Re: relion possible newer version? notice

[Roland Fehrenbacher]

> "B" == Ben Tris  writes:

Hi Ben,

B> Hello, https://tracker.debian.org/pkg/relion

B> Debian relion is on v1.4 in Debian there is worked on v2.1 but
B> there also exists v3.0.8

B> https://github.com/3dem/relion/releases

it's on my ToDo list for the coming weeks.

Best,

Roland

New relion git layout

[Roland Fehrenbacher]

Hi,

I've just uploaded a new relion version which includes a complete overhaul of
the previous packaging. It now uses dep14 allowing to work directly out
of the upstream git (see README.source). This also required the renaming
of the git branches where the master branch is now upstream's master and
debian/master is the default branch where Debian related stuff should
go. If someone intends to work on relion, she/he should get a new clone.

Cheers,

Roland

---
https://www.q-leap.com / https://qlustar.com
--- 100% Open Source HPC / Storage / Cloud Linux Cluster OS ---

Re: Qlustar 10 available - Now 100% Open Source

[Roland Fehrenbacher]

> "A" == Andreas Tille  writes:

Hi Andreas, Tony,


A> Hi Tony, On Sat, Apr 21, 2018 at 04:57:41PM +0200, Tony Travis
A> wrote:
>> Q-Leap previously offered to support Debian-Med and they attended
>> at least one Debian-Med Sprint. However, their product licensing
>> policy was restrictive and I decided not to use it. However, that
>> has now changed:
>>
>> > https://qlustar.com/news/qlustar-10-available-now-100-open-source

A> The Download page[1] says:

A>   Before downloading any parts of Qlustar, please read the
A>   Qlustar License Agreement. If you are representing a company
A>   planning to sell clusters or services based on Qlustar, please
A>   particularly note the paragraph titled COMMERCIAL RESTRICTIONS
A>   and get in touch with us.

this is the license to use Qlustar as a distro. All individual packages
by us are fully open sourced and would fit into main. But Tony is of
course right, there is nothing to package here for Debian, since the Qlustar
packages make only sense for Qlustar ... Except: We
package some generally useful stuff for Debian that is needed for
Qlustar and not yet present in Debian (see the debian HPC group).

Hope this clarifies things. Cheers and all the best for your newborn
grand child Andreas,

Roland

A> This sounds only fit for debian/non-free.  It is no argument to
A> not work on the packaging, thought.  However, doing the packaging
A> without any knowledge and systems to test is a bit hard.  I'd
A> like to see some kind of packaging model, where we teach upstream
A> the packaging and they do the actual work.  This has worked for
A> other complex software where we have no internal competence in
A> Debian Med (for instance fis-gtm).

A> Tony, if you have some contact could you make such a proposal?

A> Kind regards and thanks for the info

A> Andreas.

A> [1] https://qlustar.com/download

A> -- http://fam-tille.de

-- 
Best,

Roland

---
http://www.q-leap.com / http://qlustar.com
  --- HPC / Storage / Cloud Linux Cluster OS ---

Important News for DebMed graphics package maintainers

[Roland Fehrenbacher]

Please take this important new order into account or else ...

https://twitter.com/genetics_blog/status/827267187077373952

Sorry, couldn't help posting this to you guys :)

Cheers,

Roland

---
http://www.q-leap.com / http://qlustar.com
  --- HPC / Storage / Cloud Linux Cluster OS ---

Re: Anybody able to have a 20min talk at 3rd Swiss Galaxy Workshop, Thursday, October 20th, Freiburg (Germany)?

[Roland Fehrenbacher]

> "A" == Andreas Tille  writes:

A> Hi, I was invited to
>>
A> https://wiki.galaxyproject.org/Events/Switzerland2016
>>
A> to have a short talk about Debian Med.  Unfortunately I can not
A> make it due to some scheduling conflict.  I wonder whether
A> somebody else from the Debian Med team might be able to go.  I'd
A> support this by some slides if needed.
>>
>> if I can use your slides for the initial 2/3 of the talk and if
>> it's OK if I spend the remaining 1/3 on the Qlustar support of
>> DebMed, I'd take over.

A> For me that would be fine.  Are slides in LaTeX beamer OK?  I'd
A> need the weekend to assemble the slides.

Ok, good, so I'll go. Latex beamer produces PDF, right? I'll be using
Libreoffice/Impress. There are several options to handle this.
I suggest to discuss the followups about how to produce the
slides etc. offline, probably not so interesting for the list :)

-- 
Best,

Roland

---
http://www.q-leap.com / http://qlustar.com
  --- HPC / Storage / Cloud Linux Cluster OS ---

Re: Anybody able to have a 20min talk at 3rd Swiss Galaxy Workshop, Thursday, October 20th, Freiburg (Germany)?

[Roland Fehrenbacher]

> "A" == Andreas Tille  writes:

Hi Andreas,

A> Hi, I was invited to

A>https://wiki.galaxyproject.org/Events/Switzerland2016

A> to have a short talk about Debian Med.  Unfortunately I can not
A> make it due to some scheduling conflict.  I wonder whether
A> somebody else from the Debian Med team might be able to go.  I'd
A> support this by some slides if needed.

if I can use your slides for the initial 2/3 of the talk and if
it's OK if I spend the remaining 1/3 on the Qlustar support of DebMed,
I'd take over.

Best,

Roland

---
http://www.q-leap.com / http://qlustar.com
  --- HPC / Storage / Cloud Linux Cluster OS ---

SVN - GIT conversion (II)

[Roland Fehrenbacher]

Hi,

the next 10 packages we'll convert to GIT are:

Task Phylo:
---
probalign, fastdnaml, sigma-align, treeviewx, njplot

Task Bio:
-
wise, sim4, adun.app, gdpc, clustalo

Best,

Roland

---
http://www.q-leap.com / http://qlustar.com
  --- HPC / Storage / Cloud Linux Cluster OS ---


-- 
To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org
with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Archive: https://lists.debian.org/21787.60389.752867.861...@gargle.gargle.howl

Re: fasttree: hard-coded limit on branch length precision leads to erroneous results

[Roland Fehrenbacher]

 A == Andreas Tille andr...@an3as.eu writes:

Hi Andreas, Charles,

A On Sun, Mar 29, 2015 at 09:46:06AM +0900, Charles Plessy wrote:
 Le Sun, Mar 29, 2015 at 12:12:23AM +0100, Andreas Tille a écrit :
 
  I personally would consider a 2.1.8 backport to all relevant
  releases more usefull than spending time on old versions?  Am I
  missing something?

 Hi Andreas,

 in that case we need to decide whether removing version 2.1.4
 from Wheezy or not.

A Removing the package from Wheezy will not deinstall it from
A peoples computers.  May be we can cross thumbs that people have
A http://backports.debian.org/ in their sources.list.  I think the
A real harm in practice might not be that high.  We have currently

APopcon: 9 users (4 upd.)

A and Jessie might be released soon anyway.  I will not stop
A anybody to do the needed steps but I think we need to outweight
A the work it needs and the harm that is effectively done if we
A don't do this work.

just pushed 2.1.8-1.

Best,

Roland

--
To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org
with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Archive: https://lists.debian.org/21786.32605.213442.174...@gargle.gargle.howl

Re: SVN - GIT mass conversion

[Roland Fehrenbacher]

 Roland Fehrenbacher r...@q-leap.de writes:

Hi Andreas,

 A == Andreas Tille andr...@an3as.eu writes:
 Hi Andreas,

 fasttree is a special case I will write a separate mail about
 later.

A I've seen the commits.

A All fine with me - as I said please make sure to remove soonish
A from SVN and drop the README.status files to ensure that nobody
A else will continue working on the SVN files.

done. Please check whether it looks OK.

Best,

Roland

---
http://www.q-leap.com / http://qlustar.com
  --- HPC / Storage / Cloud Linux Cluster OS ---


-- 
To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org
with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Archive: https://lists.debian.org/21785.5277.388400.349...@gargle.gargle.howl

Re: SVN - GIT mass conversion

[Roland Fehrenbacher]

 A == Andreas Tille andr...@an3as.eu writes:

A Hi Roland, On Mon, Mar 30, 2015 at 11:17:17AM +0200, Roland
A Fehrenbacher wrote:

 done. Please check whether it looks OK.

A Thanks.  I commited some change with

A   We have no documented format for this kind of files but some
A   best practices inside this SVN archive.  Adapting to this ...

A So it is not your fault to not have found any doc - I also do not
A know about any but I think the metainformation which is now
A inside README.status might be helpful.  It would be nice if you
A could stick to this format - may be we might need it in the
A future.

Sure. So with future conversions I will do the following to the SVN
archive after GIT repo is available:

1) Delete content of trunk and commit.
2) Create README.status in the format of 
svn://svn.debian.org/debian-med/trunk/packages/fasttree/trunk/README.status
using the commit id of the commit in 1) for the field
SVNDeleteRevision.

Final questions:
- What's the meaning of the field Format in README.status?
- Will the VCS link for a package on the DebianMed webpages (and
  elsewhere on Debian pages) be automatically converted?

Best,

Roland

---
http://www.q-leap.com / http://qlustar.com
  --- HPC / Storage / Cloud Linux Cluster OS ---


-- 
To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org
with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Archive: https://lists.debian.org/21785.31761.543121.24...@gargle.gargle.howl

Re: SVN - GIT mass conversion

[Roland Fehrenbacher]

 A == Andreas Tille andr...@an3as.eu writes:

Hi Andreas,

 fasttree is a special case I will write a separate mail about
 later.

A I've seen the commits.

A All fine with me - as I said please make sure to remove soonish
A from SVN and drop the README.status files to ensure that nobody
A else will continue working on the SVN files.

I just tried to do this on alioth but don't seem to have permission to commit:

$ svn co svn://svn.debian.org/debian-med/trunk/packages/fasttree/trunk/
$ cd trunk
$ svn delete debian
Add README.status
$ svn ci
svn: Commit failed (details follow):
svn: Authorization failed

Best,

Roland

---
http://www.q-leap.com / http://qlustar.com
  --- HPC / Storage / Cloud Linux Cluster OS ---


-- 
To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org
with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Archive: https://lists.debian.org/21782.64253.651726.726...@gargle.gargle.howl

Re: fasttree: hard-coded limit on branch length precision leads to erroneous results

[Roland Fehrenbacher]

 C == Charles Plessy ple...@debian.org writes:

C Le Fri, Mar 27, 2015 at 02:10:38PM +0100, Andreas Tille a écrit :
 On Fri, Mar 27, 2015 at 11:01:29AM +0100, Roland Fehrenbacher
 wrote:

  C Do you think it would be possible to backport the change
  C for Wheezy as well ?
 
  I guess so. We have already built the package for
  Qlustar/Wheezy, so no principal problem. We'd have to rebuild
  it with a different version number suitable for the backports
  repo, but that's done in no time.  Just a question how the
  upload process to the official backport repo works. I'm not
  familiar with that.

 I admit I never cared about backports and I was hoping that
 somebody from the team would care for it.  Unfortunately this was
 not (yet) the case and I'm crossing thumbs that this will become
 better in the future.

C Actually, I have been a bit confusing: I did not mean uploading
C version 2.1.7-2 to Wheezy, but to apply the patches to 2.1.4-1 as
C a Stable update if it makes sense.

Ah, OK. There would be 2 problems with this: a) It's not clear whether
2.1.4 + patch will work OK. b) It'd be messy to figure out the 2.1.4-1
content because of missing tags. So 2.1.7-2 backport yes, fixed 2.1.4-1
no.

Best,

Roland

---
http://www.q-leap.com / http://qlustar.com
  --- HPC / Storage / Cloud Linux Cluster OS ---


--
To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org
with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Archive: https://lists.debian.org/21782.61606.309684.453...@gargle.gargle.howl

Re: fasttree: hard-coded limit on branch length precision leads to erroneous results

[Roland Fehrenbacher]

 A == Andreas Tille andr...@an3as.eu writes:

Hi Andreas,

A Hi Roland, On Fri, Mar 27, 2015 at 11:01:29AM +0100, Roland
A Fehrenbacher wrote:
C commit 5788cecbb05a4394c3fed722c47bdba5c20432ef Author:
C tbooth-guest tbooth-gu...@debian.org Date: Tue Feb 25 13:43:34
C 2014 +

C Fixed package not cleaning 100% after build.

 this is a perfect example why it's so important to tag package
 releases. Unfortunately, fasttree doesn't have any so far. So for
 someone unfamiliar with the package history, it's guesswork or
 tedious detective research to find out what went into a release
 version of the package.

A You are right.  Some maintainers in our team are a bit sloppy
A with tagging.  The rationale of them is that we have
A snapshot.debian.org.  While I do not subscribe to this opinion
A personally I understand their point.

A Apropos tagging: There are people in the team who said they will
A never tag any of their uploads to avoid that all these tags will
A consume more and more space on their harddisks.

that's one of the many places where GIT really shines versus SVN: tags and
branches have zero cost with GIT, whereas SVN makes code copies most of
the time ... 

A I also do not fully subscribe to this opinion but to find some
A compromise I deleted historical tags quite systematicly only
A leaving tags of major versions, somehow important tags (for
A whatever reason) and the last three tags.  To my (possibly poor)
A understanding this was the best compromise to invite people to do
A some tagging at all without filling up to much disk space.

A So please be prepared for a mostly incomplete tagging in SVN
A (feel free to criticise this but its hard to change the past.)

Just mentioned it to make people more aware. For the new GIT converted
repos there won't be an excuse :)

 Good job fasttree is a tiny package making things easier. Looking
 at the date of the last commit in fasttree, I assumed it must
 have been included in the jessie version.  On the other hand, the
 biolinux1 in the version number should have made me more
 suspicious ... :)

A I did an upload based upon

A apt-get source fasttree

A and afterwards importing your patches.  I stored this in the
A Jessie branch of the newly created Git repository.  Cases like
A this are not covered by our policy document (but should).  I hope
A I found a solution that is easy to understand and helpful for
A this case.
 
That was just fine.

Best,

Roland

---
http://www.q-leap.com / http://qlustar.com
  --- HPC / Storage / Cloud Linux Cluster OS ---


-- 
To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org
with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Archive: https://lists.debian.org/21782.61957.195354.483...@gargle.gargle.howl

Re: fasttree: hard-coded limit on branch length precision leads to erroneous results

[Roland Fehrenbacher]

 C == Charles Plessy ple...@debian.org writes:

Hi Charles,

C Le Thu, Mar 26, 2015 at 05:15:36PM +0100, Andreas Tille a écrit :
 On Thu, Mar 26, 2015 at 05:14:24PM +0100, Andreas Tille wrote:
   The above article describes the patch needed to prevent the
   flaw. Upstream incorporated the fix in version 2.1.8. In my
   opinion this bug is release critical and should be fixed
   before the release of jessie.
 
  Please file an RC bug!

 I'll tag #781259 as serious.

C to get the fix in Jessie at this point of the Freeze, it has to
C be limited the strict necessary changes.

C I recommend to temporarly revert the following commits:

C 
---
C commit 5788cecbb05a4394c3fed722c47bdba5c20432ef Author:
C tbooth-guest tbooth-gu...@debian.org Date: Tue Feb 25 13:43:34
C 2014 +

C Fixed package not cleaning 100% after build.

this is a perfect example why it's so important to tag package
releases. Unfortunately, fasttree doesn't have any so far. So for
someone unfamiliar with the package history, it's
guesswork or tedious detective research to find out what went into a
release version of the package. Good job fasttree is a tiny package
making things easier. Looking at the date of the last commit in
fasttree, I assumed it must have been included in the jessie version.
On the other hand, the biolinux1 in the version number should have made
me more suspicious ... :)

C I also think the upstream changelog belongs in the package,
C according to policy, so I added it.  But maybe I'm mistaken?



C git-svn-id:
C svn://svn.debian.org/debian-med/trunk/packages/fasttree/trunk@16316
C d8681a01-af0d-0410-a158-b4166a59cfaa

C commit dcef62b4c80a2c43b3c17af428e977b6535c3dc3 Author: jamessan
C james...@debian.org Date: Sun Feb 23 04:46:19 2014 +

C Move debian/upstream to debian/upstream/metadata

C git-svn-id:
C svn://svn.debian.org/debian-med/trunk/packages/fasttree/trunk@16250
C d8681a01-af0d-0410-a158-b4166a59cfaa
C 
---

C I think that the commits about VCS URL and maintainer are
C acceptable, but if the release team prefers the package without,
C the best will be to revert the commit on VCS URLs

The change of the VCS URLs was in a commit that is not part of the tag 2.1.7-2.

C and upload the changes as a Team Upload, without change of
C maintainers (this can be done when uploading version 2.1.8 after
C the release).

You guys know best what to do in such cases. Just go ahead with whatever
you think is right.

C In any case, many thanks for spotting this and preparing a
C correction so quickly !

It was a simple fix and given the findings described in the blog post
pretty important.

C Do you think it would be possible to backport the change for
C Wheezy as well ?

I guess so. We have already built the package for Qlustar/Wheezy, so no
principal problem. We'd have to rebuild it with a different version
number suitable for the backports repo, but that's done in no time.
Just a question how the upload process to the official backport repo
works. I'm not familiar with that.

-- 
Roland

---
http://www.q-leap.com / http://qlustar.com
  --- HPC / Storage / Cloud Linux Cluster OS ---


--
To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org
with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Archive: https://lists.debian.org/21781.10873.301925.713...@gargle.gargle.howl

Re: SVN - GIT mass conversion

[Roland Fehrenbacher]

 C == Charles Plessy ple...@debian.org writes:

Hi Andreas, Charles,

C Le Wed, Mar 25, 2015 at 03:23:47PM +0100, Andreas Tille a écrit :

 Another hint.  I have assembled some authors file at

 
https://anonscm.debian.org/viewvc/blends/projects/0svn2git/blends-authors?view=markup

 which probably covers several authors from Debian Med.  Please
 make sure you do not waste your time on assembling these authors
 again and also commit the authors file at some decent place (may
 be in some infrastructure Git (or just commit it to SVN :-P) to
 make sure other people will not need to redo the work that was
 just done.

C how about the following URL :)

C 
https://anonscm.debian.org/viewvc/debian-med/trunk/community/infrastructure/comitters?view=markup

Sorry, I don't get it. How exactly are these 2 files supposed to be used?

Best,

Roland

---
http://www.q-leap.com / http://qlustar.com
  --- HPC / Storage / Cloud Linux Cluster OS ---


--
To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org
with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Archive: https://lists.debian.org/21779.57121.108379.50...@gargle.gargle.howl

fasttree: hard-coded limit on branch length precision leads to erroneous results

[Roland Fehrenbacher]

Hi,

as described in detail at
http://darlinglab.org/blog/2015/03/23/not-so-fast-fasttree.html
fasttree 2.1.7 has a a serious issue for many genomic epidemiology
studies which can lead to completely wrong conclusions about research
results in biomedicine. The current version of fasttree in jessie
(2.1.7-1) has this severe deficiency.

The above article describes the patch needed to prevent the
flaw. Upstream incorporated the fix in version 2.1.8. In my opinion this
bug is release critical and should be fixed before the release of
jessie. I've already prepared a patched new package for this, so the bug
could be closed very fast after uploading that new package version.

Roland

---
http://www.q-leap.com / http://qlustar.com
  --- HPC / Storage / Cloud Linux Cluster OS ---


-- 
To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org
with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Archive: https://lists.debian.org/87oanfssug@q-leap.de

Re: SVN - GIT mass conversion

[Roland Fehrenbacher]

 A == Andreas Tille andr...@an3as.eu writes:

 Sorry, I don't get it. How exactly are these 2 files supposed to
 be used?

A Its only one file the authors file explained here:

Ahttps://wiki.debian.org/Alioth/Git#Create_the_author_file

A Charles suggested to commit this authors file at some place where
A it can easily be maintained.
 
Ah, OK, got you. I've also added an authors convert script in our
conversion process that converts a username not found in the authors file
to a git author username usern...@debian.org. This will obviously
not be correct in all circumstances, but on the other hand, it won't have
any negative consequences either. Since the authors list is pretty long
and probably close to complete), these cases will be rather rare anyway.

Here is the first list of packages, we'll convert:

Task Bio:
-
fasttree

Task NGS:
-
maq, velvet, last-align, ssake, kissplice

Task Phylo:
---
hmmer, dialign, probcons, poa, proda

fasttree is a special case I will write a separate mail about later.

Best,

Roland

---
http://www.q-leap.com / http://qlustar.com
  --- HPC / Storage / Cloud Linux Cluster OS ---


-- 
To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org
with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Archive: https://lists.debian.org/21780.5483.907290.649...@gargle.gargle.howl

Re: SVN - GIT mass conversion

[Roland Fehrenbacher]

 A == Andreas Tille andr...@an3as.eu writes:

Hi Andreas,
 
A I would not stop anybody from doing this but standardisation on
A its own would be no value in itself.

 In general I think it is, since you don't need to be expert in
 two VSC tools/packaging workflows and hence save time - higher
 productivity. It'll be quite a bit easier to help each other out
 with bug fixes in packages not maintained by oneself.

A While I agree that it is easier to be an expert in only one VCS
A you need to consider that we also have SVN experts (believe it or
A not ;-)).  I'd consider it a shame if we would loose a packager
A since the person has only knowledge in Git and does not spend its
A time to learn something else.  That's why I'd hesitate to force
A Git on all team members.
 
I think enforcement would definitely be the wrong approach. But
declaring a preferred workflow might make sense. That way newcomers
without preference won't need to make up their mind ... Just realize
it's hard to write about this without showing bias :)

A Do you have some stronger arguments for the move which would
A rectify this?

 I don't want to get into flame wars or a deeper discussion about
 this here, but for me the advantages of GIT are overwhelming and
 discussed at every corner on the net.

A We all know that there is a really large migration process from
A SVN to Git and I'll do not join a flame war about this.  I simply
A ask whether my time for conversion is larger than just carrying
A two hand full of files in a common SVN.

Sure. Of course we have automated the process as much as possible, so
it's essentially no extra work for us (at least for most packages).

A Another hint.  I have assembled some authors file at

A
https://anonscm.debian.org/viewvc/blends/projects/0svn2git/blends-authors?view=markup

A which probably covers several authors from Debian Med.  Please
A make sure you do not waste your time on assembling these authors
A again and also commit the authors file at some decent place (may
A be in some infrastructure Git (or just commit it to SVN :-P) to
A make sure other people will not need to redo the work that was
A just done.

I'll check this out.

Best,

Roland

---
http://www.q-leap.com / http://qlustar.com
  --- HPC / Storage / Cloud Linux Cluster OS ---


-- 
To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org
with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Archive: https://lists.debian.org/21779.6036.164791.157...@gargle.gargle.howl

Re: SVN - GIT mass conversion

[Roland Fehrenbacher]

 C == Charles Plessy ple...@debian.org writes:

Hi Charles,

thanks for your comments.

C Le Tue, Mar 24, 2015 at 06:02:49PM +0100, Roland Fehrenbacher a
C écrit :

 while porting DebMed packages to Qlustar, we started a mass
 conversion of SVN to GIT package repositories. Since at the
 St. Malo sprint I got the impression that having as much as
 possible of the DebMed stuff managed via GIT would be desirable
 in general, we'd also start creating new repos for these packages
 on alioth that would allow to fully switch to GIT for these
 packages at a certain date. The goal of this is to standardize
 DebianMed on GIT entirely.

C there is also an effor to propose a standard layout in Debian in
C general.  It is work in progress, but you can have a look at
C http://dep.debian.net/deps/dep14/ and at mailing list archives
C after searching with DEP-14 (or variations with/without hyphen
C etc.) as a keyword.

C (In my understanding, here standard means normalising minor
C difference between similar layouts, not forcing everybody to use
C the same layout.)

Good to know. As far as I can see, the standard git-buildpackage
structure is not incompatible with the proposal, even though the branch
names are slightly different. Should be fairly straightforward to adjust
to an agreed upon debian-wide standard later on. Would wait until that
will have appeared.

C In Debian Med, I have experimented on alternative layouts that
C follow directly upstream's Git repository instead of usign the
C source tarball as an intermediate.  I prefer that way, but I will
C be short of time to keep all my packages up to date just by
C myself in the near future, so if my Git layout is on your way to
C do good team work, do not hesitate to migrate it to a more
C standard one.

I've already noticed. We do something similar and I think that's the way
to go for upstream managed by GIT projects. When I'll get around
thinking some more about this I'll post my ideas, so maybe we can agree
upon a common structure/workflow.

C (Two main reasons why I will lack time are a) still being a young
C parent and b) still spending most of my Debian time learning
C Haskell to rewrite the Umegaya system in a hopefully bug-free
C way.)

Enjoy the time with your kids :)

Best,

Roland

---
http://www.q-leap.com / http://qlustar.com
  --- HPC / Storage / Cloud Linux Cluster OS ---


--
To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org
with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Archive: https://lists.debian.org/21779.5400.92745.849...@gargle.gargle.howl

SVN - GIT mass conversion

[Roland Fehrenbacher]

Hi,

while porting DebMed packages to Qlustar, we started a mass conversion
of SVN to GIT package repositories. Since at the St. Malo sprint I got the
impression that having as much as possible of the DebMed stuff managed
via GIT would be desirable in general, we'd also start creating new
repos for these packages on alioth that would allow to fully switch to GIT
for these packages at a certain date. The goal of this is to standardize
DebianMed on GIT entirely.

The new git repos will have the standard structure with
master/upstream/pristine-tar branches. They will include the full original SVN
history and tags as well as the latest orig.tar (from the current
version in testing) in the pristine tar branch, so that the package versions in
testing will be readily recreatable from them using git-buildpackage.

We plan to do the conversion in junks of 10 packages at a time and will
announce these packages here in advance, so that the maintainers of them
and everyone else will know about it in time and can check that the
conversion was done properly.

After a conversion will have been determined to be OK by all parties, we
should have a process to decommission the corresponding SVN repo.

If there are objections against converting certain packages (or the
whole idea), let's discuss it here.

Suggestions, comments etc. are obviously welcome.

Best,

Roland

---
http://www.q-leap.com / http://qlustar.com
  --- HPC / Storage / Cloud Linux Cluster OS ---


-- 
To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org
with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Archive: https://lists.debian.org/21777.39097.742999.56...@gargle.gargle.howl

Re: SVN - GIT mass conversion

[Roland Fehrenbacher]

 A == Andreas Tille andr...@an3as.eu writes:

Hi Andreas,

A Hi Roland, On Tue, Mar 24, 2015 at 06:02:49PM +0100, Roland
A Fehrenbacher wrote:
 Hi,

 while porting DebMed packages to Qlustar, we started a mass
 conversion of SVN to GIT package repositories. Since at the
 St. Malo sprint I got the impression that having as much as
 possible of the DebMed stuff managed via GIT would be desirable
 in general, we'd also start creating new repos for these packages
 on alioth that would allow to fully switch to GIT for these
 packages at a certain date. The goal of this is to standardize
 DebianMed on GIT entirely.

 The new git repos will have the standard structure with
 master/upstream/pristine-tar branches. They will include the full
 original SVN history and tags as well as the latest orig.tar
 (from the current version in testing) in the pristine tar branch,
 so that the package versions in testing will be readily
 recreatable from them using git-buildpackage.

 We plan to do the conversion in junks of 10 packages at a time
 and will announce these packages here in advance, so that the
 maintainers of them and everyone else will know about it in time
 and can check that the conversion was done properly.

 After a conversion will have been determined to be OK by all
 parties, we should have a process to decommission the
 corresponding SVN repo.

 If there are objections against converting certain packages (or
 the whole idea), let's discuss it here.

A No objection from my side.  However, I personally do not see the
A gain to port all packages.  While I think we have some people who
A remain in the SVN age I simply would consider my time wasted to
A do a mass conversion without any obvious profit.

we won't do all packages anyway, just those relevant for clustering
(Bio, Bio-Dev, NGS, Phylo, IMG, IMG-Dev tasks). It won't be time wasted,
because we will do it anyway for our internal use, so it's just a
question whether DebMed wants to profit as well.

A I would not stop anybody from doing this but standardisation on
A its own would be no value in itself.

In general I think it is, since you don't need to be expert in two
VSC tools/packaging workflows and hence save time - higher
productivity. It'll be quite a bit easier to help each other out with
bug fixes in packages not maintained by oneself.

A Specifically if I think about several R packages which have only
A tiny bits in SVN but may be large chunks of data in Git we just
A fill up disk space at alioth on local disks and bandwidth for no
A obvious win.

For some packages, it indeed might make not so much sense, that's why I'd
put them up for discussion.

A Do you have some stronger arguments for the move which would
A rectify this?

I don't want to get into flame wars or a deeper discussion about this
here, but for me the advantages of GIT are overwhelming and discussed at
every corner on the net. On the other hand, I definitely don't want to
force anything on any maintainer.

 Suggestions, comments etc. are obviously welcome.

A As I said I'm not against progress so if you do some move please
A make sure to drop a file according to the example in

Atrunk/packages/clustalx/trunk/README.status

OK.

Best,

Roland

---
http://www.q-leap.com / http://qlustar.com
  --- HPC / Storage / Cloud Linux Cluster OS ---


-- 
To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org
with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Archive: https://lists.debian.org/21777.49991.937330.457...@gargle.gargle.howl

Re: Is Churchill revolutionary?

[Roland Fehrenbacher]

 Gert == Gert Wollny gw.foss...@gmail.com writes:

Gert On Wed, 2015-02-11 at 17:31 +, Jorge Sebastião Soares
Gert wrote:
 Hey,

 Maybe this is one more of those articles that have been published
 lately with the intent to verify the attention reviewers and
 journals pay to submissions:
Gert I don't think so, the paper appears in a BMC journal, and so
Gert far all review I got from other journals from this publisher
Gert were quite thorough. Besides, they really applied for a patent
Gert for the method:

Gert http://www.google.com/patents/US20130311106

Gert I skimmed the paper, and what they claim is that they found a
Gert parallelization strategy that gives close to optimal scaling
Gert which really seems to make a difference when using *lots* of
Gert processors. It's not my field of work, so I can't comment on
Gert the details.

Since I'm not a Bioinformtician, I ask myself: Are there tools in DebMed
(or otherwise free) to achieve the same results, even if currently not as
performing? If so, I'd be interested to look at them and see how they can
be optimized to achieve similar performance. If their tasks are
data-parallel a lot of the performance gain might come from a great HW setup.
What would be needed is some kind of benchmark everyone in the field is
familiar with.

Cheers,

Roland

---
http://www.q-leap.com / http://qlustar.com
  --- HPC / Storage / Cloud Linux Cluster OS ---


--
To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org
with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Archive: https://lists.debian.org/21724.32876.213381.965...@gargle.gargle.howl

Re: Is Churchill revolutionary?

[Roland Fehrenbacher]

 Andreas == Andreas Tille andr...@an3as.eu writes:

Andreas Hi, On Wed, Feb 11, 2015 at 11:24:35AM -0600, Scott
Andreas Christley wrote:
 
 These are essentially data-parallel solutions. What I’ve found is
 that most of these workflows utilizing existing software,
 e.g. BWA for alignment and GATK for variant calling, ...

Andreas Anybody interested in packaging GATK

Andreashttps://github.com/broadgsa/gatk

Not sure whether their licensing permits redistribution within Debian.
Check https://github.com/broadgsa/gatk/tree/master/licensing

-- 
Roland

---
http://www.q-leap.com / http://qlustar.com
  --- HPC / Storage / Cloud Linux Cluster OS ---


--
To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org
with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Archive: https://lists.debian.org/21724.6.690063.758...@gargle.gargle.howl

Re: Is Churchill revolutionary?

[Roland Fehrenbacher]

 Andreas == Andreas Tille andr...@an3as.eu writes:

Andreas Hi Roland, On Wed, Feb 11, 2015 at 12:51:21PM +0100, Roland
Andreas Fehrenbacher wrote:

Andreas I did not found any download or even any project page of
Andreas the software.

 The link is at the very end of the article. Here for reference:
 http://churchill.nchri.org/

Andreas Ahh, my bad to do a simple web search instead of reading.
Andreas However, I can confirm that nothing happens after
Andreas Agree-ing to the license terms ... :-(

Thanks for checking. Hmm, seems to be some quickly hacked up page then ...

Andreas Somebody who has some vital interest should probably
Andreas contact the authors.

Anyone can judge the real impact of this?

Roland

---
http://www.q-leap.com / http://qlustar.com
  --- HPC / Storage / Cloud Linux Cluster OS ---


-- 
To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org
with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Archive: https://lists.debian.org/21723.30221.23789.120...@gargle.gargle.howl

Blog about recent DebMed sprint

[Roland Fehrenbacher]

Hi all,

wrote a short blog entry about the St. Malo sprint including some pics

https://www.qlustar.com/content/bioinformatics-waves-french-atlantic-coast

Roland

---
http://www.q-leap.com / http://qlustar.com
  --- HPC / Storage / Cloud Linux Cluster OS ---


-- 
To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org
with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Archive: https://lists.debian.org/21723.16734.178593.204...@gargle.gargle.howl

Re: Is Churchill revolutionary?

[Roland Fehrenbacher]

 Andreas == Andreas Tille andr...@an3as.eu writes:

Andreas Hi Roland, On Tue, Feb 10, 2015 at 06:39:30PM +0100, Roland
Andreas Fehrenbacher wrote:
 To the DebMed sequencing experts out there:

 Is this (
 http://www.gizmag.com/churchill-fast-human-genome-analysis/35944/
 ) just marketing fuzz or really as much of a breakthrough as it
 sounds?

Andreas I personally can't say.
 
 PS: I can't download the code, but you guys could check.

Andreas I did not found any download or even any project page of
Andreas the software.

The link is at the very end of the article. Here for reference:
http://churchill.nchri.org/

Cheers,

Roland

---
http://www.q-leap.com / http://qlustar.com
  --- HPC / Storage / Cloud Linux Cluster OS ---


-- 
To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org
with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Archive: https://lists.debian.org/21723.16953.736654.378...@gargle.gargle.howl

Is Churchill revolutionary?

[Roland Fehrenbacher]

To the DebMed sequencing experts out there:

Is this (
http://www.gizmag.com/churchill-fast-human-genome-analysis/35944/ ) just
marketing fuzz or really as much of a breakthrough as it sounds?

Cheers,

Roland

PS: I can't download the code, but you guys could check. Steffen, Tim, what do
you think?

---
http://www.q-leap.com / http://qlustar.com
  --- HPC / Storage / Cloud Linux Cluster OS ---


-- 
To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org
with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Archive: https://lists.debian.org/21722.16978.414477.756...@gargle.gargle.howl

New git repos

[Roland Fehrenbacher]

Hi,

just to let you all know. I just created new git repos for the following
packages we (Q-Leap DebMed team) started working on:

yaggo (already exists, migrating from svn to git)
libshark (dependency of sailfish)
g2log (dependency of sailfish)
sailfish
mpiblast

Cheers,

Roland

---
http://www.q-leap.com / http://qlustar.com
  --- HPC / Storage / Cloud Linux Cluster OS ---


-- 
To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org
with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Archive: https://lists.debian.org/21714.8373.837024.481...@gargle.gargle.howl

Re: Group image

[Roland Fehrenbacher]

 Andreas == Andreas Tille andr...@fam-tille.de writes:

Hi all,

Andreas Nice to have met you all

Andreas Andreas.

was great to be part of this sprint and especially appreciated the welcoming
atmosphere created by all of you. Looking forward to more of this :)

Special thanks to Olivier for the superb organization.

All the best,

Roland

---
http://www.q-leap.com / http://qlustar.com
  --- HPC / Storage / Cloud Linux Cluster OS ---


-- 
To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org
with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Archive: https://lists.debian.org/21713.63398.905933.47...@gargle.gargle.howl