[Debian-med-packaging] tandem-genotypes_1.8.3-1_amd64.changes REJECTED

[Steffen Möller]

Hi Torsten,

On 06.11.21 13:00, Thorsten Alteholz wrote:
> Hi Steffen,
>
> upstream states in his corresponding paper the source of all datafiles.
We agree that most references in the paper are about the analysis the
authors have performed for that paper. But those sequences are not
redistributed in the source tree.
> They are not licensed under GPL, so please add the correct ones to your debian/copyright.

You may be referring to this sentence: Tandem repeat (rmsk.txt) and gene
(refFlat.txt) annotations were obtained from the UCSC genome database
(http://genome.ucsc.edu/) [31
<https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1667-6#ref-CR31>].
We made the file hg38-disease-tr.txt, with 31 disease-associated tandem
repeats, based on Tang et al. [1
<https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1667-6#ref-CR1>].

The files redistributed in the tests folder with that name however are
not the complete files (those would be >12MB
https://googlegenomics.readthedocs.io/en/latest/use_cases/discover_public_data/ucsc_annotations.html)
but only a few lines resembling the format to make some good test cases.
I suggest to add the following to d/copyright

Files: hg*-disease-tr.txt
Copyright: 2018-2021 Martin C. Frith <mcfrith at gmail.com>
License: GPL-3.0+
Comment: As stated in the accompanying paper
  (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1667-6),
  these files are derived from work published in
  Tang H, Kirkness EF, Lippert C, Biggs WH, Fabani M, Guzman E,
Ramakrishnan S, Lavrenko V, Kakaradov B, Hou C, et al
  Profiling of short-tandem-repeat disease alleles in 12,632 human whole
genomes. Am J Hum Genet. 2017;101:700–15.

Files: debian-tests-data/*
Copyright: 2018-2021 Martin C. Frith <mcfrith at gmail.com>
License: GPL-3.0+
Comment: These files are very short to make quick and good tests that
resemble in format
  and content multi-Megabyte large annotation files. The accompanying paper
  (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1667-6)
  explicitly references refFlat.txt
  (https://googlegenomics.readthedocs.io/en/latest/use_cases/discover_public_data/ucsc_annotations.html)
  and rmsk.txt
(http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database//rmsk/./txt/.gz)
  which need to be downloaded separately.

Would that be in line with what you had in mind?

Many thanks

Steffen


>
> Thanks!
>   Thorsten
>
>
>
> ===
>
> Please feel free to respond to this email if you don't understand why
> your files were rejected, or if you upload new files which address our
> concerns.
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-packaging/attachments/20211111/c6eec25d/attachment-0001.htm>