bowtie2 packaging

2012-02-18 Thread Alex Mestiashvili
Hello , I started work on bowtie2 packaging and I see that bowtie is already packaged in svn [2]. I am wondering if any packaging job has already been done on bowtie2 ? And if not, would you ( bowtie uploaders ) mind if bowtie2 will be placed to git repository ? Regards , Alex [1]

Re: bowtie2 packaging

2012-02-18 Thread Andreas Tille
On Sat, Feb 18, 2012 at 10:52:50AM +0100, Alex Mestiashvili wrote: I started work on bowtie2 packaging and I see that bowtie is already packaged in svn [2]. I am wondering if any packaging job has already been done on bowtie2 ? Not that I would know of. And if not, would you ( bowtie

Re: Tasks pages (close to) fixed; Bibref does not seem to be updated automatically

2012-02-18 Thread Charles Plessy
Hi Andreas, I have a working implementation as a Debian package that will allow us to transfer easily the Umegaya gatherer for bibliographic information to debian-med.debian.net. I do not remember if I have the root access to that machine... Can you add me to the sudo group ? Once installed

Re: [plugw...@p10link.net: Bug#660309: tophat: broken code in configure script for determining CFLAGS]

2012-02-18 Thread Carlos Borroto
Hi Andreas, On Sat, Feb 18, 2012 at 2:42 AM, Andreas Tille andr...@an3as.eu wrote: Hi Carlos, just for the case you have not yet realised that maintainers should read the mailing list   http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging I just enabled mail

Re: Tasks pages (close to) fixed; Bibref does not seem to be updated automatically

2012-02-18 Thread Andreas Tille
Hi Charles, On Sun, Feb 19, 2012 at 12:25:17AM +0900, Charles Plessy wrote: I have a working implementation as a Debian package that will allow us to transfer easily the Umegaya gatherer for bibliographic information to debian-med.debian.net. I do not remember if I have the root access to

Re: [plugw...@p10link.net: Bug#660309: tophat: broken code in configure script for determining CFLAGS]

2012-02-18 Thread Andreas Tille
On Sat, Feb 18, 2012 at 10:28:27AM -0500, Carlos Borroto wrote: I think we can upload. Done. I also added a debian/upstream file with the references concerning the package. I will make sure to forward this issue to upstream and see if this patch or a similar solution can be included in next

copyright of cufflinks

2012-02-18 Thread Andreas Tille
Hi, as far as I can see after having studied debian/copyright of cufflinks its non-free nature is only because it contains some third party software (locfit) which contains the following phrase in its licensing agreement which otherwise should be considered free: For these reasons, the Locfit

Re: Tasks pages (close to) fixed; Bibref does not seem to be updated automatically

2012-02-18 Thread Andreas Tille
On Sat, Feb 18, 2012 at 04:53:40PM +0100, Andreas Tille wrote: I noticed this. I just verified the current data in UDD and noticed that some packages are lacking information even if the upstream file just has it (for instance mira-assembler has only DOI in UDD). May be we could track this

Re: copyright of cufflinks

2012-02-18 Thread Charles Plessy
Le Sat, Feb 18, 2012 at 07:30:17PM +0100, Andreas Tille a écrit : IMHO it might be worth trying to contact the author of this 10 year old code to verify whether this phrase remains valid these days. Any volunteer to free cufflinks (or did I missed something)? Hi Andreas, this did not

Re: bowtie2 packaging

2012-02-18 Thread Charles Plessy
Le Sat, Feb 18, 2012 at 03:03:36PM +0100, Andreas Tille a écrit : On Sat, Feb 18, 2012 at 10:52:50AM +0100, Alex Mestiashvili wrote: I started work on bowtie2 packaging and I see that bowtie is already packaged in svn [2]. I am wondering if any packaging job has already been done on bowtie2