On 06/06/16 15:05, Sascha Steinbiss wrote:
Dear Nicola, first of all many thanks for the quick reply.thanks for contacting me about the SSPACE-basic repository. The repository contains a copy of the "basic" version of SSPACE, which was released by Baseclear years ago under the GPL (v2 or later) and then discontinued.This is very nice to hear; I didn't know that but it does indeed explain this separate version and license.Then they removed all traces of this version from their websiteDoes that mean they do not support SSPACE-basic _at all_ any more? That is, do you know if they still handle, for example, bug reports? 'Discontinued' seems to suggest that...
I don't think so, but to be sure you should contact BaseClear about that.
SSPACE standard is a completely different version (at least license-wise).Got it.The first commit of the repository https://github.com/nsoranzo/sspace_basic/commit/652d24aa74a3b45774db43b3483e71e40572a553 contains an exact copy of the files I downloaded at the time from http://www.baseclear.com/download.php?file_id=1038 , the other commits are patches from me.If Baseclear have discontinued SSPACE-basic, I was wondering if you would be OK with being our upstream contact for SSPACE-basic? That means that we would possibly forward bug reports, patches, etc. from Debian to you if they address the SSPACE-basic software itself.
That would be fine for me, but unfortunately I can't guarantee I will have time/resources to fix the issues. I created the repository mainly because I wrote a Galaxy wrapper for SSPACE basic and the original download location disappeared. Also I wanted to preserve the code for anyone that wants to use it, but this is not my project or work!
I'd very happy if you package SSPACE-basic and I'd happy to accept patches to make the software more "packageable" if needed.I will look into it as soon as I find some time, and contact you with suggestions or patches if required. From what I can see without delving too much into packaging, we won't be able to include the PDF manuals without the source they were created from (LaTeX, Word, ...) also included in the repository. This is a Debian policy; if these are not available we'd have to exclude them from the packaged version. An alternative is to just make plain text versions (copy&paste?) and to include them in the repository. This would need to be done on your side as well though.
I can take a look in merging the PDF manuals and the README in 2 MarkDown files, it's all just text.
Cheers, Nicola
Thanks again for your cooperation :) Always happy to hear such welcome news and to see good software freed! Best regards Sascha-- Nicola Soranzo, Ph.D. Data Infrastructure & Algorithms group The Genome Analysis Centre (TGAC) Norwich Research Park, Norwich, NR4 7UH, UK http://www.tgac.ac.uk/sequencing-informatics/ On 04/06/16 16:49, Sascha Steinbiss wrote:Dear Dr. Soranzo, I am writing you on behalf of the Debian Med team, a group within the Debian project with the objective to package free software with relevance in biology and medicine for official Debian. I noticed that you provide a GitHub repository with the SSPACE basic source code [1], under the GPLv2 [2]. This version of SSPACE would in principle be possible to be packaged for Debian, as inclusion into the main archive requires such a free license, allowing for free redistribution. I was wondering how the version that you provide relates to the non-free version (SSPACE standard) provided by Baseclear [3]. Is the one that you provide a different or reduced-functionality version compared to theirs? Most importantly, Baseclear make no mention of any kind of free license — on the contrary, they require users to contact them to obtain the software and also handle commercial users separately, a notion that the GPL does not have. I would be glad if you could clarify how this GPL-licensed version came to be? We would be very thankful if this was a version that the original authors of SSPACE released under a free license, and would be happy to package it for Debian. Many thanks Sascha Steinbiss [1] https://github.com/nsoranzo/sspace_basic [2] https://github.com/nsoranzo/sspace_basic/blob/master/COPYING [3] http://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE