RE: Licences (Was Re: Trace Archive Proposal (was RE: Summary of 454 Format))
You can update the copyright statement to be the following in the places
in the io_lib library that refers to the 454 copyright. Do you need
more than that?
James Knight
Director of Bioinformatics Development
454 Life Sciences
-----------------------
* Copyright (c)[2001-2005] 454 Life Sciences Corporation. All Rights
Reserved.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
* MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
NONINFRINGEMENT.
*
* IN NO EVENT SHALL AUTHORS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE.
*
* Permission to use, copy, modify and distribute this software and its
* documentation for any purpose is hereby granted without fee, provided
that
* this copyright and notice appears in all copies.
-----------------
-----Original Message-----
From: James Bonfield [mailto:jkb@sanger.ac.uk]
Sent: Tuesday, September 02, 2008 12:02 PM
To: Knight, James
Subject: Licences (Was Re: Trace Archive Proposal (was RE: Summary of
454 Format))
Hello Jim,
Sorry for ressurrecting an ancient email conversation.
Debian have an issue with the licence used in io_lib, or at least the
portions from getsff.c, reasonably I guess as I understood the intent
of our email conversation without specifically understanding the
missing clauses.
Specifically Debian's problem is that io_lib's open_trace_file.c (and
maybe elsewhere) contains the 454 copyright notice disclaiming
warranty, provided "as is" and the usual bits, but does NOT state that
it may be copied, modified and redistributed.
Ie from the code:
/*
* 454 sorted format (.srt) index searching for SFF files.
* Uses a binary search.
* This function and getuint4_255 above are taken with permission
* from 454's getsff.c with the following licence:
*
* Copyright (c)[2001-2005] 454 Life Sciences Corporation. All Rights
Reserved.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
* MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
NONINFRINGEMENT.
*
* IN NO EVENT SHALL LICENSOR BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE.
*/
Compare this to the rest (almost) of the io_lib code which uses:
/*
* Copyright (c) Medical Research Council 1994. All rights reserved.
*
* Permission to use, copy, modify and distribute this software and its
* documentation for any purpose is hereby granted without fee, provided
that
* this copyright and notice appears in all copies.
*
* This file was written by James Bonfield, Simon Dear, Rodger Staden,
* as part of the Staden Package at the MRC Laboratory of Molecular
* Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
*
* MRC disclaims all warranties with regard to this software.
*/
The discussion is taking place on the debian-med mailing list. See:
http://lists.debian.org/debian-med/2008/09/msg00005.html
for reference and discussion so far. It's probably best if you could
CC debian-med@lists.debian.org with your response to this too.
Cheers,
James
On Fri, Oct 14, 2005 at 03:26:25PM -0400, Knight, James wrote:
> Feel free to take the code from getsff.c to support the sorted index.
> There are no licensing restrictions on that source code. That is what
> I'll also be doing (taking the same sorted index code to put into
> runArchive and then reworking getsff to use the new format), so the
> sorted index format for that will be the same (I'll use ".srt" as the
> magic number and "1.00" as the version, so that you can include that
in
> your code).
>
> Jim
>
> -----Original Message-----
> From: James Bonfield [mailto:jkb@sanger.ac.uk]
> Sent: Friday, October 14, 2005 6:13 AM
> To: Knight, James
> Cc: Dmitriy Volodin; mczody@broad.mit.edu; Alekseyev, Vladimir
> (NIH/NLM/NCBI); Du, Lei; Spencer, William; Lohman, Kent; Yaschenko,
> Eugene (NIH/NLM/NCBI); Toby Bloom; Margulies, Marcel;
> SKravitz@venterinstitute.org
> Subject: Re: Trace Archive Proposal (was RE: Summary of 454 Format)
>
> Hello all,
>
> Thanks Jim for the 454Reads.sff. It's helped with io_lib development
> and I can now say that I have code for reading sequences out of an SFF
> archive. It's not ideal in that currently it requires the use of
> RAWDATA to set the SFF file as a container. I'm thinking maybe being
> able to ask for entry e.g. 454Reads.sff/145046_0008_2431 would solve
> both the unique name issue and the requirement of explicitly seting
> RAWDATA to point to the archive. Any comments on this idea?
>
> I'm working on adding the hash indexing too. It's mostly working fine
> currently using my existing hash reading code, but I also want to put
> it into the SFF extraction code route (which currently is using a
> linear search). I'm happy to support the sorted (and hence binary
> searchable) index mechanism originally used in TVF too as long as I
> have permission to just rip off that code (from getsff.c?) without it
> causing any licencing issues.
>
> I'll make new io_lib source available soon.
>
> James
>
>
> --
> James Bonfield (jkb@sanger.ac.uk)
> A Staden Package developer: https://sourceforge.net/projects/staden/
>
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>
>
--
James Bonfield (jkb@sanger.ac.uk) | Hora aderat briligi. Nunc et Slythia
Tova
| Plurima gyrabant gymbolitare vabo;
A Staden Package developer: | Et Borogovorum mimzebant undique
formae,
https://sf.net/projects/staden/ | Momiferique omnes exgrabure Rathi.
--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
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