Re: Our discussions about publishing a paper on Debian-Med:
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-13-42
Cloud BioLinux: pre-configured and on-demand bioinformatics computing
for the genomics community
Konstantinos Krampis†Email author, Tim Booth†, Brad Chapman
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 07, 2018 at 03:48:05PM +0200, Steffen Möller wrote:
> I had a look at the precursor of missing Debian packages at
> https://salsa.debian.org/med-team/community/bio-linux/blob/master/debian-med_missings.txt
> . That does not look too bad. Most of these seem to have license issues.
> Qiim
rk on it just now.
>
> Bye,
>
> Tony.
>
>> On 6 Sep 2018, at 12:42, Andreas Tille wrote:
>>
>> Hi William and Tony,
>>
>> one month ago I've created the BioLinux metapackage source[1]. I had
>> expected some commits to the tasks files from yo
very interested in pushing
forward with the Bio-Linux task, but I can’t work on it just now.
Bye,
Tony.
> On 6 Sep 2018, at 12:42, Andreas Tille wrote:
>
> Hi William and Tony,
>
> one month ago I've created the BioLinux metapackage source[1]. I had
> expected so
Hi Andreas,
On 9/6/18 1:42 PM, Andreas Tille wrote:
> Hi William and Tony,
>
> one month ago I've created the BioLinux metapackage source[1]. I had
> expected some commits to the tasks files from you to make a sensible
> tasks layout which can be rendered in the usual B
Hi William and Tony,
one month ago I've created the BioLinux metapackage source[1]. I had
expected some commits to the tasks files from you to make a sensible
tasks layout which can be rendered in the usual Blends way. The fact
that there were no commits so far makes me wonder whether you
On 20/08/18 08:59, Stefan WECKX wrote:
> Hi Tony,
>
>
>
> Any update on the expected release date?
Hi, Stefan.
Sorry, I'm away on holiday in the French Pyranees just now, with only
intermittent access to my email. I'll be working in Milan afterwards
until 2 Oct before I look at the Bio-Linux
On 27/05/18 12:01, Andor J Kiss wrote:
> Hi Tony,
>
> Wow, this is great news. Do you need any help testing? Let me know if
> we can be of any help.
>
> Andor J Kiss, PhD
> Di
nteresting
once it will be open sourced.
> I would like to do something similar to what Tim did with the Galaxy
> package on Biolinux, which sadly have not being updated in a very long time
> :(.
It would be interesting to have it in Debian.
> This is a package I would love see bei
hink about preparing a package to submitting
for debian-med, but that`s a long shot.
I would like to do something similar to what Tim did with the Galaxy
package on Biolinux, which sadly have not being updated in a very long time
:(.
This is a package I would love see being submitted to Debian med in
Hi Raony,
On Thu, Mar 24, 2016 at 01:40:19PM +0100, Raony Guimaraes Corrêa Do Carmo
Lisboa Cardenas wrote:
> That was a very nice welcome! I will read carefully everything you wrote
> and the documents you suggested. I will look for something interesting to
> work on in the tasks page to get star
not yet released you have the
> > > opportunity to get stuff into 16.04 this way, without the need for a
> > > special Bio-Linux package.
>
> +1
>
> Its not even that you do not need a special package. We are striving
> for fully tested packages for all Debian Med packages in a
7:08 +0200, Andreas Tille wrote:
> Hi Tim,
>
> I noticed that BioLinux contains
>
> sickle 0.94windowed adaptive trimming tool for FASTQ files using
> quality
>
> According to Github[1] sickle is at version 1.33. One of our users
> requested this software a
Hi Tim,
I noticed that BioLinux contains
sickle0.94windowed adaptive trimming tool for FASTQ files using
quality
According to Github[1] sickle is at version 1.33. One of our users
requested this software and I would like to update the package. Would
you volunteer to commit your
On Fri, Feb 20, 2015 at 03:14:01AM +, Simon Sadedin wrote:
> Wonderful! Thanks so much for the help.
>
> I am still taking my baby steps and practising making debian packages, but
> I hope to have a package soon that hopefully I could get some feedback on.
Feel free to ask any question you mi
Wonderful! Thanks so much for the help.
I am still taking my baby steps and practising making debian packages, but
I hope to have a package soon that hopefully I could get some feedback on.
Thanks again!
Simon
On 20/02/2015 4:45 am, "Andreas Tille" wrote:
>Hi again,
>
>On Wed, Feb 18, 2015 at
Hi again,
On Wed, Feb 18, 2015 at 01:07:05PM +0100, Andreas Tille wrote:
>
> > gpars 1.2.1 : exists already, but not sufficient version
>
> Since the situation seems to be quite clear in this case I did as
> suggested above in this case (should be seen in BTS soon[1]).
Latest version uploaded t
On 02/18/2015 01:07 PM, Andreas Tille wrote:
> Hi Simon,
>
> On Wed, Feb 18, 2015 at 11:03:32AM +, Simon Sadedin wrote:
>> groovy 2.3.4 : exists already but is only version 2.0.0~beta2
> No idea where you get this version number from. But for developing new
> packages you need to build agains
Hi Simon,
On Wed, Feb 18, 2015 at 11:03:32AM +, Simon Sadedin wrote:
>
> groovy 2.3.4 : exists already but is only version 2.0.0~beta2
No idea where you get this version number from. But for developing new
packages you need to build against unstable and here we have:
$ LANG=LC_ALL apt-cach
Thanks Tim & Andreas,
Your words are very encouraging :-) When I checked in detail I found the
dependency situation is not as bad as I thought. I think these are the
minimal dependencies that are missing or not sufficient:
groovy 2.3.4 : exists already but is only version 2.0.0~beta2
gpars 1.2.1
Hi Simon,
As you've probably guessed, the correct answer is (A) but it might not
be as bad as you think because:
1) Most small Java libraries are actually very easy to package
2) Most updates to small Java libraries are trivial to push through
3) You are not alone - both Debian Med and Debian Jav
Hi Simon,
On Tue, Feb 17, 2015 at 09:32:37AM +, Simon Sadedin wrote:
> I guess I have a ³simple² question but it might be a bit of a showstopper
> - Bpipe relies on a number of java libraries that are fetched in binary
> form from online repositories at build time. If I understand Debian polic
Hi all,
I guess I have a ³simple² question but it might be a bit of a showstopper
- Bpipe relies on a number of java libraries that are fetched in binary
form from online repositories at build time. If I understand Debian policy
correctly, that is not allowable. I checked through the packages and
Hi Simon,
On Thu, Feb 05, 2015 at 11:42:13PM +, Simon Sadedin wrote:
>
> This sounds awesome, I am completely happy to go ahead to do the work to
> get it into Debian Med. Getting it available on standard Linux distros
> would be really great as well!
That's our plan. :-)
> Andreas, I woul
Hi Andreas / Tim,
This sounds awesome, I am completely happy to go ahead to do the work to
get it into Debian Med. Getting it available on standard Linux distros
would be really great as well!
Andreas, I would really enjoy to be part of the MoM program, if you have
time. What would be the first s
Hi Simon,
I'm writing you as a member of the Debian Med team.
On Thu, Feb 05, 2015 at 06:08:49PM +, Tim Booth wrote:
> It's great to hear that you are using Bio-Linux and want to contribute
> your Bpipe package. We also have a need for an effective lightweight
> pipeline system that supports
n packagers' policy manual ;-) Does that sound an OK
plan?
Cheers,
TIM
> Hello,
>
> We are big users of BioLinux here at MCRI so firstly I would like to
> say thank you for this wonderful contribution to the bioinformatics
> community.
>
> I am the author of
On Wed, Sep 28, 2011 at 10:05:19AM +0200, Steffen Möller wrote:
>
> I would try multiple distros and decide which you
> like best
Well, such a try can be time consuming - especially if you want to go
that far to install all the biological software on it. You need to find
a definition for "like b
ive usb and use it on a ms-win xp pro sp3 pc machine:
>>> gigabyte G31M-SL2 mainboard,
>>> Pentium dual core E5200 3.38Ghz (32bit),
>>> 3GB RAM,
>>> Nvidia GeForce 9500GT video-card with own 1GB memory.
>>> one samsung 120GB harddisk with two part
e E5200 3.38Ghz (32bit),
> > 3GB RAM,
> > Nvidia GeForce 9500GT video-card with own 1GB memory.
> > one samsung 120GB harddisk with two partition.
> > (usb mouse/keyboard, usb laser printer samsung ML1610, Hans-G 19" squre LCD
> > monitor with vga connection, 1280
ion, 1280x1024 on winxp)
>
> Some linux based bio-genetic programs Biolinux 5 (32bit), Debian scientific
> Biolgy blend, DNAlinux, Bioslax, Scientific linux, bioknoppix...are based on
> debian and/or ubuntu. This linux program may be more easeir for non
> familiar end users a
On Sat, 6 Sep 2008, Charles Plessy wrote:
in more than one. In the end, they look more like Debtags to me. It has
been a long time that I wonder if it will soon be necessary to split
med-bio, but I am still undecided.
As I said, I'm undecided as well, but I just had the idea to add some
struct
On Sat, 6 Sep 2008, Steffen Moeller wrote:
I personally feel that there is not overly much more that people
really use and that is freely available but not packaged by us ...
ok, a few do come to mind. But not overly much, really.
Thanks for reviewing. It would be really great if somebody mor
On Sat, 06 Sep 2008 22:20:49 +0200, Steffen Moeller wrote:
> Steffen
>
> Who has just installed Ubuntu on a nice machine whose e1000 ethernet
> card was not recognised by the Debian installer
My laptop has an e1000:
$ lspci | grep -i net
00:19.0 Ethernet controller: Intel Corporation 82562GT 10
Hi Andreas,
Andreas Tille wrote:
>
>http://envgen.nox.ac.uk/bioinformatics/
>
I looked through their "protein" category and can stress that
Debian-Med has not need whatsoever to shy off. We just don't
list every binary that EMBOSS comes with as a separate program.
I personally feel that there
On Sat, 6 Sep 2008, Charles Plessy wrote:
my last email exchange with them was two years ago and it left me with
the impression that they do not generate their binary Debian packages
from Debian source packages, but with some tool similar to
"checkinstall".
Well, I do not know checkinstall, bu
n would be to make out tasks pages more comlete and thus
> indirectly advertising BioLinux - which hopefully makes them happy about
> our team. ;-)
>
> Once this is done we should try to catch the "low hanging fruits" which
> might be a nice completion for Debian Med and th
Hi,
at
http://envgen.nox.ac.uk/bioinformatics/
you can fand some search form to find the software which is included into
BioLinux. I started reviewing the packages they builded and started adding
information to our tasks files. They have several packages for software
on our preliminary
Hi,
I just noticed the BioLinux-BR Project in Brasilia and I have to say: I like it.
My question is now: Does BioInformatics in Brasila work different than in other
parts of the world, where people are using Debian. You people seems to have
done an amazingly good job in providing many biological
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