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deweylab / RSEM

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
http://deweylab.biostat.wisc.edu/rsem/
GNU General Public License v3.0
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Please clarify license of IDR source code in pRSEM directory #41

Closed mr-c closed 7 years ago

mr-c commented 7 years ago

Thank you for releasing RSEM & pRSEM as free software!

However there are some problems with the third-party source code included (and in some cases, modified) inside the pRSEM directory:

For example, the version of idr that was modified appears to have been never released under any license I can find, as https://sites.google.com/site/anshulkundaje/projects/idr/idrCode.tar.gz?attredirects=0 has not licensing information nor does https://sites.google.com/site/anshulkundaje/projects/idr

Version 1.0, 1.1, and 1.11 of IDR is licensed LGPL (>= 2.0), but the code doesn't appear to be the version adapted here. The version 1.2 on cran is licensed GPL-2+ https://cran.r-project.org/web/packages/idr/ and version 2.0+ on Github are also licensed GPL-2+

Without proof that the 2010 version of IDR was released under any free or open source license means that Debian cannot distribute pRSEM. Without a license it also means that you can not distribute that code or your modifications.

pliu55 commented 7 years ago

Thanks for bringing up this issue. The IDR code is a slightly modified version from https://sites.google.com/site/anshulkundaje/projects/idr, which is supposedly under MIT license. I am wondering if we asked the author of https://sites.google.com/site/anshulkundaje/projects/idr to add an MIT license to https://sites.google.com/site/anshulkundaje/projects/idr, would that solve the issue here? If so, I will contact the author about it.

mr-c commented 7 years ago

Thank you @pliu55 for the response. Yep, that would suffice, though it would be better to upgrade to the latest IDR release from https://github.com/nboley/idr

pliu55 commented 7 years ago

The author of IDR added GPLv2 license. Please check it out: https://sites.google.com/site/anshulkundaje/projects/idr/#TOC-Code-for-IDR-Analysis and let me know if this issue can be closed.

DieTANG commented 7 years ago

Hello, I can't find the rsem-parse-alignments file in RSEM. Is this not included in RSEM?

bli25wisc commented 7 years ago

@DieTANG You should first compile RSEM by typing 'make' and then 'rsem-parse-alignments' will appear.