Program_Licenses.md

The StaPH-B/docker-builds repository is licensed under GNU GPLv3 as of 2020-01-16 (commit: https://github.com/StaPH-B/docker-builds/commit/a4f6e3c7cd7f82aab5117f6f48a292a48cc1091a )

In this repository you will find numerous dockerfiles, but no source code of the programs we have built docker images for. The one exception to this is Serotypefinder, which is licensed under Apache 2.0, and allows for the re-distribution of the source code.

The licenses of the open-source software that is contained in these Docker images should be listed in each dockerfile's metadata, but is also listed in the table below.

Software	License	Link to license
ABRicate	GNU GPLv2	https://github.com/tseemann/abricate/blob/master/LICENSE
artic-ncov2019-epi2me	MPL 2.0	https://github.com/epi2me-labs/wf-artic/blob/master/LICENSE
any2fasta	GNU GPLv3	https://github.com/tseemann/any2fasta/blob/master/LICENSE
ARIBA	GNU GPLv3	https://github.com/sanger-pathogens/ariba/blob/master/LICENSE
Augur	GNU Affero GPLv3	https://github.com/nextstrain/augur/blob/master/LICENSE.txt
Auspice	GNU Affero GPLv3	https://github.com/nextstrain/auspice/blob/master/LICENSE.txt
BBTools	non-standard - see licence.txt and legal.txt that is included in docker image under /bbmap/docs/; Also on sourceforge repo for BBTools	https://jgi.doe.gov/disclaimer/
bcftools	MIT or GNU GPLv3 (depends on how bcftools was compiled, I believe GNU GPLv3 applies here)	https://github.com/samtools/bcftools/blob/develop/LICENSE
bedtools	MIT	https://github.com/arq5x/bedtools2/blob/master/LICENSE
blast+	Public Domain	https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/scripts/projects/blast/LICENSE
bowtie2	GNU GPLv3	https://github.com/BenLangmead/bowtie2/blob/master/LICENSE
BWA	GNU GPLv3	https://github.com/lh3/bwa/blob/master/COPYING
Canu Racon Minimap2	GNU GPLv3 (Canu), MIT (Racon), MIT (Minimap2)	https://github.com/marbl/canu/blob/master/README.license.GPL https://github.com/isovic/racon/blob/master/LICENSE https://github.com/lh3/minimap2/blob/master/LICENSE.txt
centroid	GitHub No License	https://github.com/https://github.com/stjacqrm/centroid
CDC-SPN	GitHub No License	https://github.com/BenJamesMetcalf/Spn_Scripts_Reference
cfsan-snp-pipeline	non-standard license see -->	https://github.com/CFSAN-Biostatistics/snp-pipeline/blob/master/LICENSE.txt
Circlator	GNU GPLv3	https://github.com/sanger-pathogens/circlator/blob/master/LICENSE
colorid	MIT	https://github.com/hcdenbakker/colorid/blob/master/LICENSE
datasets-sars-cov-2	Apache 2.0	https://github.com/CDCgov/datasets-sars-cov-2/blob/master/LICENSE
dragonflye	GNU GPLv3	https://github.com/rpetit3/dragonflye/blob/main/LICENSE
DSK	GNU Affero GPLv3	https://github.com/GATB/dsk/blob/master/LICENSE
emm-typing-tool	GNU GPLv3	https://github.com/phe-bioinformatics/emm-typing-tool/blob/master/LICENCE
emboss	GNU GPLv3	http://emboss.sourceforge.net/licence/
EToKi	GNU GPLv3	https://github.com/zheminzhou/EToKi/blob/master/LICENSE
FastANI	Apache v2.0	https://github.com/ParBLiSS/FastANI/blob/master/LICENSE
Fastp	MIT	https://github.com/OpenGene/fastp/blob/master/LICENSE
FastTree	GNU GPLv2	http://www.microbesonline.org/fasttree/
FastQC	GNU GPLv3	https://github.com/s-andrews/FastQC/blob/master/LICENSE.txt
fastq-scan	MIT	https://github.com/rpetit3/fastq-scan/blob/master/LICENSE
Freebayes	MIT	https://github.com/freebayes/freebayes/blob/master/LICENSE
Filtlong	GNU GPLv3	https://github.com/rrwick/Filtlong/blob/master/LICENSE
FLASH	GNU GPLv3	https://github.com/ebiggers/flash/blob/master/COPYING
Flye	BSD-3	https://github.com/fenderglass/Flye/blob/flye/LICENSE
Freyja	BSD-2	https://github.com/andersen-lab/Freyja/blob/main/LICENSE
GAMBIT	GNU aGPLv3	https://github.com/jlumpe/gambit/blob/master/LICENSE
GAMMA	Apache 2.0	https://github.com/rastanton/GAMMA/blob/main/LICENSE
Genotyphi	GNU GPLv3	https://github.com/katholt/genotyphi/blob/main/LICENSE
Hmmer	BSD-3	http://eddylab.org/software/hmmer/Userguide.pdf
htslib	MIT	https://github.com/samtools/htslib/blob/develop/LICENSE
iqtree	GNU GPLv2	https://github.com/Cibiv/IQ-TREE/blob/master/LICENSE
iqtree2	GNU GPLv2	https://github.com/iqtree/iqtree2/blob/master/LICENSE
IRMA	GNU GPLv3	https://wonder.cdc.gov/amd/flu/irma/disclaimer.html
iVar	GNU GPLv3	https://github.com/andersen-lab/ivar/blob/master/LICENSE
Kaptive	GNU GPLv3	https://github.com/katholt/Kaptive/blob/master/LICENSE
Kleborate	GNU GPLv3	https://github.com/katholt/Kleborate/blob/master/LICENSE
kma	Apache v2.0	https://bitbucket.org/genomicepidemiology/kma/src/master/
Kraken	GNU GPLv3	https://github.com/DerrickWood/kraken/blob/master/LICENSE
Kraken2	MIT	https://github.com/DerrickWood/kraken2/blob/master/LICENSE
kSNP3	BSD	available in zipped kSNP archive on sourceforge or in docker image under /kSNP3.1_Linux_package/THE BSD OPENSOURCE LICENSE.pdf
kSNP4	BSD	available in zipped kSNP archive on sourceforge or in docker image under /opt/kSNP4 Linux package/Documentation/THE BSD OPENSOURCE LICENSE.pdf
legsta	GNU GPLv3	https://github.com/tseemann/legsta/blob/master/LICENSE
liftoff	GNU GPLv3	https://github.com/agshumate/Liftoff/blob/master/LICENSE.md
Lyve-SET	MIT	https://github.com/lskatz/lyve-SET/blob/master/LICENSE
Mafft	BSD	https://mafft.cbrc.jp/alignment/software/license.txt
Mash	non-standard license (see link)	https://github.com/marbl/Mash/blob/master/LICENSE.txt
mashtree	GNU GPLv3	https://github.com/lskatz/mashtree/blob/master/LICENSE
MaSuRCA	GNU GPLv3	https://github.com/alekseyzimin/masurca/blob/master/LICENSE.txt
Medaka	Mozilla Public License 2.0	https://github.com/nanoporetech/medaka/blob/master/LICENSE.md
Metaphlan	MIT	https://github.com/biobakery/MetaPhlAn/blob/3.0/license.txt
minimap2	MIT	https://github.com/lh3/minimap2/blob/master/LICENSE.txt
miniasm	MIT	https://github.com/lh3/miniasm/blob/master/LICENSE.txt
minipolish	GNU GPLv3	https://github.com/rrwick/Minipolish/blob/main/LICENSE
mlst	GNU GPLv2	https://github.com/tseemann/mlst/blob/master/LICENSE
Mugsy	Artistic License 2.0	Archived in: https://sourceforge.net/projects/mugsy/files/mugsy_x86-64-v1r2.3.tgz
MultiQC	GNU GPLv3	https://github.com/ewels/MultiQC/blob/master/LICENSE
Mummer	The Artistic License 2.0	https://github.com/mummer4/mummer/blob/master/LICENSE.md
Mykrobe	MIT	https://github.com/Mykrobe-tools/mykrobe/blob/master/LICENSE
NanoPlot	GNU GPLv3	https://github.com/wdecoster/NanoPlot/blob/master/LICENSE
NCBI AMRFinderPlus	Public Domain	https://github.com/ncbi/amr/blob/master/LICENSE
NCBI Datasets	Public Domain	https://github.com/ncbi/datasets/blob/master/pkgs/ncbi-datasets-cli/LICENSE.md
NCBI table2asn	Public Domain	unknown
ngmaster	GNU GPLv3	https://github.com/MDU-PHL/ngmaster/blob/master/LICENSE
OrthoFinder	GNU GPLv3	https://github.com/davidemms/OrthoFinder/blob/master/License.md
Panaroo	MIT	https://github.com/gtonkinhill/panaroo/blob/master/LICENSE
Pangolin	GNU GPLv3	https://github.com/cov-lineages/pangolin/blob/master/LICENSE.txt
pasty	Apache 2.0	https://github.com/rpetit3/pasty/blob/main/LICENSE
pbptyper	MIT	https://github.com/rpetit3/pbptyper/blob/main/LICENSE
Phyml	GNU GPLv3	https://github.com/stephaneguindon/phyml/blob/master/COPYING
Piggy	GNU GPLv3	https://github.com/harry-thorpe/piggy/blob/master/LICENSE
Pilon	GNU GPLv2	https://github.com/broadinstitute/pilon/blob/master/LICENSE
Piranha	GNU GPLv3	https://github.com/polio-nanopore/piranha/blob/main/LICENSE
PlasmidSeeker	BSD 3-Clause	https://github.com/bioinfo-ut/PlasmidSeeker/blob/master/LICENSE
pmga	GNU GPLv2	https://github.com/rpetit3/pmga/blob/master/LICENSE
PopPUNK	Apache 2.0	https://github.com/bacpop/PopPUNK/blob/master/LICENSE
Prokka	GNU GPLv3	https://raw.githubusercontent.com/tseemann/prokka/master/doc/LICENSE.Prokka
pyGenomeViz	MIT	https://github.com/moshi4/pyGenomeViz/blob/main/LICENSE
QUAST	GNU GPLv2	https://github.com/ablab/quast/blob/master/LICENSE.txt
QuickSNP	GNU GPLv3	https://github.com/k-florek/QuickSNP/blob/main/LICENSE
racon	MIT	https://github.com/isovic/racon/blob/master/LICENSE
rasusa	MIT	https://github.com/mbhall88/rasusa/blob/master/LICENSE
raven	MIT	https://github.com/lbcb-sci/raven/blob/master/LICENSE
RAxML RAxML Next Generation	GNU GPLv3 (RAxML), GNU Affero GPLv3 (RAxML Next Generation)	https://github.com/stamatak/standard-RAxML/blob/master/gpl-3.0.txt https://github.com/amkozlov/raxml-ng/blob/master/LICENSE.txt
ResFinder	Apache 2.0	https://bitbucket.org/genomicepidemiology/resfinder/src/master/
Roary	GNU GPLv3	https://github.com/sanger-pathogens/Roary/blob/master/GPL-LICENSE
SalmID	MIT	https://github.com/hcdenbakker/SalmID/blob/master/LICENSE
Samtools	GNU GPLv3	https://github.com/samtools/samtools/blob/develop/LICENSE
SeqKit	MIT	https://github.com/shenwei356/seqkit/blob/master/LICENSE
SeqSero	GNU GPLv2	https://github.com/denglab/SeqSero/blob/master/LICENSE
SeqSero2	GNU GPLv2	https://github.com/denglab/SeqSero2/blob/master/LICENSE
seqyclean	MIT	https://github.com/ibest/seqyclean/blob/master/LICENSE
seqtk	MIT	https://github.com/lh3/seqtk/blob/master/LICENSE
Seroba	GNU GPLv3	https://github.com/sanger-pathogens/seroba/blob/master/LICENSE
SerotypeFinder	Apache 2.0	https://bitbucket.org/genomicepidemiology/serotypefinder/
shigatyper	non-standard license see -->	https://github.com/CFSAN-Biostatistics/shigatyper/blob/master/LICENSE
ShigEiFinder	GNU GPLv3	https://github.com/LanLab/ShigEiFinder/blob/main/LICENSE
Shovill	GNU GPLv3	https://github.com/tseemann/shovill/blob/master/LICENSE
SISTR	Apache 2.0	https://github.com/phac-nml/sistr_cmd/blob/master/LICENSE
SKA	MIT	https://github.com/simonrharris/SKA/blob/master/LICENSE
SKESA	Public Domain	https://github.com/ncbi/SKESA/blob/master/LICENSE
Smalt	GNU GPLv3	https://www.sanger.ac.uk/tool/smalt-0/
SnpEff	MIT	https://github.com/pcingola/SnpEff/blob/master/LICENSE.md
Snippy	GNU GPLv2	https://github.com/tseemann/snippy/blob/master/LICENSE
snp-dists	GNU GPLv3	https://github.com/tseemann/snp-dists/blob/master/LICENSE
SNP-sites	GNU GPLv3	https://github.com/sanger-pathogens/snp-sites/blob/master/LICENSE
SNVPhyl-tools	Apache 2.0	https://github.com/phac-nml/snvphyl-tools/blob/master/LICENSE
SPAdes	GNU GPLv2	https://github.com/ablab/spades/blob/spades_3.13.0/assembler/LICENSE
SRA-toolkit	Public Domain	https://github.com/ncbi/sra-tools/blob/master/LICENSE
SRST2	BSD	https://github.com/katholt/srst2/blob/master/LICENSE.txt
Staramr	Apache 2.0	https://github.com/phac-nml/staramr/blob/master/LICENSE
TBProfiler	GNU GPLv3	https://github.com/jodyphelan/TBProfiler/blob/master/LICENSE
TipToft	GNU GPLv3	https://github.com/andrewjpage/tiptoft/blob/master/LICENSE
Tostadas	Apache-2.0 license	https://github.com/CDCgov/tostadas/blob/master/LICENSE
Treemmer	GNU GPLv3	https://github.com/fmenardo/Treemmer/blob/master/COPYING
Trimmomatic	GNU GPLv3	https://github.com/usadellab/Trimmomatic/blob/main/distSrc/LICENSE
Trycycler	GNU GPLv3	https://github.com/rrwick/Trycycler/blob/master/LICENSE
Unicycler	GNU GPLv3	https://github.com/rrwick/Unicycler/blob/master/LICENSE
VADR	Public Domain	https://github.com/nawrockie/vadr/blob/master/LICENSE
VIBRANT	GNU GPLv3	https://github.com/AnantharamanLab/VIBRANT/blob/master/LICENSE
VIGOR4	GNU GPLv3	https://github.com/JCVenterInstitute/VIGOR4/blob/master/LICENSE.txt
VirSorter2	GNU GPLv2	https://github.com/jiarong/VirSorter2/blob/master/LICENSE
wtdbg2	GNU GPLv3	https://github.com/ruanjue/wtdbg2/blob/master/LICENSE.txt