Add licenses

[sjackman]

@whoiswillma Hi, William. I maintain this third-party tap Brewsci/bio. I hear that you may have a script to automatically add licenses when it can be determined from GitHub or the source tarball. Would you be interested in either running that script for Brewsci/bio and opening a PR or sharing that script with me? Thank you!

cc @SeekingMeaning

[whoiswillma]

I'm working on fetching the license information right now. Here's the script in the meantime: https://github.com/MLH-Fellowship/brew/blob/license-fetch/Library/Homebrew/dev-cmd/license.rb

[whoiswillma]

Here is the report.csv file that's generated. Looks like license information was found for about 170 formulae.

Report file

``` pathvisio,,,curl: (60) SSL: no alternative certificate subject name matches target host name 'www.pathvisio.org' abricate,GPL-2.0,github, abyss-explorer,GPL-3.0,github, adam,NOASSERTION,github, ale,NOASSERTION,github, andi,GPL-3.0,github, any2fasta,GPL-3.0,github, apbspdb2pqr,,github, arcs,GPL-3.0,github, arks,,github, astral,Apache-2.0,github, bali-phy,GPL-2.0,github, bam2fastx,BSD-3-Clause-Clear,github, bamm,GPL-2.0,github, bandage,GPL-3.0,github, barrnap,NOASSERTION,github, bazam,LGPL-2.1,github, bcalm,MIT,github, beast2,LGPL-2.1,github, berokka,GPL-3.0,github, bfc,MIT,github, bifrost,BSD-2-Clause,github, biobloomtools,NOASSERTION,github, biomake,BSD-3-Clause,github, bonsai,MIT,github, bowtie,Artistic-2.0,github, bracken,GPL-3.0,github, breseq,NOASSERTION,github, bwa-mem2,NOASSERTION,github, cannoli,NOASSERTION,github, canu,,github, cd-hit,GPL-2.0,github, centrifuge,GPL-3.0,github, circlator,GPL-3.0,github, clonalframeml,GPL-3.0,github, cluster-picker,GPL-3.0,github, crumble,NOASSERTION,github, cutadapt,MIT,github, das_tool,NOASSERTION,github, dehomopolymerate,GPL-3.0,github, delly,,github, discovardenovo,,, disty,MIT,github, dwgsim,GPL-2.0,github, e-mem,GPL-3.0,github, easel,NOASSERTION,github, ema,MIT,github, epa-ng,AGPL-3.0,github, exabayes,NOASSERTION,github, express,Artistic-2.0,github, fasta,NOASSERTION,github, fastani,Apache-2.0,github, fastp,MIT,github, fastq-pair,MIT,github, fermi-lite,MIT,github, figtree,,github, filtlong,GPL-3.0,github, finch-rs,MIT,github, flowcraft,GPL-3.0,github, flye,NOASSERTION,github, abacas,,, aragorn,,, art,,, artemis,,, ascp,,, bbtools,,, bioperl,,, blast-legacy,,, blat,,, bodr,CC0-1.0,, busco,MIT,, cap3,,, circos,GPL-3.0,, clustal-omega,GPL-2.0,, clustal-w,GPL-3.0,, consel,,, dida,,, dsh-bio,GPL-3.0,, edirect,,, elph,NOASSERTION,, emboss,GPL-2.0,, exonerate,GPL-3.0,, fasttree,,, fastuniq,,, flash,GPL-3.0,, fraggenescan,,, freebayes,MIT,github, fwdpp,GPL-3.0,github, gappa,GPL-3.0,github, gatk,BSD-3-Clause,github, gblocks,,, gemma,GPL-3.0,github, genewise,,, genome-painter,GPL-3.0,github, gepard,MIT,github, gfakluge,MIT,github, gfalint,MIT,github, gfaview,,github, ghostz,,, gmap-gsnap,,, groot,MIT,github, gzstream,,, harvest-tools,NOASSERTION,github, hh-suite,GPL-3.0,github, hisat2,GPL-3.0,github, hmmer2,,, humann2,NOASSERTION,, idba,,github, indel-seq-gen,,, indelible,,, infernal,NOASSERTION,, iqtree,GPL-2.0,github, iqtree2,GPL-2.0,github, ispcr,,, iva,GPL-3.0,github, ivar,GPL-3.0,github, jellyfish,NOASSERTION,github, jspecies,,, k8,,github, kaiju,GPL-3.0,github, kalign,GPL-3.0,github, kat,GPL-3.0,github, kent-tools,,, kma,,, kmc,,github, kmergenie,,, kounta,GPL-3.0,github, kr,NOASSERTION,, kraken,GPL-3.0,github, kraken2,MIT,github, kssd,NOASSERTION,github, last,GPL-3.0,, lastz,MIT,github, legsta,GPL-3.0,github, libbigwig,MIT,github, libdivsufsort,MIT,github, libgff,,github, libpll,AGPL-3.0,github, libsequence,GPL-3.0,github, light-assembler,GPL-3.0,github, lighter,GPL-3.0,github, links-scaffolder,GPL-3.0,github, lofreq,NOASSERTION,github, lrsim,MIT,github, lsd2,GPL-2.0,github, magic-blast,NOASSERTION,, maker,NOASSERTION,, mapcaller,MIT,github, mash,NOASSERTION,github, masurca,GPL-3.0,github, matplotlib,,github, maxbin2,NOASSERTION,, mcl,NOASSERTION,, megahit,GPL-3.0,github, meme,,, metabat,,, blast@2.2,,, metaphlan,,, mhap,Apache-2.0,github, minced,GPL-3.0,github, minia,AGPL-3.0,github, miniasm,MIT,github, minigraph,MIT,github, minimap,MIT,github, minimap2,NOASSERTION,github, mir-prefer,NOASSERTION,github, mlst,GPL-2.0,github, mmtf-cpp,MIT,github, mosdepth,MIT,github, mothur,GPL-3.0,github, mp-est,,, mpboot,,, mrbayes,GPL-3.0,github, mreps,GPL-2.0,github, mummer,,, muscle,,, nanofilt,,, nanopolish,MIT,github, newick-utils,NOASSERTION,, nextflow,Apache-2.0,github, nextgenmap,NOASSERTION,github, ngmaster,GPL-2.0,github, ngmerge,MIT,github, nonpareil,Artistic-2.0,github, ntcard,MIT,github, ntedit,GPL-3.0,github, nthits,MIT,github, ntjoin,GPL-3.0,github, nullarbor,GPL-2.0,github, nxtrim,NOASSERTION,github, oases,GPL-3.0,github, oma,NOASSERTION,, orfm,LGPL-3.0,github, paml,,, pandaseq,GPL-3.0,github, panito,NOASSERTION,github, parasail,NOASSERTION,github, parsnp,NOASSERTION,github, peat,GPL-2.0,github, phlawd,GPL-2.0,github, phylip,,, phylobayes,,github, phyml,GPL-3.0,github, phyx,GPL-3.0,github, pilon,NOASSERTION,github, pirate,GPL-3.0,github, porechop,GPL-3.0,github, portcullis,GPL-3.0,github, pplacer,GPL-3.0,github, prank,,github, prokka,,github, pullseq,NOASSERTION,github, pymol,NOASSERTION,github, quast,NOASSERTION,github, quickmerge,GPL-3.0,github, quicktree,Apache-2.0,github, quip,BSD-3-Clause,, r2r,,, r8s,GPL-3.0,, racon,MIT,github, rails,GPL-3.0,github, rapidnj,,, rasusa,MIT,github, raven-assembler,MIT,github, raxml,,github, rcorrector,GPL-3.0,github, realphy,GPL-3.0,, repaq,MIT,github, repeatmasker,,, rmblast,,, roary,GPL-3.0,github, rtg-tools,BSD-2-Clause,github, salmid,MIT,github, salmon,GPL-3.0,github, sambamba,GPL-2.0,github, samblaster,MIT,github, samclip,GPL-3.0,github, sdsl-lite,NOASSERTION,github, sepp,GPL-3.0,github, seq-gen,,github, seqan@2,NOASSERTION,github, seqan@3,NOASSERTION,github, seqkit,MIT,github, sga,,github, shovill,GPL-3.0,github, sibelia,NOASSERTION,github, simulate-pcr,,, ska,MIT,github, skesa,NOASSERTION,github, smalt,GPL-3.0,, snap,,, snippy,GPL-2.0,github, snoscan,NOASSERTION,, snp-dists,GPL-3.0,github, snp-sites,NOASSERTION,github, snpeff,,, solexaqa,,, sortmerna,GPL-3.0,github, souporcell,MIT,github, squeakr,BSD-3-Clause,github, stacks,GPL-3.0,, staden-io-lib,NOASSERTION,github, star-aligner,MIT,github, stringtie,MIT,github, subread,GPL-3.0,, sumaclust,,, swipe,AGPL-3.0,github, taxonkit,MIT,github, tbl2asn,,, tigmint,GPL-3.0,github, transabyss,NOASSERTION,github, transdecoder,NOASSERTION,github, treepl,,github, trimadap,,github, trimal,GPL-3.0,github, trimmomatic,GPL-3.0,, trinity,NOASSERTION,github, trnascan,NOASSERTION,, unicycler,GPL-3.0,github, unikmer,MIT,github, uniqtag,MIT,github, varscan,,github, varsim,BSD-2-Clause,github, vcf2phylip,GPL-3.0,github, vcflib,,github, velvet,GPL-2.0,github, velvetoptimiser,GPL-2.0,github, verticalize,MIT,github, viennarna,NOASSERTION,, virulign,GPL-2.0,github, vmatch,ISC,, vt,MIT,github, webin-cli,Apache-2.0,github, wiggletools,NOASSERTION,github, wish,GPL-3.0,github, wtdbg2,GPL-3.0,github, xmatchview,GPL-3.0,github, xssp,,github, ```

How would you like me to submit the code changes? When I added license info to homebrew-core Mike wanted each file to have its own commit, and to not submit a PR to avoid useless CI runs.

[sjackman]

One commit per file, and please do open a PR. It will almost certainly time out or fail for some other reason, but I'll squash merge it without updating the files. I just want the PR to record the change.

[sjackman]

Thank you, Will! 🏆

[whoiswillma]

Always glad to help 😀

Just a heads up: the script had an SSL issue with pathvisio. Seems like that was a known thing when the formula was merged? https://github.com/brewsci/homebrew-bio/pull/45

[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.