Re: Bio-Linux
Hi Tony, On Mon, Aug 06, 2018 at 11:48:58AM +0200, Tony Travis wrote: > > Please have a look at > > > > https://salsa.debian.org/blends-team/biolinux > > > > To have some content I have choosen a copy of med-bio for biolinux-desktop > > and med-bio-dev for biolinux-server which is definitely *not* sensible, but > > works as a test case. Please adapt the tasks (including the Description in > > the top) to your preference. Once you have something reasonable I'll setup > > the websentinel config to have tasks pages for BioLinux. > > I've just had a look, but I see all packages set as 'Recommends' - How > do I configure them to be installed? Recommends are installed on default installations. You need to force apt by --no-install-recommends in case you want to stop apt from doing this and this is how metapackages should work. You once installed apt-get install med-bio and got all the Recommends, right? > The main packages in the server metapackage are the Apache web server > and Galaxy, plus the x2go server. Neither of these are useful on a > 'live' USB/DVD or minimal install on a low-spec PC. Just add these packages to the server package (and for sure remove what needs to be removed. It seems there is some packaging work left for galaxy server). > > Please check all files for spelling issues etc. There is no point in > > manually editing debian/control or biolinux-tasks.desc since these are > > autogenerated. You get them by > > > > make dist > > > > Hope this helps over the first hurdle but keep on asking here. I'll be > > more responsive soon (just in the train back home from DebConf). > > It helps a LOT! :-) > > Thanks for the effort to merge BioLinux and Debian Med - I'm positive > > about a great and productive cooperation > > Me too :-) Happy to contribute to BioLinux Andreas. -- http://fam-tille.de
New version of bali-phy
Hi Andreas, I pushed a new version of bali-phy (version 3.3) to the salsa repo. The debian build process hasn't changed this round, but the package has some nice improvements. Can you please upload it for me? -BenRI
Re: Bio-Linux
On 06/08/18 11:12, Andreas Tille wrote: > Hi William and Tony, > > On Fri, Aug 03, 2018 at 03:22:01PM +0100, William McCaffery wrote: >> That sounds reasonable, especially if we want to keep them as discreet >> projects. If Andreas would be willing to set this up that would be great. > > Please have a look at > > https://salsa.debian.org/blends-team/biolinux > > To have some content I have choosen a copy of med-bio for biolinux-desktop > and med-bio-dev for biolinux-server which is definitely *not* sensible, but > works as a test case. Please adapt the tasks (including the Description in > the top) to your preference. Once you have something reasonable I'll setup > the websentinel config to have tasks pages for BioLinux. Hi, Andreas. I've just had a look, but I see all packages set as 'Recommends' - How do I configure them to be installed? >> As far as I can tell from the Debian documentation and what we've discussed, >> the complete set of Bio-Linux tasks would simply be Tim's original package >> list, divided into desktop and server tasks. I would ask your preference on >> whether we would use the reduced list I created which only has packages in >> sid (although this has some issues with virtual packages) or the compete >> set. I know that the documentation states the latter, but I don't know if >> all of the packages are still useful to Bio-Linux. As for separating >> Bio-Linux server and client packages, I can go through Tim's packages and >> try and create a list of packages for a server task for review. The main packages in the server metapackage are the Apache web server and Galaxy, plus the x2go server. Neither of these are useful on a 'live' USB/DVD or minimal install on a low-spec PC. > Please check all files for spelling issues etc. There is no point in > manually editing debian/control or biolinux-tasks.desc since these are > autogenerated. You get them by > > make dist > > Hope this helps over the first hurdle but keep on asking here. I'll be > more responsive soon (just in the train back home from DebConf). It helps a LOT! > Thanks for the effort to merge BioLinux and Debian Med - I'm positive > about a great and productive cooperation Me too :-) Tony. -- Minke Informatics Limited, Registered in Scotland - Company No. SC419028 Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) tel. +44(0)19755 63548http://minke-informatics.co.uk mob. +44(0)7985 078324mailto:tony.tra...@minke-informatics.co.uk
Re: Bio-Linux
Hi William and Tony, On Fri, Aug 03, 2018 at 03:22:01PM +0100, William McCaffery wrote: > That sounds reasonable, especially if we want to keep them as discreet > projects. If Andreas would be willing to set this up that would be great. Please have a look at https://salsa.debian.org/blends-team/biolinux To have some content I have choosen a copy of med-bio for biolinux-desktop and med-bio-dev for biolinux-server which is definitely *not* sensible, but works as a test case. Please adapt the tasks (including the Description in the top) to your preference. Once you have something reasonable I'll setup the websentinel config to have tasks pages for BioLinux. > As far as I can tell from the Debian documentation and what we've discussed, > the complete set of Bio-Linux tasks would simply be Tim's original package > list, divided into desktop and server tasks. I would ask your preference on > whether we would use the reduced list I created which only has packages in > sid (although this has some issues with virtual packages) or the compete > set. I know that the documentation states the latter, but I don't know if > all of the packages are still useful to Bio-Linux. As for separating > Bio-Linux server and client packages, I can go through Tim's packages and > try and create a list of packages for a server task for review. Please check all files for spelling issues etc. There is no point in manually editing debian/control or biolinux-tasks.desc since these are autogenerated. You get them by make dist Hope this helps over the first hurdle but keep on asking here. I'll be more responsive soon (just in the train back home from DebConf). Thanks for the effort to merge BioLinux and Debian Med - I'm positive about a great and productive cooperation Andreas. -- http://fam-tille.de
Re: picard-tools status
- Mail original - > De: "andreas" > À: "debian-med" > Envoyé: Lundi 6 Août 2018 10:03:12 > Objet: Re: picard-tools status > On Mon, Aug 06, 2018 at 09:34:29AM +0200, olivier sallou wrote: >> I see that picard-tools has not been updated to v2.18.2. >> >> libbarclay-java and libgatk-native-bindings-java are still in experimental >> (needed for picard-tools) >> >> Any reason for being stuck in experimental? > > No, please upload to unstable if you have time. I'm on train ride > back from DebConf, Andreas. ok, I have uploaded them to unstable (in progress). I have updated them as well as picard-tools to re-introduce unit tests (were blocks by a bug in an other lib that is fixed now). Once available in unstable, we should be able to build and push picard-tools to sid. Olivier > > -- > http://fam-tille.de
Re: picard-tools status
On Mon, Aug 06, 2018 at 09:34:29AM +0200, olivier sallou wrote: > I see that picard-tools has not been updated to v2.18.2. > > libbarclay-java and libgatk-native-bindings-java are still in experimental > (needed for picard-tools) > > Any reason for being stuck in experimental? No, please upload to unstable if you have time. I'm on train ride back from DebConf, Andreas. -- http://fam-tille.de
picard-tools status
Hi, I see that picard-tools has not been updated to v2.18.2. libbarclay-java and libgatk-native-bindings-java are still in experimental (needed for picard-tools) Any reason for being stuck in experimental? Olivier
