Hi Charles, On 4 May 2010 21:01, Charles Plessy <ple...@debian.org> wrote: > Le Tue, May 04, 2010 at 06:30:26PM -0700, Shaun Jackman a écrit : >> >> I've packaged GMAP: >> Align mRNA and EST sequences to a genome >> GMAP: Genomic Mapping and Alignment Program >> GSNAP: Genomic Short-read Nucleotide Alignment Program >> >> The ITP is here: >> http://bugs.debian.org/580277 >> >> The git repository is here: >> git://git.debian.org/git/debian-med/gmap.git >> http://git.debian.org/?p=debian-med/gmap.git > > Dear Shaun, > > thank you very much for helping us to stay up to date in the field of > next-generation sequencing. Just out of curiosity, will you use the > package yourself, or did you prepare it for a friend or a colleague? > > I had a look at your package and have the following comments: > > - It is non-free: > > ‘Distribution of this Package as part of a commercial software product > requires > prior arrangement with the Developers.’ > > I updated debian/control accordingly.
Thanks. > Since this license is not compatible with > the GPL, I recommend that you chose another license for your packaging > work, in > order to avoid headaches in the future. Can you recommend a license that is DFSG free and compatible with the upstream license? > - We will have to be careful when doing modifications. > > ‘Distribution of a modified version of this Package requires prior > arrangement with the Developers.’ > > I am not sure of what it means for the manpages you wrote. If you have > written them > using the output of the programs as a template, they are a derivative of > them, > and the above may mean that we need agreement of the upstream developpers > before > redistributing them. But anyway, manpages are better to be forwarded > upstream. Have > you contacted them? I'm in contact with the upstream author, but not yet regarding the Debian package. I'll forward the man pages upstream. > - Location of the databases. > > I have seen ‘-DGMAPDB=\"/usr/share/gmap\"’ in the build logs. Does that > mean that the > users will have to install their databases there, or is there a way to > override > this path? In general, I think Debian users expect /usr/share to be > completely under > the control of the packaging system. Perhaps another path would be better? The default location can be overridden by a command line option (-D) or an environment variable (GMAPDB). How about /var/cache/gmap? http://www.pathname.com/fhs/pub/fhs-2.3.html#VARCACHEAPPLICATIONCACHEDATA > - Package description. How about this one: > > Description: spliced and SNP-tolerant alignment programs for mRNA and short > reads > This package contains the GMAP and GSMAP programs to align biological > sequences, and additional utilities to manage genome databases in GMAP/GSNAP > format. GMAP (Genomic Mapping and Alignment Program) is a tool for aligning > cDNAs (complementary DNA) to reference genomes. GSNAP (Genomic Short-read > Nucleotide Alignment Program) is a tool for aligning single and paired-end > sequence reads as short as 14 nt and of arbitrarily long length. It can do de > novo discovery of splice sites (including interchromosomal splicing) or use a > datbase of known splice sites. It also tolerates known single nucleotide > polymorphisms (SNPs) and can align bisulfite-treated DNA. I edited and reformatted your description. How's this look? Description: spliced and SNP-tolerant alignment for mRNA and short reads This package contains the programs GMAP and GSNAP as well as utilities to manage genome databases in GMAP/GSNAP format. GMAP (Genomic Mapping and Alignment Program) is a tool for aligning EST, mRNA and cDNA sequences. GSNAP (Genomic Short-read Nucleotide Alignment Program) is a tool for aligning single and paired-end transcriptome reads. Both tools can use a database of * known splice sites and identify novel splice sites. * known single nucleotide polymorphisms (SNPs). GSNAP can align bisulfite-treated DNA. > Maybe it would be good to propose to the authors to proofread this > description, > so that we are sure that I did not under- or over-estimate the possibilities > of their programs. I believe these claims are correct, but of course it wouldn't hurt to check. Cheers, Shaun -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/aanlktink2siybtb_crmnhlhqrhpfvnn_8te5v_5sz...@mail.gmail.com
