From tbooth at ceh.ac.uk Wed Dec 3 09:06:18 2014 From: tbooth at ceh.ac.uk (Tim Booth) Date: Wed, 3 Dec 2014 14:06:18 +0000 Subject: [Bio-linux-dev] Galaxy config In-Reply-To: <54733C3A.7080103@abdn.ac.uk> References: <54733C3A.7080103@abdn.ac.uk> Message-ID: <1417615578.26424.41.camel@wllt1771.nerc-wallingford.ac.uk> Hi Tony, Sorry it took so long to reply to this. Many things on my TODO list as usual. The answer is "possibly" since galaxy configuration is a bit of a mess, with some things allowing sub-configurations, some things being monolithic and others being hacked to allow migration to the Tool Shed. Basically, all your custom configs should be converted to shed modules and loaded via the Tool Shed mechanism, and if you don't want to do this there are ways around it but they are hacky. The newest Galaxy brings in major changes and I don't have the time to get it working as a package just now, so I'm staying with the version I have for the duration of BL8, but of course I'll add fixes and security/stability patches. By the way, are you still operating as Minke Informatics? The website is a dead link today, or at least an error code from the server. Cheers, TIM On Mon, 2014-11-24 at 14:10 +0000, Tony Travis wrote: > Hi, Tim. > > I've just realised that a Bio-Linux Galaxy update overwrote my custom > Galaxy config for "osiris": > > https://bitbucket.org/osiris_phylogenetics > > Is there a way to include sub-configs in Galaxy to prevent this? > > BTW, I think "osiris" might be a useful addition to BL Galaxy. > > Thanks, > > Tony. > > -- > Dr. A.J.Travis, University of Aberdeen, Institute of Biological and > Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen > AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396 > http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis > > > The University of Aberdeen is a charity registered in Scotland, No SC013683. > Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683. > _______________________________________________ > Bio-Linux-dev mailing list > Bio-Linux-dev at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705 From tony.travis at abdn.ac.uk Wed Dec 3 09:35:38 2014 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Wed, 3 Dec 2014 14:35:38 +0000 Subject: [Bio-linux-dev] Galaxy config In-Reply-To: <1417615578.26424.41.camel@wllt1771.nerc-wallingford.ac.uk> References: <54733C3A.7080103@abdn.ac.uk> <1417615578.26424.41.camel@wllt1771.nerc-wallingford.ac.uk> Message-ID: <547F1FBA.1080408@abdn.ac.uk> On 03/12/14 14:06, Tim Booth wrote: > Hi Tony, > > Sorry it took so long to reply to this. Many things on my TODO list as > usual. > > The answer is "possibly" since galaxy configuration is a bit of a mess, > with some things allowing sub-configurations, some things being > monolithic and others being hacked to allow migration to the Tool Shed. > Basically, all your custom configs should be converted to shed modules > and loaded via the Tool Shed mechanism, and if you don't want to do this > there are ways around it but they are hacky. Hi, Tim. OK, I'll learn how to do it properly :-) > The newest Galaxy brings in major changes and I don't have the time to > get it working as a package just now, so I'm staying with the version I > have for the duration of BL8, but of course I'll add fixes and > security/stability patches. > > By the way, are you still operating as Minke Informatics? The website > is a dead link today, or at least an error code from the server. Yes, I'm still operating as Minke Informatics but I've had to change my ISP because the one I was using was impossible to communicate with and had become very unreliable. My email is now working again, but I've not transferred my web pages yet. Bye, Tony. -- Dr. A.J.Travis, University of Aberdeen, Institute of Biological and Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396 http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis The University of Aberdeen is a charity registered in Scotland, No SC013683. Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683. From tony.travis at abdn.ac.uk Tue Dec 16 13:26:05 2014 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Tue, 16 Dec 2014 18:26:05 +0000 Subject: [Bio-linux-dev] Mapmaker Message-ID: <5490793D.80306@abdn.ac.uk> Hi, Tim. I've ported Mapmaker 3.0b to Bio-Linux 8. Based on Patches for compiling Mapmaker3 under Mac OS: http://ftp.kaist.ac.kr/macports/release/ports/science/mapm3/ mailto:ryandesign at macports.org Original Mapmaker 3.0b sources obtained from: http://www.broadinstitute.org/ftp/distribution/software/mapmaker3/ mailto:mapmaker at genome.wi.mit.edu This is quite old software, but it is still widely used under e.g. "dosbox" and I thought it was worth porting it to Bio-Linux to get a native version. I've verified that the results from analysing the sample data using the native Linux version of agree with results obtained using the DOS version. Please let me know if you think this would be worth packaging for Bio-Linux/Debian-Med. I've tried to contact the upstream developers at the Broad institute, but my email to was bounced. I'm in touch with the developer of the Mac port already. Thanks, Tony. -- Dr. A.J.Travis, University of Aberdeen, Institute of Biological and Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396 http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis The University of Aberdeen is a charity registered in Scotland, No SC013683. Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683. -------------- next part -------------- A non-text attachment was scrubbed... Name: mapm3.patch Type: text/x-patch Size: 22782 bytes Desc: not available URL: