bio-linux-desktop

2019-05-31 Thread Tony Travis
Hi, Andreas. Sorry about my slow progress on this project... I've been creating "bio-linux-desktop" .iso's manually from the 'task' you created and even though not all of the packages were installed the resulting .iso is already > 6GB, which is too big to writ

Re: FW: Bio linux download

2019-05-20 Thread Dylan Aïssi
Hi Tony, Le lun. 20 mai 2019 à 22:21, Tony Travis a écrit : > Hi, Dylan. > > I've installed the "metaphlan2" package from Ubuntu "bionic-proposed" > successfully, with no errors reported. If "metaphlan2" is installed, > "med-bio" will install without errors in Ubuntu-MATE 18.04.2 LTS: > Thanks f

Re: FW: Bio linux download

2019-05-20 Thread Tony Travis
On 24/04/2019 20:29, Dylan Aïssi wrote: Hi Graham, Le mer. 24 avr. 2019 à 21:19, Graham Inggs a écrit : Is this LP: #1777165 [1]? Let's get this fixed, I'm happy to sponsor a SRU [2] upload. I am preparing the fix [1], I will ping you when it is ready. Best, Dylan [1] https://salsa.debi

Re: FW: Bio linux download

2019-04-25 Thread Tony Travis
On 25/04/2019 19:11, Graham Inggs wrote: On Wed, 24 Apr 2019 at 23:42, Tony Travis wrote: I reported the bug and provided a patch - What else should I have done? Subscribing the 'ubuntu-sponsors' team to the bug would have made it visible to someone who could have done the upload for you. It

Re: FW: Bio linux download

2019-04-25 Thread Graham Inggs
On Wed, 24 Apr 2019 at 23:42, Tony Travis wrote: > I reported the bug and provided a patch - What else should I have done? Subscribing the 'ubuntu-sponsors' team to the bug would have made it visible to someone who could have done the upload for you. It's mostly only the packages supported by Ca

Re: FW: Bio linux download

2019-04-24 Thread Tony Travis
On 24/04/2019 21:20, Graham Inggs wrote: Hi On Wed, 24 Apr 2019 at 21:30, Dylan Aïssi wrote: I am preparing the fix [1], I will ping you when it is ready. Uploaded, thanks! For future reference, the general procedure to get a fix into Ubuntu is to attach a patch and subscribe 'ubuntu-sponso

Re: FW: Bio linux download

2019-04-24 Thread Graham Inggs
Hi On Wed, 24 Apr 2019 at 21:30, Dylan Aïssi wrote: > I am preparing the fix [1], I will ping you when it is ready. Uploaded, thanks! For future reference, the general procedure to get a fix into Ubuntu is to attach a patch and subscribe 'ubuntu-sponsors' to the bug. Regards Graham

Re: FW: Bio linux download

2019-04-24 Thread Graham Inggs
Hi Tony On Wed, 24 Apr 2019 at 16:32, Tony Travis wrote: > [Note: There is a problem installing "metaphlan2" under Ubuntu 18.04] Is this LP: #1777165 [1]? Let's get this fixed, I'm happy to sponsor a SRU [2] upload. Regards Graham [1] https://pad.lv/1777165 [2] https://wiki.ubuntu.com/StableR

Re: FW: Bio linux download

2019-04-24 Thread Dylan Aïssi
Hi Graham, Le mer. 24 avr. 2019 à 21:19, Graham Inggs a écrit : > > Is this LP: #1777165 [1]? Let's get this fixed, I'm happy to sponsor > a SRU [2] upload. > I am preparing the fix [1], I will ping you when it is ready. Best, Dylan [1] https://salsa.debian.org/med-team/metaphlan2/commits/ubu

Re: FW: Bio linux download

2019-04-24 Thread Tony Travis
On 24/04/2019 14:55, Timms-Wilson, Tracey wrote: *From:*Shaun Allingham [mailto:s.alling...@derby.ac.uk] *Sent:* 24 April 2019 14:37 *To:* Timms-Wilson, Tracey *Subject:* Bio linux download Hi, I am trying to download Biolinux on a USB stick but once i have finished the initial download the

Re: Bio-Linux 8 EOL

2019-03-27 Thread Andreas Tille
Hi Tony, On Wed, Mar 27, 2019 at 12:21:33PM +, Tony Travis wrote: > apt install x2goserver > > Also install these security packages: > > apt install fail2ban > apt install rkhunter > apt install chkrootkit I'd recommend to add these packages to the bio-l

Bio-Linux 8 EOL

2019-03-27 Thread Tony Travis
Hi, Bio-Linux 8 will reach its EOL (End Of Life) in April 2019 when Ubuntu 14.04 LTS reaches its EOL and Bio-Linux 8 will no longer be supported. Bio-Linux 9 is still a work in progress, but I recommend replacing any Bio-Linux 8 instances with a clean install of Ubuntu-MATE 18.04 LTS

Re: Galaxy under Bio-Linux 9

2019-03-11 Thread Tony Travis
Hi, Casey. Thanks for your helpful reply. In fact, I know Tim well and I worked with him on Bio-Linux for many years. The Debian Med team are looking into the possibility of packaging Galaxy ‘properly’ as opposed to Tim’s hand-crafted binary .deb, for which there was never a source .deb

Re: Galaxy under Bio-Linux 9

2019-03-11 Thread Casey Bergman
o get this information. Sorry I can't be more helpful. Best regards, Casey > On Mar 9, 2019, at 10:01, Tony Travis > wrote: > > Hi, Casey. > > I'm at the 2019 Debian-Med Sprint in Vilnius and we are discussing how to > package Galaxy for Bio-Linux in Debian-Med.

Galaxy under Bio-Linux 9

2019-03-09 Thread Tony Travis
Hi, Casey. I'm at the 2019 Debian-Med Sprint in Vilnius and we are discussing how to package Galaxy for Bio-Linux in Debian-Med. Because you were one of the people who developed the Galaxy instance that Tim created a binary .deb package for, I suggested that we contact you to find out i

Galaxy under Bio-Linux 9

2019-03-09 Thread Tony Travis
Hi, Simon. I'm at the 2019 Debian-Med Sprint in Vilnius and we are discussing how to package Galaxy for Bio-Linux in Debian-Med. Because you were one of the people who developed the Galaxy instance that Tim created a binary .deb package for, I suggested that we contact you to find out i

Bio-Linux 9 alpha on CyVerse

2018-11-19 Thread Tony Travis
Hi, I've created a public Bio-Linux 9-alpha image on CyVerse Atmosphere: > https://atmo.cyverse.org/application/images/1617 We were unable to image an instance based on Ubuntu-MATE 18.04 (Bionic) for some reason so, until we find out why, I've made a version based on Ubuntu-MATE

Bio-Linux 9 alpha on CyVerse Atmosphere

2018-11-04 Thread Tony Travis
Hi, I've created a public VM image of Bio-Linux 9 alpha (development) on CyVerse Atmosphere as "Bio-Linux-9-ajtravis-20181105": > https://atmo.cyverse.org/application/images/1596 You need an account on CyVerse with Atmosphere enabled to use it: > https://user.cyverse.org/r

Bio-Linux 9 alpha on CyVerse Atmosphere

2018-11-04 Thread Tony Travis
Hi, I've created a public VM image of Bio-Linux 9 alpha (development) on CyVerse Atmosphere as "Bio-Linux-9-ajtravis-20181105": > https://atmo.cyverse.org/application/images/1596 You need an account on CyVerse with Atmosphere enabled to use it: > https://user.cyverse.org/r

Re: Bio-Linux 9

2018-10-14 Thread Andreas Tille
Hi Tony, On Mon, Oct 15, 2018 at 01:18:15AM +0100, Tony Travis wrote: > I'm now back from Milan and working part-time at the University of > Aberdeen again. We are upgrading all our Bio-Linux 8 (Ubuntu 14.04 LTS) > machines to Ubuntu-MATE 18.04 LTS + med-bio + med-bio-dev as proto

Bio-Linux 9

2018-10-14 Thread Tony Travis
Hi, I'm now back from Milan and working part-time at the University of Aberdeen again. We are upgrading all our Bio-Linux 8 (Ubuntu 14.04 LTS) machines to Ubuntu-MATE 18.04 LTS + med-bio + med-bio-dev as prototypes to use during the development of Bio-Linux 9. So far the only problem

Re: [Bio-linux-list] FW: biolinux

2018-09-26 Thread Tony Travis
On 26/09/18 13:48, Simon Wagstaff wrote: > Hi Tony, > We have an increasing number of people working with Galaxy on Biolinux 8. I > understand that previous upgrades of Ubuntu break the BL version of Galaxy > but I was wondering if there are plans to include Galaxy in the Bio-Linux

Re: Bio-Linux

2018-09-14 Thread Andreas Tille
On Fri, Sep 14, 2018 at 03:09:46PM +0100, Tony Travis wrote: > > Neither me nor William are Members of biolinux, which is why we can't > push changes. Please add us as members and make me one of the owners. You asked for membership in Blends team and I added you - so you should be able to push (p

Re: Bio-Linux

2018-09-14 Thread Tony Travis
On 14/09/18 06:56, Andreas Tille wrote: > On Thu, Sep 13, 2018 at 10:32:54PM +0100, Tony Travis wrote: >> >> I've cloned the repo you created and started going through it making the >> changes, but this is a major change and it might be better to start over >&g

Re: Bio-Linux

2018-09-13 Thread Andreas Tille
On Thu, Sep 13, 2018 at 10:32:54PM +0100, Tony Travis wrote: > > I've cloned the repo you created and started going through it making the > changes, but this is a major change and it might be better to start over > with a repo called "bio-linux". I have some routine an

Re: Bio-Linux

2018-09-13 Thread Tony Travis
illiam. I should have made it clear that I want the task to be called Bio-Linux with meta-packages "bio-linux-desktop" and "bio-linux-server". I've cloned the repo you created and started going through it making the changes, but this is a major change and it might be be

Re: Bio-Linux

2018-09-13 Thread Andreas Tille
ges" and metapackages. The term metapackage is just a hint for human beeings that this package has basically no content than dependencies. > Ideally, I would like "bio-linux-server" to include "bio-linux-desktop" > so we don't have to duplicate a list of depen

Re: Bio-Linux

2018-09-13 Thread Tony Travis
On 09/09/18 17:18, Tony Travis wrote: > [...] > I want our "bio-linux-server" meta-package to be a superset of the > "bio-linux-desktop" meta-package. A Bio-Linux server is a GUI terminal > server supporting remote MATE desktops and and needs the complete MAT

Re: Bio-Linux

2018-09-12 Thread Andreas Tille
On Wed, Sep 12, 2018 at 08:15:01PM +0100, William McCaffery wrote: > Hi Andreas, > > I've been attempting to push, but I've been getting > > remote: You are not allowed to push code to this project. > fatal: unable to access > 'https://salsa.debian.org/blends-team/biolinux.git/': The requested UR

Bio-Linux

2018-09-12 Thread William McCaffery
Hi Andreas, I've been attempting to push, but I've been getting remote: You are not allowed to push code to this project. fatal: unable to access 'https://salsa.debian.org/blends-team/biolinux.git/': The requested URL returned error: 403 Any idea what might be causing it? Thanks, William

Re: Bio-Linux

2018-09-09 Thread Tony Travis
exclusively server packages, or would it contain normal bio-linux packages >> as well as server packages? > > This needs to be answered by Tony (or any other Bio-Linux expert). Hi, William and Andreas. Bio-Linux 8 contains 'server' packages that are not really needed on the

Re: Bio-Linux

2018-09-08 Thread Andreas Tille
Hi William, On Sat, Sep 08, 2018 at 06:56:32PM +0100, William McCaffery wrote: > I understand that I need to replace it; this may have been more of a > subjective question -- would we want the server package to contain > exclusively server packages, or would it contain normal bio-linux

Re: Bio-Linux

2018-09-08 Thread William McCaffery
all those recommends from that task and replace it by something that makes sense for Bio-Linux. I personally can not tell what makes sense since I need to admit that I do not know Bio-Linux sufficiently enough. Just feel free to change *everything* and do not assume any sensible content i

Re: Bio-Linux

2018-09-08 Thread Andreas Tille
sk of Debian Med. You possibly need to remove all those recommends from that task and replace it by something that makes sense for Bio-Linux. I personally can not tell what makes sense since I need to admit that I do not know Bio-Linux sufficiently enough. Just feel free to change *everything*

Re: Bio-Linux

2018-09-08 Thread William McCaffery
t virtual packages, would these cause any issues with the package? Before the bio-linux repo was created I had experimented with a meta-package, and had a few issues with them. For example, at least one of them appears to no longer have any normal packages attributed to it. I admit I do not unders

ELPH+Re: Bio-Linux' Caftools -> experimental Fwd: Processing of caftools_2.0.2-1_amd64.changes

2018-08-31 Thread Steffen Möller
t; That would be really cool. Please record it on our Software Liberation > page[1]. > > BTW, what is the reason to upload the package to experimental? Missing man pages, lack of documentation, and  wanted to actively involve the Bio-Linux folks in the package before it his main. To uns

Re: Bio-Linux' Caftools -> experimental Fwd: Processing of caftools_2.0.2-1_amd64.changes

2018-08-26 Thread Andreas Tille
Hi, On Fri, Aug 24, 2018 at 05:10:07PM +0200, Steffen Möller wrote: > This is another Bio-Tools package. I kind of like to have it, but I tend > to think this is mostly of historic interest. This does not mean that we > should not have it, very much the opposite, it was once instrumental for > get

Bio-Linux' Caftools -> experimental Fwd: Processing of caftools_2.0.2-1_amd64.changes

2018-08-24 Thread Steffen Möller
Hello Tony, This is another Bio-Tools package. I kind of like to have it, but I tend to think this is mostly of historic interest. This does not mean that we should not have it, very much the opposite, it was once instrumental for getting the worm genome together, and many others. Because of the s

Re: Bio-Linux

2018-08-22 Thread Steffen Möller
to start with this to spent our time in a sensible >> manner. I'm also offering mentoring to learn how to properly package >> inside the Debian Med team[1]. >> >>> The https://blends.debian.org/med/tasks/bio pages have that yellow >>> section that lists a

Re: Bio-Linux

2018-08-16 Thread Tony Travis
On 16/08/18 13:39, Andreas Tille wrote: > On Thu, Aug 16, 2018 at 12:47:21PM +0200, Tony Travis wrote: >>> >>>> The https://blends.debian.org/med/tasks/bio pages have that yellow >>>> section that lists a few bio-linux ones. How would you (Andreas and >>

Re: Bio-Linux

2018-08-16 Thread Andreas Tille
On Thu, Aug 16, 2018 at 12:47:21PM +0200, Tony Travis wrote: > > > >> The https://blends.debian.org/med/tasks/bio pages have that yellow > >> section that lists a few bio-linux ones. How would you (Andreas and > >> Tony) feel about moving them to the Bio-Linux l

Re: Bio-Linux

2018-08-16 Thread Tony Travis
#x27;m also offering mentoring to learn how to properly package > inside the Debian Med team[1]. > >> The https://blends.debian.org/med/tasks/bio pages have that yellow >> section that lists a few bio-linux ones. How would you (Andreas and >> Tony) feel about moving them to the Bio

Re: Bio-Linux

2018-08-15 Thread Andreas Tille
side I would be particularly interested to learn about the > packages that Bio-Linux wants to see redistributed with them but that > are yet not in Debian. We actually have this kind of documentation since our latest sprint. Unfortunately it seems to be in a simila maintenance situation that ov

Re: Bio-Linux

2018-08-15 Thread Steffen Möller
ks 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. from my side I would be particularly interested to learn about the packages that Bi

Re: [Bio-linux-list] Bio-Linux 9

2018-08-14 Thread Andreas Tille
Hi Tony, On Tue, Aug 14, 2018 at 06:13:22PM +0200, Tony Travis wrote: > On 14/08/18 13:33, Steffen Möller wrote: > >> However, we've not yet managed to enable 'persistence' on a 'live' USB. > > > > Hm. Hm. Hm. How was that again. I propose to ha

Re: [Bio-linux-list] Bio-Linux 9

2018-08-14 Thread Tony Travis
ersistence' on a 'live' USB. > > Hm. Hm. Hm. How was that again. I propose to have the Bio-Linux task > working and we can then address this on Debian Devel. We also need to think > about cloud setups. Hi, Steffen. Do you mean we should NOT discuss how to create a '

Re: [Bio-linux-list] Bio-Linux 9

2018-08-14 Thread Steffen Möller
lp in any way please let me know. > Hi, Simon. > > Thanks very much for your interest in Bio-Linux and your offer to help. +1 > At present, Will is creating a meta-package for "bio-linux-desktop" with > help from Andreas Tille and the Debian-Med team. Our plan is to migrate &g

Re: [Bio-linux-list] Bio-Linux 9

2018-08-14 Thread Tony Travis
On 13/08/18 14:31, Simon Wagstaff wrote: > Hi Will, > This is great news. > > Very much appreciate the effort you and Tony continue to put into the project. > > If I can help in any way please let me know. Hi, Simon. Thanks very much for your interest in Bio-Linux and your

Re: Bio-Linux

2018-08-08 Thread William McCaffery
inel 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

Re: Bio-Linux

2018-08-06 Thread Andreas Tille
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

Re: Bio-Linux

2018-08-06 Thread Tony Travis
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 preferenc

Re: Bio-Linux

2018-08-06 Thread Andreas Tille
ething 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

Re: Bio-Linux

2018-08-03 Thread William McCaffery
Hi Tony, 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. 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

Re: Bio-Linux

2018-08-03 Thread Tony Travis
On 31/07/18 19:50, William McCaffery wrote: > [...] > In regards to the suggestion of a separate source package, what would > that involve? Personally I don't think that having the name > med-bio-linux-desktop would be an issue, since, as far as I'm aware the > package w

Re: Bio-Linux

2018-08-03 Thread Tony Travis
On 28/07/18 00:45, Andreas Tille wrote: > [...] > OK, I understood that full med-bio and med-bio-dev are to heavy for a > live system. Just for my personal understanding: Is Bio-Linux > targeting at live media *exclusively*? Hi, Andreas. Not exclusively, the "Bio-Linux

Re: Bio-Linux

2018-08-01 Thread Steffen Möller
;> -file a WNPP bug report, > This is only needed for new source packages. As long as you stick to > debian-med source package there is no need for a WNPP bug. > >> -Create a new task in Debian med in the blends repository > Yes. > >> -Add to this task all packages current

Re: Bio-Linux

2018-08-01 Thread Andreas Tille
ou stick to debian-med source package there is no need for a WNPP bug. > -Create a new task in Debian med in the blends repository Yes. > -Add to this task all packages currently in Bio-Linux even if they aren't > currently packaged in sid so that if they are added in the future t

Re: Bio-Linux

2018-07-31 Thread William McCaffery
Hi, If we were to create a new task within deb-med, would I be correct in saying that I would have to: -file a WNPP bug report, -Create a new task in Debian med in the blends repository -Add to this task all packages currently in Bio-Linux even if they aren't currently packaged in s

Re: Bio-Linux

2018-07-27 Thread Andreas Tille
maintenance > > effort. If we add new packages these will be mentioned there (and I have > > also developed tools to verify that everything is really included so you > > are safe that no new package will be missing). > > I want to create a 'bio-linux-desktop' meta-pa

Re: Bio-Linux

2018-07-27 Thread Andreas Tille
[Got confirmation from William to quote him in public - please everybody rise your opinion here. Thank you.] - Forwarded message from Andreas Tille - Hi William, On Thu, Jul 26, 2018 at 05:50:52PM +0100, William McCaffery wrote: > I've been working with Tony on Bio-linux 9,

Re: Digressions (Re: Bio-Linux 9)

2018-07-09 Thread Tony Travis
hed in > Nature Methods: > [...] Hi, Charles and Michael. Bio-Linux is an APT-managed system, and Bio-Linux 9 will be based on "med-bio" and "med-bio-dev". Although I'm running an APT-managed system, I do sometimes find it difficult to live under the constraints im

Re: Digressions (Re: Bio-Linux 9)

2018-07-09 Thread Michael Crusoe
2018-07-06 5:16 GMT+03:00 Charles Plessy : > Le Sun, Jun 24, 2018 at 11:26:32AM +0100, Tony Travis a écrit : > > On 24/06/18 01:21, Charles Plessy wrote: > > > > > > Very much agreed. I see how bioconda is slowly overtaking us, just by > > > providing an essential feature: the ability to install

Re: Digressions (Re: Bio-Linux 9)

2018-07-05 Thread Charles Plessy
Le Sun, Jun 24, 2018 at 11:26:32AM +0100, Tony Travis a écrit : > On 24/06/18 01:21, Charles Plessy wrote: > > > > Very much agreed. I see how bioconda is slowly overtaking us, just by > > providing an essential feature: the ability to install software via a > > package manager without having to

Re: omegaMap in salsa -> bio-linux co-maintenance?

2018-07-03 Thread Tony Travis
On 03/07/18 15:34, Steffen Möller wrote: > Hello, > > I just contributed an initial packaging of > https://blends.debian.org/med/tasks/bio#omegamap (yellow bio-linux > package) to salsa (https://salsa.debian.org/med-team/omegamap). @Tony, > how would you feel about becoming on

omegaMap in salsa -> bio-linux co-maintenance?

2018-07-03 Thread Steffen Möller
Hello, I just contributed an initial packaging of https://blends.debian.org/med/tasks/bio#omegamap (yellow bio-linux package) to salsa (https://salsa.debian.org/med-team/omegamap). @Tony, how would you feel about becoming one of the Uploaders? I thought this may help. The package needs a bit of

Re: Digressions (Re: Bio-Linux 9)

2018-06-24 Thread Tony Travis
conflicting versions of supporting software for a given pipeline can't be installed on the same system. The issue of having to ask a system admin to install packages is not the main issue. In the case of Bio-Linux 8, I use "Bioconda" to run QIIME for precisely this reason and I int

Digressions (Re: Bio-Linux 9)

2018-06-23 Thread Charles Plessy
Le Sat, Jun 23, 2018 at 11:45:04AM +0200, Steffen Möller a écrit : > > And if we just remove that red section? After all, we do have ITPs for > what red is meant to express. So, I would rather have red as an indication > of a delta to conda - or to bio-linux to stay in the thread. Hi

Re: Bio-Linux 9

2018-06-23 Thread Steffen Möller
is outdated and will possibly never > be packaged. And if we just remove that red section? After all, we do have ITPs for what red is meant to express. So, I would rather have red as an indication of a delta to conda - or to bio-linux to stay in the thread. To digress a bit - to care for sin

Re: Bio-Linux 9

2018-06-22 Thread Andreas Tille
On Fri, Jun 22, 2018 at 05:53:40PM +0200, Steffen Möller wrote: > > @all, anybody who minds if I remove all software from our red list that > has stale URLs? Hexamer came to mind. Ohters just needs an update of > their URL like GenoGrapher and yet again others should possibly be > removed because

Re: Bio-Linux 9

2018-06-22 Thread Steffen Möller
On 6/21/18 5:41 PM, Andreas Tille wrote: > Hi William, > > On Thu, Jun 21, 2018 at 03:39:46PM +0100, William wrote: >> Over the next six weeks I'll be working with Tony Travis to build an alpha >> release of Bio Linux 9, which will see a switch from using the NERC >

Re: Bio-Linux 9

2018-06-21 Thread Andreas Tille
Hi William, On Thu, Jun 21, 2018 at 03:39:46PM +0100, William wrote: > Over the next six weeks I'll be working with Tony Travis to build an alpha > release of Bio Linux 9, which will see a switch from using the NERC > repositories to Debian sid, as imported into Ubuntu. We

Bio-Linux 9

2018-06-21 Thread William
Hi, Over the next six weeks I'll be working with Tony Travis to build an alpha release of Bio Linux 9, which will see a switch from using the NERC repositories to Debian sid, as imported into Ubuntu. We hope that this release will have most of the functionality seen in our Bio-Linux

AW: [Bio-linux-devel] phoenix clinical trial management system integration

2018-06-09 Thread Rene Krenn
@an3as.eu] Gesendet: Dienstag, 22. Mai 2018 10:00 An: Rene Krenn ; Debian Med Project List Cc: 'Kojzar, Harald' ; 'Trajanoski, Slave' Betreff: Re: [Bio-linux-devel] phoenix clinical trial management system integration [Removing bio-linux-de...@bioinformatics.org from CC

Re: Tetra from Bio-Linux - lost?

2018-05-31 Thread Steffen Möller
a. In my mission to >> turn yellow packages into green I thought that I should go and package >> that one up. Do you have the source tree anywhere, still? > Hi, Steffen. > > Sorry about my slow reply, I've been busy teaching... > > Bela Tiwari and Tim Booth created b

Re: [Bio-linux-list] FW: biolinux

2018-05-27 Thread Tony Travis
re.org/wiki/User:Andor_J_Kiss  > > On Mon, 2018-04-16 at 12:29 +0100, Tony Travis wrote: >> [...] >> Yes, we are planning a release of Bio-Linux 9 but it will be based on >> Ubuntu-MATE 18.04 LTS not 16.04. >> >> The new version of Bio-Linux will include many pac

Re: Tetra from Bio-Linux - lost?

2018-05-23 Thread Tony Travis
that I should go and package > that one up. Do you have the source tree anywhere, still? Hi, Steffen. Sorry about my slow reply, I've been busy teaching... Bela Tiwari and Tim Booth created binary-only Debian packages for the initial releases of Bio-Linux before I was involved in

trace2dbest Re: Tetra from Bio-Linux - lost?

2018-05-23 Thread Steffen Möller
welcome you as an uploader. Another Bio-Linux package by the same group with interest in ESTs is "Partigene". Should there be some interest, by Tony or someone else, I happily offer to share a screen via Skype while packaging that one, too. Best, Steffen On 5/22/18 8:03 PM, Andreas T

Re: Tetra from Bio-Linux - lost?

2018-05-22 Thread Andreas Tille
Hi, I tried https://web.archive.org/ but failed. This mail is just a hint that this sometimes works as last resort but it did not in this case. Kind regards Andreas. On Tue, May 22, 2018 at 07:16:24PM +0200, Steffen Möller wrote: > Hi Tony, > > The tool "tetra" > (https://bmcbioinforma

Tetra from Bio-Linux - lost?

2018-05-22 Thread Steffen Möller
Hi Tony, The tool "tetra" (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-5-163) has lost its presence on http://www.megx.net/tetra. In my mission to turn yellow packages into green I thought that I should go and package that one up. Do you have the source tree anywhere, st

Re: [Bio-linux-devel] phoenix clinical trial management system integration

2018-05-22 Thread Andreas Tille
[Removing bio-linux-de...@bioinformatics.org from CC since I understood Tony that it is not relevant for this list.] Hi Rene, On Tue, May 22, 2018 at 09:13:45AM +0200, Rene Krenn wrote: > > ok regarding packaging, jfyi this is the script to get (and build) it on a > minimal debia

AW: [Bio-linux-devel] phoenix clinical trial management system integration

2018-05-22 Thread Rene Krenn
-processor. Another optional one would be the public subject signup portal, which is a perl dancer webapp. regards, rene -Ursprüngliche Nachricht- Von: Andreas Tille [mailto:andr...@an3as.eu] Gesendet: Dienstag, 22. Mai 2018 08:02 An: Tony Travis Cc: bio-linux-de...@bioinformatics.org

Re: [Bio-linux-devel] phoenix clinical trial management system integration

2018-05-21 Thread Andreas Tille
should subscribe in any case this list since the mentoring is done in public.) > Hi, Rene. > > Bio-Linux is a platform for bioinformatics, rather than collecting and > analysing clinical trials data. It looks like a good target for the task "Research"[3] which has no existi

Re: [Bio-linux-devel] phoenix clinical trial management system integration

2018-05-19 Thread Tony Travis
lp with > packaging. Hi, Rene. Bio-Linux is a platform for bioinformatics, rather than collecting and analysing clinical trials data. However, many packages from Debian-Med are included in Bio-Linux and the two projects work together to avoid duplication of effort packaging the same bioinformati

Porting to Bio-Linux and publicity work (Was: RRID update on salsa on packages starting with A+B)

2018-04-04 Thread Andreas Tille
Hi, On Wed, Apr 04, 2018 at 02:36:57PM +0200, Steffen Möller wrote: > > In my PoV there is not too much of a conceptional difference between porting > to Bio-Linux and having backports within Debian. We need to address both. > Just who should do all that. Backporting to Debian stab

Re: Updating Bio-Linux

2018-04-01 Thread Tony Travis
On 01/04/18 11:41, Abdulrahman MI wrote: > Dear tony > > Thanks for bio-linux  > I have questions  > How to update the tools like SPAdes, etc to most recent release. Hi, Abdulrahman. You have two options: Compile version 3.11.1 from source: > http://cab.spbu.ru/software/s

Re: Bio-Linux vs Debian-Med package lists [update]

2018-03-22 Thread Andreas Tille
on. Could you provide a patch for the package description[2] to reflect this fact a bit better. I'd love to provide thorough information to the users of the package and for sure I would add the package to med-bio once it becomes clear to the reader why it is there. I have in mind something

Re: Bio-Linux vs Debian-Med package lists [update]

2018-03-22 Thread Tony Travis
he "aplpack" package is for plotting all sorts of biological results. At present, Bio-Linux takes these from Michael Rutter's Ubuntu PPA: > https://launchpad.net/~marutter/+archive/ubuntu/c2d4u Thanks again, Tony. -- Minke Informatics Limited, Registered in Scotland - Company N

Re: Bio-Linux vs Debian-Med package lists [update]

2018-03-22 Thread Andreas Tille
Hi Tony, I just commited the following change: diff --git a/debian-med_missings.txt b/debian-med_missings.txt index bdd6826..53add22 100644 --- a/debian-med_missings.txt +++ b/debian-med_missings.txt @@ -156,13 +156,8 @@ r-bioc-zlibbioc: r-bioc-deseq: - Debian has r-bioc-deseq2 is r-bioc-dese

Re: Bio-Linux vs Debian-Med package lists [update]

2018-03-12 Thread Tony Travis
If I do not hear from you I will soon remove those packages > from the list that are obvious false positives. Hi, Andreas. I compared the Bio-Linux 'master' list of packages added to Ubuntu in the Bio-Linux .iso with your Debian-Med/Bio* tasks. The false positives appear to be p

Re: Bio-Linux vs Debian-Med package lists [update]

2018-03-11 Thread Andreas Tille
Debian-Med Sprint in Barcelona. > > > > I've compared our Bio-Linux 'master' package list used to create the > > 'live/install' USB stick with your "med-bio*" list of 'Recommends:'. > > > > Updated to remove ',

Re: Bio-Linux vs Debian-Med package lists [update]

2018-02-12 Thread Andreas Tille
Hi Tony, thanks for the comparison. On Sun, Feb 11, 2018 at 07:21:20PM +0100, Tony Travis wrote: > Re: Our discussion at the 2018 Debian-Med Sprint in Barcelona. > > I've compared our Bio-Linux 'master' package list used to create the > 'live/install' U

Bio-Linux vs Debian-Med package lists [update]

2018-02-11 Thread Tony Travis
Hi, Andreas. Re: Our discussion at the 2018 Debian-Med Sprint in Barcelona. I've compared our Bio-Linux 'master' package list used to create the 'live/install' USB stick with your "med-bio*" list of 'Recommends:'. Updated to remove ',' from

Re: Bio-Linux vs Debian-Med package lists

2018-02-11 Thread Andreas Tille
Hi Tony, no idea why your mail did not made it to the list - I'm answering to what I've bounced here. On Sun, Feb 11, 2018 at 09:46:50AM +0100, Tony Travis wrote: > I've compared our Bio-Linux 'master' package list used to create the > 'live/install

Fwd: Bio-Linux vs Debian-Med package lists

2018-02-11 Thread Tony Travis
--- Begin Message --- Hi, Andreas. Re: Our discussion at the 2018 Debian-Med Sprint in Barcelona. I've compared our Bio-Linux 'master' package list used to create the 'live/install' USB stick with your "med-bio*" list of 'Recommends:'. Bye, Tony.

Re: [Bio-linux-dev] Bringing the Artemis package officially into Debian

2015-09-24 Thread Afif Elghraoui
Hello, On الأربعاء 23 أيلول 2015 03:03, Steffen Möller wrote: > > On 23.09.2015 09:26, Andreas Tille wrote: >> thanks again for your push on artemis packaging. > Indeed. A big "wow!" also from my side. >> On Tue, Sep 22, 2015 at 08:51:59PM -0700, Afif Elghraoui wrote: >>> Following the earlier em

Re: [Bio-linux-dev] Bringing the Artemis package officially into Debian

2015-09-23 Thread Andreas Tille
On Wed, Sep 23, 2015 at 12:03:21PM +0200, Steffen Möller wrote: > >>That is, except for > >>jemAlign.jar, which I can find no trace of anywhere on the internet > >>other than Artemis's bundle and an email thread on Debian Med where > >>Andreas is also looking for its source. The Artemis upstream re

Re: [Bio-linux-dev] Bringing the Artemis package officially into Debian

2015-09-23 Thread Steffen Möller
On 23.09.2015 09:26, Andreas Tille wrote: Hi Afif, thanks again for your push on artemis packaging. Indeed. A big "wow!" also from my side. On Tue, Sep 22, 2015 at 08:51:59PM -0700, Afif Elghraoui wrote: Following the earlier email exchange, I had started some draft packaging for Artemis [1]

Re: [Bio-linux-dev] Bringing the Artemis package officially into Debian

2015-09-23 Thread Andreas Tille
Hi Afif, thanks again for your push on artemis packaging. On Tue, Sep 22, 2015 at 08:51:59PM -0700, Afif Elghraoui wrote: > Following the earlier email exchange, I had started some draft packaging > for Artemis [1]. At a cursory look, it seems that all the Java > dependencies are now available fr

Re: [Bio-linux-dev] Bringing the Artemis package officially into Debian

2015-09-22 Thread Afif Elghraoui
Hi, Jim, Sascha, and all, Following the earlier email exchange, I had started some draft packaging for Artemis [1]. At a cursory look, it seems that all the Java dependencies are now available from Debian packages. That is, except for jemAlign.jar, which I can find no trace of anywhere on the inte

Re: [Bio-linux-dev] Bringing the Artemis package officially into Debian

2015-09-22 Thread Sascha Steinbiss
Hi all, > Have you contacted the team at Sanger developing Artemis ? They are almost > certainly happy to help out with any upstream issues you might have. I am working closely with the Pathogen Informatics team at Sanger, who maintain Artemis at the moment. While there is currently no dedicate

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