Re: jh_build seeks in .pc folder (Was: Request for sponsoring: beagle)

2016-04-26 Thread Andreas Tille
Hi Dylan, On Tue, Apr 26, 2016 at 11:24:50PM +0200, Dylan wrote: > Hi Andreas, > Thank you for the upload. > I suppose that you don't know why my gbp import-orig remove the src folder. That's a wrong wording. Import-orig just imports the files and directories that are found in the main folder of

Re: jh_build seeks in .pc folder (Was: Request for sponsoring: beagle)

2016-04-26 Thread Dylan
Hi Andreas, Thank you for the upload. I suppose that you don't know why my gbp import-orig remove the src folder. Best regards, Dylan

Re: jh_build seeks in .pc folder (Was: Request for sponsoring: beagle)

2016-04-24 Thread Dylan
Hi Andreas, 2016-04-23 0:15 GMT+02:00 Andreas Tille : > On Fri, Apr 22, 2016 at 10:21:37PM +0200, Dylan wrote: >> >> Sorry for the following question, but how can I keep the top level src >> directory? git-import-orig automatically remove it and I do not find >> any option to keep it. > > Strange.

Re: jh_build seeks in .pc folder (Was: Request for sponsoring: beagle)

2016-04-22 Thread Andreas Tille
On Fri, Apr 22, 2016 at 10:21:37PM +0200, Dylan wrote: > > Sorry for the following question, but how can I keep the top level src > directory? git-import-orig automatically remove it and I do not find > any option to keep it. Strange. What exact command did you used? The correct command is

Re: jh_build seeks in .pc folder (Was: Request for sponsoring: beagle)

2016-04-22 Thread Dylan
Hi, Thank you Andreas, 2016-04-18 8:31 GMT+02:00 Emmanuel Bourg : > Le 18/04/2016 08:21, Andreas Tille a écrit : > >> Do you have any hint or is this a bug in jh_build? > > This looks like a bug in jh_build. That said, you could also keep the > top level src directory from the upstream tarball and

Re: Request for sponsoring: beagle

2016-04-18 Thread Olivier Sallou
- Mail original - > De: "Dylan" > À: "Debian Med Project" > Envoyé: Lundi 18 Avril 2016 08:11:05 > Objet: Re: Request for sponsoring: beagle > > Hi, > According to ftpmaster's comments, I removed the embedded copy of > htsjdk and I pat

Re: Request for sponsoring: beagle

2016-04-17 Thread Afif Elghraoui
على الأحد 17 نيسـان 2016 ‫23:11، كتب Dylan: > I also asked to upstream the source file of the pdf and he sent me a > docx file. I do not find any information about how to integrate > correctly a pdf from a docx file. So, I do not package the pdf > anymore. I suppose it's possible to generate the

Re: jh_build seeks in .pc folder (Was: Request for sponsoring: beagle)

2016-04-17 Thread Emmanuel Bourg
Le 18/04/2016 08:21, Andreas Tille a écrit : > Do you have any hint or is this a bug in jh_build? This looks like a bug in jh_build. That said, you could also keep the top level src directory from the upstream tarball and instruct jh_build to look for sources in this directory only. That would av

jh_build seeks in .pc folder (Was: Request for sponsoring: beagle)

2016-04-17 Thread Andreas Tille
Hi Debian Java experts, I admit I have not checked myself but Dylan reports that jh_build seeks in .pc folder which is wrong. The package in question is in Git https://anonscm.debian.org/git/debian-med/beagle.git Do you have any hint or is this a bug in jh_build? Kind regards Andreas

Re: Request for sponsoring: beagle

2016-04-17 Thread Dylan
Hi, According to ftpmaster's comments, I removed the embedded copy of htsjdk and I patched some files to refer to the new htsjdk. But with this new patch, beagle FTBFS because jh_build searches .java files in .pc folder. So, I remove the .pc folder just before calling jh_build. I do not think it is

Re: Request for sponsoring: beagle

2016-03-30 Thread Dylan
Hi Afif, 2016-03-29 9:19 GMT+02:00 Afif Elghraoui : > No problem. By the way, I noticed you had an emacs modeline in your > debian/rules file. There are emacs modes for the debian packaging files > in the dpkg-dev-el package. If you install that, emacs will work very > well with debian/* Thanks f

Re: Request for sponsoring: beagle

2016-03-29 Thread Afif Elghraoui
على الإثنين 28 آذار 2016 ‫01:05، كتب Dylan: >> On Sat, Mar 26, 2016 at 09:59:09PM +0100, Andreas Tille wrote: >>> Uploaded - thanks for your work. Andreas. >> >> And probably beaten. ;-) Thanks a lot Afif! > > > > Thank you both! > No problem. By the way, I noticed you had an emacs modelin

Re: Request for sponsoring: beagle

2016-03-28 Thread Dylan
> On Sat, Mar 26, 2016 at 09:59:09PM +0100, Andreas Tille wrote: >> Uploaded - thanks for your work. Andreas. > > And probably beaten. ;-) Thanks a lot Afif! Thank you both! Dylan

Re: Request for sponsoring: beagle

2016-03-26 Thread Afif Elghraoui
على السبت 26 آذار 2016 ‫14:01، كتب Andreas Tille: >> Uploaded - thanks for your work. Andreas. > And probably beaten. ;-) Thanks a lot Afif! > No problem! I do, however, think it's time something is done abou the race conditions. I have a suggestion that I'm going to post to the thread where

Re: Request for sponsoring: beagle

2016-03-26 Thread Andreas Tille
On Sat, Mar 26, 2016 at 09:59:09PM +0100, Andreas Tille wrote: > Uploaded - thanks for your work. Andreas. And probably beaten. ;-) Thanks a lot Afif! > On Sat, Mar 26, 2016 at 07:55:07PM +0100, Dylan wrote: > > Hi all, > > Could someone sponsor this new package [1] ? > > > > Package name: be

Re: Request for sponsoring: beagle

2016-03-26 Thread Andreas Tille
Uploaded - thanks for your work. Andreas. On Sat, Mar 26, 2016 at 07:55:07PM +0100, Dylan wrote: > Hi all, > Could someone sponsor this new package [1] ? > > Package name: beagle > URL: https://faculty.washington.edu/browning/beagle/beagle.html > License: GPL3+ > Programming Lang: Java > Descrip

Re: Request for sponsoring: beagle

2016-03-26 Thread Afif Elghraoui
Hi, Dylan, على السبت 26 آذار 2016 ‫11:55، كتب Dylan: > Hi all, > Could someone sponsor this new package [1] ? > Done. > Package name: beagle > URL: https://faculty.washington.edu/browning/beagle/beagle.html > License: GPL3+ > Programming Lang: Java > Description: Genotypic imputation that works

Request for sponsoring: beagle

2016-03-26 Thread Dylan
Hi all, Could someone sponsor this new package [1] ? Package name: beagle URL: https://faculty.washington.edu/browning/beagle/beagle.html License: GPL3+ Programming Lang: Java Description: Genotypic imputation that works on phased genotypes. Beagle performs genotype calling, genotype phasing, impu