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
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
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
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
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
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
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
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
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
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
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
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
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
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.
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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*
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
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
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
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
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
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
>>
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
#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
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
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
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
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 '
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
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
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
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
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
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
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
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
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
;> -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
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
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
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
[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,
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
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
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
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
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
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
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
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
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
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
>
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
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
@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
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.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
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
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
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
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
[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
-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
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
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
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
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
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
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
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
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
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 ',
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
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
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
--- 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.
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
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
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]
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
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
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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