon

• [ ] sambamba

• [ ] samblaster

• [ ] samtools@0.1

• [ ] scarpa

• [ ] sdsl-lite

• [ ] seq-gen

• [ ] seqan

• [ ] seqdb

• [ ] sequel

• [x] sga

• [ ] shrimp

• [ ] sickle

• [ ] simulate-pcr

• [ ] skewer

• [ ] smalt

• [ ] smrtanalysis

• [x] snap

• [ ] snap-aligner

• [x] snoscan

• [ ] snp-sites

• [ ] snpeff

• [ ] soapdenovo

• [ ] sortmerna

• [ ] spaced

• [ ] spici

• [ ] squeezambler

• [ ] ssake

• [ ] stacks

• [x] stringtie

• [ ] swarm

• [ ] tabtk

• [ ] tagdust

• [ ] tasr

• [x] tbl2asn

• [ ] tophat

• [ ] trans-abyss

• [ ] trans_proteomic_pipeline

• [x] transdecoder

• [ ] transrate-tools

• [x] trf

• [ ] trimadap

• [x] trimal

• [x] trimmomatic

• [ ] trinity

• [x] trnascan

• [ ] ucsc-genome-browser

• [x] unicycler

• [ ] uproc

• [ ] vague

• [ ] varscan

• [ ] vcake

• [ ] vcflib

• [ ] velvet

• [ ] velvetoptimiser

• [x] viennarna

• [ ] vsearch

• [ ] vt

• [ ] weblogo

• [ ] wiggletools

• [ ] yaha

[scpeters]

For the formulae that didn't already go into core, is there a way to redirect from homebrew/science to this tap? My colleague was very confused that homebrew/science/matplotlib could not be found, but it would be nice if they could get a notice to check brewsci/science/matplotlib. Maybe this is an issue for brew?

[sjackman]

For the formulae that didn't already go into core, is there a way to redirect from homebrew/science to this tap?

Yes, there is, but the Homebrew maintainers decided not to do that due to security concerns, because Brewsci is maintained by different people than Homebrew. It is posted in the README.md of Homebrew/science now: https://github.com/Homebrew/homebrew-science#readme

[stale[bot]]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs.

[sjackman]

This migration process is well under way, and this checklist is no longer up to date. Closing this tracking issue, as it's no longer useful.