Re: Primer3

[Andreas Tille]

Hi Canberk,

On Mon, Jun 27, 2016 at 04:38:07AM +0300, Canberk Koç wrote:
> I manage to finish fixes can you control them please . If i do something
> wrong i work on it immediately.

I think the changes you have commited are doing what they should do.  I
uploaded (after adding a lintian-override about empty directories which
are really intended and no mistake - please check that you understand
what lintian-overrides are doing).

So I've set you Midterm evaluation to pass.
 
> Thanks for guidence and help.

You are welcome.  Did you made up your mind about muscle?  Did you
contacted upstream (if so please always CC this mailing list).  If
not I would recommend that you write something like

  "I'm contacting you on behalf of the Debian Med team ..."

(Please do a web search for this string at
site:lists.debian.org/debian-med to get some sensible expression.)  Than
explain the intention og the GSoC project and ask for some sensible test
upstream might imagine.

Other interesting target packages are

 perlprimer
 vcftools (I'll convert this one to Git currently)
 gdpc

Please try to get three packages per week at minimum - better more.
Please also let the list know if you see stumbling stones (and let me
know if you have personal issues that prevent you from commiting the
mentioned amount).

Kind regards

Andreas.

-- 
http://fam-tille.de

Re: Primer3

[Canberk Koç]

Hello Andreas,

Thanks for trusting me,guidance and give pass.
I'm researching for muscle actually but i think contacting to upstream is a
more effective way so if i can't figure what should i do i will do it .
I start to work on packages now.

Best Regards




Canberk Koç
[image: https://]about.me/canberkkoc


2016-06-27 10:04 GMT+03:00 Andreas Tille :

> Hi Canberk,
>
> On Mon, Jun 27, 2016 at 04:38:07AM +0300, Canberk Koç wrote:
> > I manage to finish fixes can you control them please . If i do something
> > wrong i work on it immediately.
>
> I think the changes you have commited are doing what they should do.  I
> uploaded (after adding a lintian-override about empty directories which
> are really intended and no mistake - please check that you understand
> what lintian-overrides are doing).
>
> So I've set you Midterm evaluation to pass.
>
> > Thanks for guidence and help.
>
> You are welcome.  Did you made up your mind about muscle?  Did you
> contacted upstream (if so please always CC this mailing list).  If
> not I would recommend that you write something like
>
>   "I'm contacting you on behalf of the Debian Med team ..."
>
> (Please do a web search for this string at
> site:lists.debian.org/debian-med to get some sensible expression.)  Than
> explain the intention og the GSoC project and ask for some sensible test
> upstream might imagine.
>
> Other interesting target packages are
>
>  perlprimer
>  vcftools (I'll convert this one to Git currently)
>  gdpc
>
> Please try to get three packages per week at minimum - better more.
> Please also let the list know if you see stumbling stones (and let me
> know if you have personal issues that prevent you from commiting the
> mentioned amount).
>
> Kind regards
>
> Andreas.
>
> --
> http://fam-tille.de
>
>

Bug#828189: marked as done (ITP: r-bioc-dnacopy -- R package: DNA copy number data analysis)

[Debian Bug Tracking System]

Your message dated Mon, 27 Jun 2016 08:02:14 +
with message-id 
and subject line Bug#828189: fixed in r-bioc-dnacopy 1.46.0-1
has caused the Debian Bug report #828189,
regarding ITP: r-bioc-dnacopy -- R package: DNA copy number data analysis
to be marked as done.

This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)


-- 
828189: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=828189
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: wnpp
Severity: wishlist
Owner: Debian Med team 

* Package name: r-bioc-dnacopy
  Version : 1.46.0
  Upstream Author : Venkatraman E. Seshan 
* URL : 
http://www.bioconductor.org/packages/release/bioc/html/DNAcopy.html
* License : GPL-2.0+
  Programming Lang: R
  Description : R package: DNA copy number data analysis

 Implements the circular binary segmentation (CBS) algorithm to segment DNA
 copy number data and identify genomic regions with abnormal copy number.
 .
 This package is for analyzing array DNA copy number data, which is usually
 (but not always) called array Comparative Genomic Hybridization (array CGH)
 data It implements a methodology for finding change-points in these data which
 are points after which the (log) test over reference ratios have changed
 location. This model is that the change-points correspond to positions where
 the underlying DNA copy number has changed. Therefore, change-points can be
 used to identify regions of gained and lost copy number. We also provide a
 function for making relevant plots of these data.

This is a dependency for r-cran-pscbs and will be team maintained by the Debian 
Med team
--- End Message ---
--- Begin Message ---
Source: r-bioc-dnacopy
Source-Version: 1.46.0-1

We believe that the bug you reported is fixed in the latest version of
r-bioc-dnacopy, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 828...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Michael R. Crusoe  (supplier of updated 
r-bioc-dnacopy package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)


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Date: Sat, 25 Jun 2016 13:58:30 -0700
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Binary: r-bioc-dnacopy
Architecture: source amd64
Version: 1.46.0-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Description:
 r-bioc-dnacopy - R package: DNA copy number data analysis
Closes: 828189
Changes:
 r-bioc-dnacopy (1.46.0-1) unstable; urgency=medium
 .
   * Initial release. (Closes: #828189)
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Re: request for sponsorship: r-cran-r.cache r-cran-future r-cran-globals r-cran-listev r-bioc-dnacopy

[Andreas Tille]

On Sun, Jun 26, 2016 at 09:30:36PM +0200, Andreas Tille wrote:
> > Good catch; I've updated r-cran-r.cache, r-cran-future, r-cran-globals, and
> > r-cran-listenv.
> 
> Uploaded with exception of r-cran-future which Build-Depends
> r-cran-globals and r-cran-listenv.  I tend to wait with uploads to new
> until all preconditions are available in unstable.

I now uploaded r-cran-future since Build-Depends are there now.  Please
note:  I did some changes to the packaging.  Most importantly R:Depends
does *not* resolve package dependencies (which sucks, I know, but nobody
feels obliged to write a proper R packaging support).  So you always need
to repeat the Build-Depends inside Depends.
  
Kind regards

   Andreas. 

-- 
http://fam-tille.de

Re: request for sponsorship: r-cran-r.cache r-cran-future r-cran-globals r-cran-listev r-bioc-dnacopy

[Michael Crusoe]

Pe 27 iun. 2016 4:54 a.m., "Andreas Tille"  a scris:
>
> On Sun, Jun 26, 2016 at 09:30:36PM +0200, Andreas Tille wrote:
> > > Good catch; I've updated r-cran-r.cache, r-cran-future,
r-cran-globals, and
> > > r-cran-listenv.
> >
> > Uploaded with exception of r-cran-future which Build-Depends
> > r-cran-globals and r-cran-listenv.  I tend to wait with uploads to new
> > until all preconditions are available in unstable.
>
> I now uploaded r-cran-future since Build-Depends are there now.  Please
> note:  I did some changes to the packaging.  Most importantly R:Depends
> does *not* resolve package dependencies (which sucks, I know, but nobody
> feels obliged to write a proper R packaging support).  So you always need
> to repeat the Build-Depends inside Depends.

Oof, sorry for forgetting this!

> Kind regards
>
>Andreas.
>
> --
> http://fam-tille.de
>

Bug#828197: marked as done (ITP: r-cran-future -- R package: A Future API for R)

[Debian Bug Tracking System]

Your message dated Mon, 27 Jun 2016 13:00:52 +
with message-id 
and subject line Bug#828197: fixed in r-cran-future 1.0.0-1
has caused the Debian Bug report #828197,
regarding ITP: r-cran-future -- R package: A Future API for R
to be marked as done.

This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)


-- 
828197: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=828197
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: wnpp
Severity: wishlist
Owner: Debian Med team 

* Package name: r-cran-future
  Version : 1.0.0
  Upstream Author : Henrik Bengtsson 
* URL : https://github.com/HenrikBengtsson/future
* License : LGPL-2.1+
  Programming Lang: R
  Description : R package: A Future API for R

In programming, a future is an abstraction for a value that may be available
 at some point in the future. The state of a future can either be unresolved or
 resolved. As soon as it is resolved, the value is available. Futures are
 useful constructs in for instance concurrent evaluation, e.g. parallel
 processing and distributed processing on compute clusters. The purpose of this
 package is to provide a lightweight interface for using futures in R.

A dependency of r-cran-pscbs, team maintained by Debian Med
--- End Message ---
--- Begin Message ---
Source: r-cran-future
Source-Version: 1.0.0-1

We believe that the bug you reported is fixed in the latest version of
r-cran-future, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 828...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Michael R. Crusoe  (supplier of updated r-cran-future 
package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)


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Version: 1.0.0-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Description:
 r-cran-future - R package: A Future API for R
Closes: 828197
Changes:
 r-cran-future (1.0.0-1) unstable; urgency=medium
 .
   * Initial release. (Closes: #828197)
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RRID: a namespace for research software

[Michael Crusoe]

http://identifiers.org/rrid/

Example: http://identifiers.org/rrid/RRID:SCR_001156

Where would be the best place to incorporate this into Debian? We are
adding support for this into the CWL spec so it would be nice to have a
resolver that give a Debian package name for a given RRID.

-- 
Michael R. Crusoe
Community Engineer & Co-founder
Common Workflow Language project
https://impactstory.org/u/-0002-2961-9670
michael.cru...@gmail.com
+32 (0) 2 808 25 58
+1 480 627 9108

http://upstream-metadata.debian.net/

[Olivier Sallou]

Hi Charles,

http://upstream-metadata.debian.net/ seems unavailable, connections
remain waiting.

Olivier

-- 
Olivier Sallou
IRISA / University of Rennes 1
Campus de Beaulieu, 35000 RENNES - FRANCE
Tel: 02.99.84.71.95

gpg key id: 4096R/326D8438  (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335  D26D 78DC 68DB 326D 8438

Re: http://upstream-metadata.debian.net/

[Andreas Tille]

On Mon, Jun 27, 2016 at 04:14:55PM +0200, Olivier Sallou wrote:
> Hi Charles,
> 
> http://upstream-metadata.debian.net/ seems unavailable, connections
> remain waiting.

Charles, I think you should do

   echo "upstream-metadata   in  a  117.121.245.165" | gpg --clearsign | mail 
chan...@db.debian.org 

If I remember correctly it was on the same host as blends.debian.net
and this was moved by GPLhost.

Hope this helps

Andreas.

-- 
http://fam-tille.de

Re: RRID: a namespace for research software

[Andreas Tille]

On Mon, Jun 27, 2016 at 10:04:40AM -0400, Michael Crusoe wrote:
> http://identifiers.org/rrid/
> 
> Example: http://identifiers.org/rrid/RRID:SCR_001156
> 
> Where would be the best place to incorporate this into Debian? We are
> adding support for this into the CWL spec so it would be nice to have a
> resolver that give a Debian package name for a given RRID.

Add a new field to debian/upstream/metadata ?

Kind regards

   Andreas.

-- 
http://fam-tille.de

Orthanc 1.1.0

[Sebastien Jodogne]

Dear all,

I have just packaged the newest upstream version of Orthanc (1.1.0):
http://anonscm.debian.org/cgit/debian-med/orthanc.git/

Could someone check the package and upload it if everything is OK? 
Thanks in advance!


Regards,
Sébastien-

Re: Galaxy project producing their own Debian packages

[Michael Crusoe]

Hoopla,

I'm at the Galaxy Community Conference sitting next to Nate Coraor.

Nate is enthusiastic about Galaxy becoming properly packaged for Debian. He
is well aware of how hacky his current package is :-)

On Thu, Jun 16, 2016 at 11:07 AM, Olivier Sallou 
wrote:

>
>
> On 06/16/2016 08:43 AM, Michael Crusoe wrote:
> >
> > Vezi Tweetul lui @natefoo:
> > https://twitter.com/natefoo/status/743306923026440194
> >
> > https://depot.galaxyproject.org/nate/dpkg/
> >
> nice, but easy for them. Galaxy installs many things at run time from
> remote locations (pypi and others). So not easy to fit in Debian as all
> dependencies not to be Debian packages.
>
> Olivier
>
> --
> Olivier Sallou
> IRISA / University of Rennes 1
> Campus de Beaulieu, 35000 RENNES - FRANCE
> Tel: 02.99.84.71.95
>
> gpg key id: 4096R/326D8438  (keyring.debian.org)
> Key fingerprint = 5FB4 6F83 D3B9 5204 6335  D26D 78DC 68DB 326D 8438
>
>


-- 
Michael R. Crusoe
Community Engineer & Co-founder
Common Workflow Language project
https://impactstory.org/u/-0002-2961-9670
michael.cru...@gmail.com
+32 (0) 2 808 25 58
+1 480 627 9108

Re: Galaxy project producing their own Debian packages

[Michael Crusoe]

Python packages that need packaging:

bx-python
wchartype
dictobj
bioblend
requests-toolbelt
pulsar-galaxy-lib
sqlalchemy-migrate
svgwrite

This should a complete list, Nate promises that there are no hidden sub
dependencies.

They also use a custom fork of pysam

On Mon, Jun 27, 2016 at 2:34 PM, Michael Crusoe 
wrote:

> Hoopla,
>
> I'm at the Galaxy Community Conference sitting next to Nate Coraor.
>
> Nate is enthusiastic about Galaxy becoming properly packaged for Debian.
> He is well aware of how hacky his current package is :-)
>
> On Thu, Jun 16, 2016 at 11:07 AM, Olivier Sallou 
> wrote:
>
>>
>>
>> On 06/16/2016 08:43 AM, Michael Crusoe wrote:
>> >
>> > Vezi Tweetul lui @natefoo:
>> > https://twitter.com/natefoo/status/743306923026440194
>> >
>> > https://depot.galaxyproject.org/nate/dpkg/
>> >
>> nice, but easy for them. Galaxy installs many things at run time from
>> remote locations (pypi and others). So not easy to fit in Debian as all
>> dependencies not to be Debian packages.
>>
>> Olivier
>>
>> --
>> Olivier Sallou
>> IRISA / University of Rennes 1
>> Campus de Beaulieu, 35000 RENNES - FRANCE
>> Tel: 02.99.84.71.95
>>
>> gpg key id: 4096R/326D8438  (keyring.debian.org)
>> Key fingerprint = 5FB4 6F83 D3B9 5204 6335  D26D 78DC 68DB 326D 8438
>>
>>
>
>
> --
> Michael R. Crusoe
> Community Engineer & Co-founder
> Common Workflow Language project
> https://impactstory.org/u/-0002-2961-9670
> michael.cru...@gmail.com
> +32 (0) 2 808 25 58
> +1 480 627 9108
>



-- 
Michael R. Crusoe
Community Engineer & Co-founder
Common Workflow Language project
https://impactstory.org/u/-0002-2961-9670
michael.cru...@gmail.com
+32 (0) 2 808 25 58
+1 480 627 9108

Re: IQtree failed build time test

[Andreas Tille]

Hi Tung,

I've attached the full build log of the Debian package.

Hope this helps

  Andreas.

On Mon, Jun 27, 2016 at 09:55:06AM +, Tung Nguyen wrote:
> Dear Andreas,
> 
> Could you provide us the gcc version and flags that were used for build?
> Currently we have no idea what might have went wrong. On our system,
> everything works fine.
> 
> Cheers
> Tung
> 
> On Fri, Jun 24, 2016 at 10:19 PM Andreas Tille  wrote:
> 
> > Hi,
> >
> > I intended to upgrade the IQtree Debian package.  When trying to build
> > it some of the build time tests failed.  The script
> >
> >sh example.short
> >
> > is used to test the functionality.  Here is the output:
> >
> >
> > time sh example.short
> > Executing tests using /build/iqtree-1.4.2+dfsg/obj-x86_64-linux-gnu/iqtree
> > ...
> > IQ-TREE version 1.4.2 for Linux 64-bit built Jun 24 2016
> > Copyright (c) 2011-2015 Nguyen Lam Tung, Olga Chernomor, Arndt von
> > Haeseler and Bui Quang Minh.
> >
> > Host:energija (SSE4.1, 7 GB RAM)
> > Command: /build/iqtree-1.4.2+dfsg/obj-x86_64-linux-gnu/iqtree -s
> > example.phy
> > Seed:318091 (Using SPRNG - Scalable Parallel Random Number Generator)
> > Time:Fri Jun 24 20:00:40 2016
> > Kernel:  SSE3
> >
> > NOTE: Consider using the multicore version because your CPU has 2 cores!
> >
> > Reading alignment file example.phy ... Phylip format detected
> > Alignment most likely contains DNA/RNA sequences
> > Alignment has 44 sequences with 384 columns and 355 patterns (322
> > informative sites)
> > Gap/Ambiguity  Composition  p-value
> >1  FL-1-103 19.53%failed  0.00%
> >2  OSH-1-10319.53%failed  0.00%
> >3  CEU-1-10319.53%failed  0.79%
> >4  TH-1-103 19.53%failed  0.10%
> >5  CAa1-103 19.53%failed  0.14%
> >6  CAb1-103 19.53%failed  0.00%
> >7  SI-1-103 19.53%failed  0.00%
> >8  LU-1-103 19.53%failed  0.01%
> >9  SU-1-103 19.53%failed  0.00%
> >   10  RP-56-175 6.25%failed  4.72%
> >   11  A-14-133  6.25%failed  3.08%
> >   12  PR-57-176 6.25%passed 63.84%
> >   13  PY-61-180 6.25%passed 69.25%
> >   14  MGI-58-1767.03%failed  0.05%
> >   15  SCR-58-1776.25%passed 94.64%
> >   16  SA-60-179 6.25%passed 66.43%
> >   17  BR-60-179 6.25%passed 27.40%
> >   18  CPL-58-1776.25%passed 55.10%
> >   19  LTU-59-1786.25%passed 28.43%
> >   20  TSP-58-1776.25%passed 51.74%
> >   21  YBN-56-1756.25%passed 72.08%
> >   22  AN-56-175 6.25%passed 52.14%
> >   23  HI-60-179 6.25%passed 51.36%
> >   24  ANA-56-1756.25%passed 88.34%
> >   25  ZE-48-166 7.03%failed  0.05%
> >   26  EAT-48-1667.03%passed 14.40%
> >   27  YSA-46-1647.03%passed  6.42%
> >   28  TH-52-170 7.03%passed 20.58%
> >   29  LA-68-186 7.03%passed 10.46%
> >   30  GR-854-9782.34%failed  0.02%
> >   31  MO-29-154 1.56%failed  0.00%
> >   32  OE-36-161 1.56%passed 15.04%
> >   33  EME-43-1681.56%failed  1.16%
> >   34  LRE-46-1711.56%failed  0.00%
> >   35  P6-2-107 17.19%passed 44.21%
> >   36  HO-1-106 17.19%passed 14.57%
> >   37  SP-1-106 17.19%failed  2.41%
> >   38  PA-1-105 17.97%failed  0.00%
> >   39  NE-2-109 15.62%passed 53.11%
> >   40  IFE-2-10915.62%passed 63.82%
> >   41  HS-9-115 16.41%failed  0.03%
> >   42  RVI-7-11415.62%failed  0.12%
> >   43  IFE-8-11515.62%passed 39.01%
> >   44  RVI-5-11215.62%failed  0.04%
> >   TOTAL10.87%  22 sequences failed composition chi2 test
> > (p-value<5%; df=3)
> >
> > Create initial parsimony tree by phylogenetic likelihood library (PLL)...
> > STACK TRACE FOR DEBUGGING:
> > 1   funcAbort()
> > 2   ()
> > 3   allocateParsimonyDataStructures()
> > 4   pllComputeRandomizedStepwiseAdditionParsimonyTree()
> > 5   IQTree::computeInitialTree(std::__cxx11::basic_string > std::char_traits, std::allocator >&, LikelihoodKernel)
> > 6   runTreeReconstruction(Params&, std::__cxx11::basic_string > std::char_traits, std::allocator >&, IQTree&,
> > std::vector >&)
> > 7   runPhyloAnalysis(Params&, Checkpoint*)
> > 8   main()
> > 9   __libc_start_main()
> > 10   _start()
> >
> > *** IQ-TREE CRASHES WITH SIGNAL SEGMENTATION FAULT
> > *** For bug report please send to developers:
> > ***Log file: example.phy.log
> > ***Alignment files (if possible)
> > Command terminated by signal 11
> > 0.00user 0.00system 0:00.01elapsed 57%CPU (0avgtext+0avgdata
> > 6888maxresident)k
> > 152inputs+8outputs (1major+318minor)pagefaults 0swaps
> > IQ-TREE multicore version 1.4.2 for Linux 64-bit built Jun 24 2016
> > Copyright (c) 2011-2015 Nguyen Lam Tung, O

Re: Orthanc 1.1.0

[Andreas Tille]

Uploaded, thanks for your work on this, Andreas.

On Mon, Jun 27, 2016 at 04:59:22PM +0200, Sebastien Jodogne wrote:
> Dear all,
> 
> I have just packaged the newest upstream version of Orthanc (1.1.0):
> http://anonscm.debian.org/cgit/debian-med/orthanc.git/
> 
> Could someone check the package and upload it if everything is OK? Thanks in
> advance!
> 
> Regards,
> Sébastien-
> 
> 

-- 
http://fam-tille.de

Bug#828796: ITP: r-bioc-geneplotter -- R package of functions for plotting genomic data

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
Owner: Debian Med team 

* Package name: r-bioc-geneplotter
  Version : 1.50.0
  Upstream Author : Bioconductor Package Maintainer 

* URL : http://bioconductor.org/packages/geneplotter/
* License : Artistic-2.0
  Programming Lang: R
  Description : R package of functions for plotting genomic data

geneplotter contains plotting functions for microarrays

Dependency for r-bioc-deseq2; team mainted by Debian Med

Re: http://upstream-metadata.debian.net/

[Charles Plessy]

Le Mon, Jun 27, 2016 at 04:21:23PM +0200, Andreas Tille a écrit :
> On Mon, Jun 27, 2016 at 04:14:55PM +0200, Olivier Sallou wrote:
> > Hi Charles,
> > 
> > http://upstream-metadata.debian.net/ seems unavailable, connections
> > remain waiting.
> 
> Charles, I think you should do
> 
>echo "upstream-metadata   in  a  117.121.245.165" | gpg --clearsign | mail 
> chan...@db.debian.org 
> 
> If I remember correctly it was on the same host as blends.debian.net
> and this was moved by GPLhost.

Hi Olivier and Andreas,

I just updated the IP address, thanks for the hint.  I realised some time ago
that the service was unavailable, but I thought it was caused by the upgrade
to Jessie...

The fact that Olivier is the first to report the problem in public suggests
that not many people have a use of this service.  Earlier this year, I started
a discussion about terminating upstream-metadata.debian.net and there was not
much objections against it.

In 2014, the service was affected by a bug that I could not resolve, and I
could not get any help for it.

https://lists.debian.org/debian-qa/2014/06/msg00022.html

Altogether I am blocked and it is clear that I will not be able to provide
a good quality of service alone.

As a pet project, I tried a couple of times to reimplement the whole system
in Haskell, but I still have to iron out my skills on simple issues such as
the handling of command-line options, etc.

Altogether, while I am satisfied that I could start this project and provide a
prototype, I also realise that the design is very naive, for instance I admit
that I do not know what would happen in case of concurrent access to the
database.

So in my opinion, it can not continue at a one-man project.

Have a nice day

-- 
Charles Plessy
Tsurumi, Kanagawa, Japan

Re: Galaxy project producing their own Debian packages

[Olivier Sallou]

- Mail original -

> De: "Michael Crusoe" 
> À: "Olivier Sallou" 
> Cc: "Debian Med Project List" , "Nate Coraor"
> 
> Envoyé: Lundi 27 Juin 2016 21:04:21
> Objet: Re: Galaxy project producing their own Debian packages

> Python packages that need packaging:

> bx-python
> wchartype
> dictobj
> bioblend
> requests-toolbelt
> pulsar-galaxy-lib
> sqlalchemy-migrate
> svgwrite

you mean all other Galaxy dependencies are already available as packages and 
only those ones are missing in Debian ? 

an other point is Galaxy uses specific versions of packages (which is quite 
usual), but may not work with latest releases of those. Would need testing. 

We would need in Debian to deactivate Galaxy startup in virtualenv as well as 
skip any auto install. 

Olivier 

> This should a complete list, Nate promises that there are no hidden sub
> dependencies.

> They also use a custom fork of pysam

> On Mon, Jun 27, 2016 at 2:34 PM, Michael Crusoe < michael.cru...@gmail.com >
> wrote:

> > Hoopla,
> 

> > I'm at the Galaxy Community Conference sitting next to Nate Coraor.
> 

> > Nate is enthusiastic about Galaxy becoming properly packaged for Debian. He
> > is well aware of how hacky his current package is :-)
> 

> > On Thu, Jun 16, 2016 at 11:07 AM, Olivier Sallou < olivier.sal...@irisa.fr
> > >
> > wrote:
> 

> > > On 06/16/2016 08:43 AM, Michael Crusoe wrote:
> > 
> 
> > > >
> > 
> 
> > > > Vezi Tweetul lui @natefoo:
> > 
> 
> > > > https://twitter.com/natefoo/status/743306923026440194
> > 
> 
> > > >
> > 
> 
> > > > https://depot.galaxyproject.org/nate/dpkg/
> > 
> 
> > > >
> > 
> 
> > > nice, but easy for them. Galaxy installs many things at run time from
> > 
> 
> > > remote locations (pypi and others). So not easy to fit in Debian as all
> > 
> 
> > > dependencies not to be Debian packages.
> > 
> 

> > > Olivier
> > 
> 

> > > --
> > 
> 
> > > Olivier Sallou
> > 
> 
> > > IRISA / University of Rennes 1
> > 
> 
> > > Campus de Beaulieu, 35000 RENNES - FRANCE
> > 
> 
> > > Tel: 02.99.84.71.95
> > 
> 

> > > gpg key id: 4096R/326D8438 ( keyring.debian.org )
> > 
> 
> > > Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
> > 
> 

> > --
> 
> > Michael R. Crusoe
> 
> > Community Engineer & Co-founder
> 
> > Common Workflow Language project
> 
> > https://impactstory.org/u/-0002-2961-9670
> 
> > michael.cru...@gmail.com
> 
> > +32 (0) 2 808 25 58
> 
> > +1 480 627 9108
> 

> --
> Michael R. Crusoe
> Community Engineer & Co-founder
> Common Workflow Language project
> https://impactstory.org/u/-0002-2961-9670
> michael.cru...@gmail.com
> +32 (0) 2 808 25 58
> +1 480 627 9108

Re: http://upstream-metadata.debian.net/

[Olivier Sallou]

- Mail original -
> De: "Charles Plessy" 
> À: debian-med@lists.debian.org
> Envoyé: Mardi 28 Juin 2016 03:25:12
> Objet: Re: http://upstream-metadata.debian.net/
> 
> Le Mon, Jun 27, 2016 at 04:21:23PM +0200, Andreas Tille a écrit :
> > On Mon, Jun 27, 2016 at 04:14:55PM +0200, Olivier Sallou wrote:
> > > Hi Charles,
> > > 
> > > http://upstream-metadata.debian.net/ seems unavailable, connections
> > > remain waiting.
> > 
> > Charles, I think you should do
> > 
> >echo "upstream-metadata   in  a  117.121.245.165" | gpg --clearsign |
> >mail chan...@db.debian.org
> > 
> > If I remember correctly it was on the same host as blends.debian.net
> > and this was moved by GPLhost.
> 
> Hi Olivier and Andreas,
> 
> I just updated the IP address, thanks for the hint.  I realised some time ago
> that the service was unavailable, but I thought it was caused by the upgrade
> to Jessie...
> 
> The fact that Olivier is the first to report the problem in public suggests
> that not many people have a use of this service.  Earlier this year, I
> started
> a discussion about terminating upstream-metadata.debian.net and there was not
> much objections against it.
> 
> In 2014, the service was affected by a bug that I could not resolve, and I
> could not get any help for it.
> 
> https://lists.debian.org/debian-qa/2014/06/msg00022.html
> 
> Altogether I am blocked and it is clear that I will not be able to provide
> a good quality of service alone.

Well, maybe in this case, service should be stopped and website reference 
removed from metadata related Wiki. By the way, the git repo referenced does 
not exists either.

Olivier



> 
> As a pet project, I tried a couple of times to reimplement the whole system
> in Haskell, but I still have to iron out my skills on simple issues such as
> the handling of command-line options, etc.
> 
> Altogether, while I am satisfied that I could start this project and provide
> a
> prototype, I also realise that the design is very naive, for instance I admit
> that I do not know what would happen in case of concurrent access to the
> database.
> 
> So in my opinion, it can not continue at a one-man project.

> 
> Have a nice day
> 
> --
> Charles Plessy
> Tsurumi, Kanagawa, Japan
> 
> 

Re: Galaxy project producing their own Debian packages

[Nate Coraor]

On Tuesday, June 28, 2016, Olivier Sallou  wrote:

>
>
> --
>
> *De: *"Michael Crusoe"  >
> *À: *"Olivier Sallou"  >
> *Cc: *"Debian Med Project List"  >, "Nate
> Coraor" 
> >
> *Envoyé: *Lundi 27 Juin 2016 21:04:21
> *Objet: *Re: Galaxy project producing their own Debian packages
>
> Python packages that need packaging:
>
> bx-python
> wchartype
> dictobj
> bioblend
> requests-toolbelt
> pulsar-galaxy-lib
> sqlalchemy-migrate
> svgwrite
>
>
> you mean all other Galaxy dependencies are already available as packages
> and only those ones are missing in Debian ?
>

Correct


> an other point is Galaxy uses specific versions of packages (which is
> quite usual), but may not work with latest releases of those. Would need
> testing.
>

Thankfully in the last few months we have updated to using recent versions
of our dependencies. The goal is to be compatible with current versions of
our dependencies going forward.


> We would need in Debian to deactivate Galaxy startup in virtualenv as well
> as skip any auto install.
>

The auto-install of dependencies and creation of a virtualenv only happens
when running from source. If installed as a traditional Python package, it
should behave normally.

--nate


> Olivier
>
>
> This should a complete list, Nate promises that there are no hidden sub
> dependencies.
>
> They also use a custom fork of pysam
>
> On Mon, Jun 27, 2016 at 2:34 PM, Michael Crusoe  > wrote:
>
>> Hoopla,
>>
>> I'm at the Galaxy Community Conference sitting next to Nate Coraor.
>>
>> Nate is enthusiastic about Galaxy becoming properly packaged for Debian.
>> He is well aware of how hacky his current package is :-)
>>
>> On Thu, Jun 16, 2016 at 11:07 AM, Olivier Sallou > > wrote:
>>
>>>
>>>
>>> On 06/16/2016 08:43 AM, Michael Crusoe wrote:
>>> >
>>> > Vezi Tweetul lui @natefoo:
>>> > https://twitter.com/natefoo/status/743306923026440194
>>> >
>>> > https://depot.galaxyproject.org/nate/dpkg/
>>> >
>>> nice, but easy for them. Galaxy installs many things at run time from
>>> remote locations (pypi and others). So not easy to fit in Debian as all
>>> dependencies not to be Debian packages.
>>>
>>> Olivier
>>>
>>> --
>>> Olivier Sallou
>>> IRISA / University of Rennes 1
>>> Campus de Beaulieu, 35000 RENNES - FRANCE
>>> Tel: 02.99.84.71.95
>>>
>>> gpg key id: 4096R/326D8438  (keyring.debian.org)
>>> Key fingerprint = 5FB4 6F83 D3B9 5204 6335  D26D 78DC 68DB 326D 8438
>>>
>>>
>>
>>
>> --
>> Michael R. Crusoe
>> Community Engineer & Co-founder
>> Common Workflow Language project
>> https://impactstory.org/u/-0002-2961-9670
>> michael.cru...@gmail.com
>> 
>> +32 (0) 2 808 25 58
>> +1 480 627 9108
>>
>
>
>
> --
> Michael R. Crusoe
> Community Engineer & Co-founder
> Common Workflow Language project
> https://impactstory.org/u/-0002-2961-9670
> michael.cru...@gmail.com
> 
> +32 (0) 2 808 25 58
> +1 480 627 9108
>
>
>