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brewsci / homebrew-bio

:beer::microscope: Bioinformatics formulae for the Homebrew package manager (macOS and Linux)
http://brewsci.github.io/homebrew-bio
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Updates #1

Open sjackman opened 6 years ago

sjackman commented 6 years ago

Subscribe to this issue to receive updates about Brewsci/bio.

sjackman commented 6 years ago

🎉 New formula arcs in Brewsci/bio for Linux and macOS! 🍺 brew install brewsci/bio/arcs 🏡 https://github.com/bcgsc/arcs 📖 https://doi.org/10.1093/bioinformatics/btx675

sjackman commented 6 years ago

🎉 New formula minimap2 in Brewsci/bio for Linux and macOS! 🍺 brew install brewsci/bio/minimap2 🏡 https://github.com/lh3/minimap2 📖 https://arxiv.org/abs/1708.01492

sjackman commented 6 years ago

🎉 New formula fastani in Brewsci/bio for Linux and macOS! 🍺 brew install brewsci/bio/fastani 🏡 https://github.com/ParBLiSS/FastANI 📖 https://doi.org/10.1101/225342

sjackman commented 6 years ago

🎉 New formula tbl2asn in Brewsci/bio for Linux and macOS! 🍺 brew install brewsci/bio/tbl2asn 🏡 https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/

sjackman commented 6 years ago

🎉 New formula miniasm in Brewsci/bio for Linux and macOS! 🍺 brew install brewsci/bio/miniasm 🏡 https://github.com/lh3/miniasm 📖 https://doi.org/10.1093/bioinformatics/btw152

sjackman commented 6 years ago

🎉 New formula canu in Brewsci/bio for Linux and macOS! 🍺 brew install brewsci/bio/canu 🏡 https://canu.readthedocs.io/ 📖 https://doi.org/10.1101/gr.215087.116

sjackman commented 6 years ago

🎉 New formula busco in Brewsci/bio for Linux and macOS! 🍺 brew install brewsci/bio/busco 🏡 http://busco.ezlab.org 📖 https://doi.org/10.1093/bioinformatics/btv351

sjackman commented 6 years ago

🎉 New formula gepard in Brewsci/bio for Linux and macOS! 🍺 brew install brewsci/bio/gepard 🏡 http://cube.univie.ac.at/gepard 📖 https://doi.org/10.1093/bioinformatics/btm039

sjackman commented 6 years ago

🎉 New formula gatk in Brewsci/bio for Linux and MacOS! 🍺 brew install brewsci/bio/gatk 🏠 https://software.broadinstitute.org/gatk/ 📖 https://doi.org/10.1101/gr.107524.110

sjackman commented 6 years ago

🎉 New formula metaphlan in Brewsci/bio for Linux and MacOS! 🍺 brew install brewsci/bio/metaphlan 🏠 https://huttenhower.sph.harvard.edu/metaphlan 📖 https://doi.org/10.1038/nmeth.2066

sjackman commented 6 years ago

🎉 New formula fwdpp in Brewsci/bio for Linux and MacOS! 🍺 brew install brewsci/bio/fwdpp 🏠 https://molpopgen.github.io/fwdpp/ 📖 https://doi.org/10.1534/genetics.114.165019

sjackman commented 6 years ago

🎉 New formula pathvisio in Brewsci/bio for Linux and MacOS! 🍺 brew install brewsci/bio/pathvisio 🏡 https://www.pathvisio.org/ 📖 https://doi.org/10.1371/journal.pcbi.1004085

sjackman commented 6 years ago

🎉 New formula kat in Brewsci/bio for Linux and MacOS! 🍺 brew install brewsci/bio/kat 🏡 https://github.com/TGAC/KAT 📖 https://doi.org/10.1093/bioinformatics/btw663

tseemann commented 6 years ago

🎉 New formula ascp in Brewsci/bio for Linux and MacOS! 🍺 brew install brewsci/bio/ascp 🏠 https://asperasoft.com/

tseemann commented 6 years ago

🎉 New formula figtree in Brewsci/bio for Linux and MacOS! 🍺 brew install brewsci/bio/figtree 🏠 http://tree.bio.ed.ac.uk/software/figtree/

tseemann commented 6 years ago

🎉 New formula gepard in Brewsci/bio for Linux and MacOS! 🍺 brew install brewsci/bio/gepard 🏠 http://cube.univie.ac.at/gepard 📖 https://doi.org/10.1093/bioinformatics/btm039

tseemann commented 6 years ago

🎉 New formula blast-legacy in Brewsci/bio for Linux and MacOS! 🍺 brew install brewsci/bio/blast-legacy :book: https://doi.org/10.1093/nar/25.17.3389

tseemann commented 6 years ago

🎉 New formula kr in Brewsci/bio for Linux and MacOS! 🍺 brew install brewsci/bio/kr 🏠 http://guanine.evolbio.mpg.de/cgi-bin/kr2/kr.cgi.pl

tseemann commented 6 years ago

🎉 New formula light-assembler in Brewsci/bio for Linux and MacOS! 🍺 brew install brewsci/bio/light-assembler 🏠 https://github.com/SaraEl-Metwally/LightAssembler 📖 https://doi.org/10.1093/bioinformatics/btw470

tseemann commented 6 years ago

🎉 New formula ispcr in Brewsci/bio for Linux and MacOS! 🍺 brew install brewsci/bio/ispcr 🏠 http://hgwdev.cse.ucsc.edu/~kent/src/

tseemann commented 6 years ago

🎉 New formula jspecies in Brewsci/bio for Linux and MacOS! 🍺 brew install brewsci/bio/jspecies 🏠 https://imedea.uib-csic.es/jspecies/index.html 📖 https://doi.org/10.1073/pnas.0906412106

tseemann commented 6 years ago

🎉 New formula lofreq in Brewsci/bio for Linux and MacOS! 🍺 brew install brewsci/bio/lofreq 🏠 https://csb5.github.io/lofreq/ 📖 https://10.1093/nar/gks918

tseemann commented 6 years ago

🎉 New formula snp-dists in Brewsci/bio for Linux and MacOS! 🍺 brew install brewsci/bio/snp-dists 🏠 https://github.com/tseemann/snp-dists

sjackman commented 6 years ago

🎉 New formula nanopolish in Brewsci/bio for Linux and MacOS! 🍺 brew install brewsci/bio/nanopolish 🏠 https://github.com/jts/nanopolish 📖 https://doi.org/10.1038/nmeth.3444

tseemann commented 6 years ago

🎉 New formula trimmomatic in Brewsci/bio for Linux and MacOS! 🍺 brew install brewsci/bio/trimmomatic 🏠 http://www.usadellab.org/cms/?page=trimmomatic 📖 https://doi.org/10.1093/bioinformatics/btu170

tseemann commented 6 years ago

🎉 New formula panito in Brewsci/bio for Linux and MacOS! 🍺 brew install brewsci/bio/panito 🏠 https://github.com/sanger-pathogens/panito

sjackman commented 6 years ago

🎉 New formula salmon in Brewsci/bio for Linux and MacOS! 🍺 brew install brewsci/bio/salmon 🏠 https://github.com/COMBINE-lab/salmon 📖 https://doi.org/10.1038/nmeth.4197

tseemann commented 6 years ago

🎉 New formula gzstream in Brewsci/bio for Linux and MacOS! 🍺 brew install brewsci/bio/gzstream 🏠 https://www.cs.unc.edu/Research/compgeom/gzstream/

sjackman commented 6 years ago

🎉 New formula sga in Brewsci/bio for Linux and MacOS! 🍺 brew install brewsci/bio/sga 🏠 https://github.com/jts/sga 📖 https://doi.org/10.1101/gr.126953.111

sjackman commented 6 years ago

🎉 New formula racon in Brewsci/bio for Linux and MacOS! 🍺 brew install brewsci/bio/racon 🏠 https://github.com/isovic/racon 📖 https://doi.org/10.1101/gr.214270.116

sjackman commented 6 years ago

🎉 New formula gfakluge in Brewsci/bio for Linux and MacOS! 🍺 brew install brewsci/bio/gfakluge 🏡 https://github.com/edawson/gfakluge

tseemann commented 6 years ago

🎉 New formula bandage in Brewsci/bio for Linux! 🍺 brew install brewsci/bio/bandage 🏠 https://rrwick.github.io/Bandage/ 📖 https://doi.org/10.1093/bioinformatics/btv383

tseemann commented 6 years ago

🎉 New formula flash in Brewsci/bio for Linux and MacOS! 🍺 brew install brewsci/bio/brewsci/bio/flash 🏠 https://ccb.jhu.edu/software/FLASH/ 📖 https://doi.org/10.1093/bioinformatics/btr507

sjackman commented 6 years ago

🎉 New formula lighter in Brewsci/bio for Linux and MacOS! 🍺 brew install brewsci/bio/lighter 🏡 https://github.com/mourisl/Lighter 📖 https://doi.org/10.1186/s13059-014-0509-9

sjackman commented 6 years ago

🎉 New formula ntcard in Brewsci/bio for Linux and MacOS! 🍺 brew install brewsci/bio/ntcard 🏠 https://github.com/bcgsc/ntCard 📖 https://doi.org/10.1093/bioinformatics/btw832

tseemann commented 6 years ago

🎉 New formula mash in Brewsci/bio for Linux and MacOS! 🍺 brew install brewsci/bio/mash 🏠 https://github.com/marbl/Mash 📖 https://doi.org/10.1186/s13059-016-0997-x

tseemann commented 6 years ago

🎉 New formula kmc in Brewsci/bio for Linux! 🍺 brew install brewsci/bio/kmc 🏠 http://sun.aei.polsl.pl/kmc/ 📖 https://doi.org/10.1093/bioinformatics/btv022

(the macos failure needs to be revisited)

tseemann commented 6 years ago

🎉 New formula shovill in Brewsci/bio for Linux and MacOS! 🍺 brew install brewsci/bio/shovill 🏠 https://github.com/tseemann/shovill

(not really for MacOS as kmc is linux only)

sjackman commented 6 years ago

🎉 New formula trf in Brewsci/bio for Linux and MacOS! 🍺 brew install brewsci/bio/trf 🏠 https://tandem.bu.edu/trf/trf.html 📖 https://doi.org/10.1093/nar/27.2.573

sjackman commented 6 years ago

🎉 New formula rmblast in Brewsci/bio for Linux and MacOS! 🍺 brew install brewsci/bio/rmblast 🏠 http://www.repeatmasker.org/RMBlast.html

sjackman commented 6 years ago

🎉 New formula repeatmasker in Brewsci/bio for Linux and MacOS! 🍺 brew install brewsci/bio/repeatmasker 🏡 http://www.repeatmasker.org/

tseemann commented 6 years ago

🎉 New formula infernal in Brewsci/bio for Linux and MacOS! 🍺 brew install brewsci/bio/infernal 🏠 http://eddylab.org/infernal/ 📖 https://doi.org/10.1093/bioinformatics/btp157

tseemann commented 6 years ago

🎉 New formula easel in Brewsci/bio for Linux and MacOS! 🍺 brew install brewsci/bio/easel 🏠 http://eddylab.org/infernal/

tseemann commented 6 years ago

🎉 New formula squeakr in Brewsci/bio for Linux and MacOS! 🍺 brew install brewsci/bio/squeakr 🏠 https://github.com/splatlab/squeakr 📖 https://dx.doi.org/10.1093/bioinformatics/btx636

tseemann commented 6 years ago

🎉 New formula minced in Brewsci/bio for Linux and MacOS! 🍺 brew install brewsci/bio/minced 🏠 https://github.com/ctSkennerton/minced

tseemann commented 6 years ago

🎉 New formula aragorn in Brewsci/bio for Linux and MacOS! 🍺 brew install brewsci/bio/aragorn 🏠 http://mbio-serv2.mbioekol.lu.se/ARAGORN/ 📖 https://doi.org/10.1093/nar/gkh152

tseemann commented 6 years ago

🎉 New formula barrnap in Brewsci/bio for Linux and MacOS! 🍺 brew install brewsci/bio/barrnap 🏠 https://github.com/tseemann/barrnap

tseemann commented 6 years ago

🎉 New formula magic-blast in Brewsci/bio for Linux and MacOS! 🍺 brew install brewsci/bio/magic-blast 🏠 https://ncbi.github.io/magicblast/

sjackman commented 6 years ago

🎉 New formula snappy in Brewsci/bio for Linux and MacOS! 🍺 brew install brewsci/bio/snappy 🏡 https://google.github.io/snappy/

tseemann commented 6 years ago

🎉 New formula phyml in Brewsci/bio for Linux and MacOS! 🍺 brew install brewsci/bio/phyml 🏠 http://www.atgc-montpellier.fr/phyml/ 📖 https://doi.org/10.1093/sysbio/syq010