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BenLangmead / bowtie

An ultrafast memory-efficient short read aligner
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SeqAn license info is not enough? #106

Closed junaruga closed 3 years ago

junaruga commented 4 years ago

I noticed this bowtie's SeqAn licenses might be not enough.

I was reading the license document about SeqAn. Though I could not find SeqAn 1.1, I was reading SeqAn 1.4.2 (The latest version of 1.X).

https://github.com/seqan/seqan/tree/seqan-v1.4.2

The SeqAn library itself, the tests and demos are licensed under the very permissing 3-clause BSD License. The licenses for the applications themselves can be found in the LICENSE files.

SeqAn itself's license is BSD license. So, maybe BSD.txt is also necessary under SeqAn-1.1/? https://github.com/seqan/seqan/blob/seqan-v1.4.2/LICENSE

$ git clone https://github.com/seqan/seqan.git

$ cd seqan

$ git checkout seqan-v1.4.2

$ find . -name LICENSE
./extras/apps/searchjoin/LICENSE
./extras/apps/param_chooser/LICENSE
./extras/apps/fx_tools/LICENSE
./extras/apps/bs_tools/LICENSE
./extras/apps/breakpoint_calculator/LICENSE
./extras/apps/sgip/LICENSE
./extras/apps/variant_comp/LICENSE
./extras/apps/ngs_roi/R/ngsroi/LICENSE
./extras/apps/ngs_roi/tool_shed/LICENSE
./extras/apps/ngs_roi/LICENSE
./extras/apps/rep_sep/LICENSE
./extras/apps/insegt/LICENSE
./extras/apps/alf/LICENSE
./extras/apps/seqan_flexbar/LICENSE
./extras/apps/razers3/LICENSE
./extras/apps/mason2/LICENSE
./extras/apps/gustaf/LICENSE
./extras/include/seqan/LICENSE
./util/py_lib/seqan/LICENSE
./util/cmake/ctd/LICENSE
./util/skel/app_template/LICENSE
./LICENSE
./core/demos/LICENSE
./core/apps/mason/LICENSE
./core/apps/splazers/LICENSE
./core/apps/dfi/LICENSE
./core/apps/samcat/LICENSE
./core/apps/razers/LICENSE
./core/apps/seqcons/LICENSE
./core/apps/razers2/LICENSE
./core/apps/fiona/LICENSE
./core/apps/seqan_tcoffee/LICENSE
./core/apps/tree_recon/LICENSE
./core/apps/sak/LICENSE
./core/apps/stellar/LICENSE
./core/apps/micro_razers/LICENSE
./core/apps/snp_store/LICENSE
./core/apps/rabema/LICENSE
./core/apps/sam2matrix/LICENSE
./core/apps/pair_align/LICENSE
./core/include/seqan/LICENSE

As a reference, in case of Fedora sequan (1.X) package, the license is managed as License: BSD and GPLv3+ and LGPLv3+. https://src.fedoraproject.org/rpms/seqan/blob/master/f/seqan.spec#_5

%files
%license BSD.txt GPLv3+.txt LGPLv3+.txt

I am not sure that it is right.

junaruga commented 4 years ago

I got an idea about how to check the license in seqan from the maintainer of seqan Fedora PRM package. That is to use with licensecheck command.

$ find . -name LICENSE | xargs licensecheck | sort | uniq | grep -v UNKNOWN | grep -v "No copyright"
./LICENSE: BSD 3-clause "New" or "Revised" License
./core/apps/micro_razers/LICENSE: GNU Lesser General Public License (v3)
./core/apps/pair_align/LICENSE: GNU Lesser General Public License (v3 or later)
./core/apps/sak/LICENSE: GNU Lesser General Public License (v3 or later)
./core/apps/sam2matrix/LICENSE: BSD 3-clause "New" or "Revised" License
./core/apps/seqan_tcoffee/LICENSE: GNU Lesser General Public License (v3 or later)
./core/apps/seqcons/LICENSE: GNU Lesser General Public License (v3 or later)
./core/apps/splazers/LICENSE: GNU Lesser General Public License (v3)
./core/apps/stellar/LICENSE: GNU Lesser General Public License (v3)
./core/apps/tree_recon/LICENSE: GNU Lesser General Public License (v3 or later)
./core/demos/LICENSE: BSD 3-clause "New" or "Revised" License
./core/include/seqan/LICENSE: BSD 3-clause "New" or "Revised" License
./extras/apps/alf/LICENSE: BSD 3-clause "New" or "Revised" License
./extras/apps/breakpoint_calculator/LICENSE: GPL (v3 or later)
./extras/apps/bs_tools/LICENSE: BSD 3-clause "New" or "Revised" License
./extras/apps/fx_tools/LICENSE: BSD 3-clause "New" or "Revised" License
./extras/apps/gustaf/LICENSE: BSD 3-clause "New" or "Revised" License
./extras/apps/mason2/LICENSE: BSD 3-clause "New" or "Revised" License
./extras/apps/ngs_roi/LICENSE: BSD 3-clause "New" or "Revised" License
./extras/apps/ngs_roi/R/ngsroi/LICENSE: BSD 3-clause "New" or "Revised" License
./extras/apps/ngs_roi/tool_shed/LICENSE: BSD 3-clause "New" or "Revised" License
./extras/apps/param_chooser/LICENSE: GNU Lesser General Public License (v3)
./extras/apps/rep_sep/LICENSE: GNU Lesser General Public License (v3)
./extras/apps/searchjoin/LICENSE: BSD 3-clause "New" or "Revised" License
./extras/apps/seqan_flexbar/LICENSE: BSD 3-clause "New" or "Revised" License
./extras/apps/sgip/LICENSE: GNU Lesser General Public License (v3)
./extras/apps/variant_comp/LICENSE: GNU Lesser General Public License (v3)
./extras/include/seqan/LICENSE: BSD 3-clause "New" or "Revised" License
./util/cmake/ctd/LICENSE: BSD 3-clause "New" or "Revised" License
./util/py_lib/seqan/LICENSE: BSD 3-clause "New" or "Revised" License
./util/skel/app_template/LICENSE: BSD 3-clause "New" or "Revised" License

Or for the files used to compile, it could be like this. -r is the recursive option.

 $ licensecheck -r ./* | grep -v UNKNOWN | grep -v "No copyright"
ch4rr0 commented 4 years ago

Hello @junaruga, we plan on getting rid of seqan for the next bowtie release.

junaruga commented 4 years ago

Hi @ch4rr0 That's actually good news for me. Thank you for considering about it.

junaruga commented 3 years ago

I would close this ticket, as I confirmed SeqAn was removed in this repository at the commit: https://github.com/BenLangmead/bowtie/commit/3945d8c7856286813cf7422c871e97db95908e29 . Thank you for the work!