Re: [MoM] deepnano getting info from maintainer

[Andreas Tille]

On Wed, Mar 08, 2017 at 02:26:48PM +0100, Andreas Tille wrote:
> So
> now its just waiting whether ftpmaster has some comments and than the
> package can migrate to the Debian archive.

Package was accepted and is now available in unstable.  I added the
project as successful MoM effort to the Wiki page[1]
 
> Thanks for your (and Afif's) work on this

Thanks again - any other takers for a MoM project?

Kind regards

  Andreas.


[1] https://wiki.debian.org/DebianMed/MoM

-- 
http://fam-tille.de

Re: [MoM] deepnano getting info from maintainer

[Andreas Tille]

Hi Çağrı,

On Wed, Mar 08, 2017 at 02:41:18PM +0300, Çağrı ULAŞ wrote:
> I change watchdog with python-watchdog and try
> 
> deepnano_basecall_no_metrichor --watch 
> 
> I couldn't understand what it's doing exactly.
> 
> $ deepnano_basecall_no_metrichor --watch .
> loading complement net
> done
> loading 2D net
> done
> Watch dir: .
> Starting Observerer
> 
> But it's not run while python-watchdog not installed. So I switched them.

OK, thanks for checking.  Since it is used for a certain functionality
I upgraded from Suggests to Recommends and uploaded the package.  So
now its just waiting whether ftpmaster has some comments and than the
package can migrate to the Debian archive.

Thanks for your (and Afif's) work on this

  Andreas.
 
> 2017-03-06 20:59 GMT+03:00 Andreas Tille :
> 
> > On Wed, Feb 22, 2017 at 08:20:01PM +0100, Andreas Tille wrote:
> > > On Wed, Feb 22, 2017 at 10:10:12PM +0300, Çağrı ULAŞ wrote:
> > > > But i think, this watchdog is not watchdog package, it's
> > python-watchdog.
> > > > I'll try this parameter and push changes in tomorrow.
> > >
> > > Good we talked about this. ;-)
> >
> > Hmmm, you claimed to push something "tomorrow" - but I have not yet seen
> > any commit.  Just lets finish this package.
> >
> > Kind regards
> >
> >   Andreas.
> >
> > --
> > http://fam-tille.de
> >
> >
> 
> 
> -- 
> *Çağrı ULAŞ*
> about.me/cagriulas

-- 
http://fam-tille.de

Re: [MoM] deepnano getting info from maintainer

[Andreas Tille]

On Wed, Feb 22, 2017 at 08:20:01PM +0100, Andreas Tille wrote:
> On Wed, Feb 22, 2017 at 10:10:12PM +0300, Çağrı ULAŞ wrote:
> > But i think, this watchdog is not watchdog package, it's python-watchdog.
> > I'll try this parameter and push changes in tomorrow.
> 
> Good we talked about this. ;-)

Hmmm, you claimed to push something "tomorrow" - but I have not yet seen
any commit.  Just lets finish this package.

Kind regards

  Andreas.

-- 
http://fam-tille.de

Re: [MoM] deepnano getting info from maintainer

[Çağrı ULAŞ]

But i think, this watchdog is not watchdog package, it's python-watchdog.
I'll try this parameter and push changes in tomorrow.

2017-02-22 21:51 GMT+03:00 Çağrı ULAŞ :

> ​​
> Hi Andreas,
>
> In README.md file they said:
>
> If you want to watch a directory for new files, first install:
>>
>>- watchdog==0.8.3
>>
>> And then use (the output parameter has no effect, we output separate
>> fasta files for each fast5 file):
>> OMP_NUM_THREADS=1 python basecall_no_metrichor.py --watch 
>
> watchdog version is fixed there but didn't test this feature with watchdog
> package in sid
>
> or version 0.8.3 though.
>
> Regards.
>
> 2017-02-22 11:45 GMT+03:00 Andreas Tille :
>
>> Hi Çağrı,
>>
>> On Wed, Feb 22, 2017 at 01:45:56AM +0300, Çağrı ULAŞ wrote:
>> > I made some changes and will push them soon. Add manpages for scripts,
>> > changes in testsuite etc.
>>
>> Sounds good.
>>
>> I checked this and noticed you added "Suggests: watchdog".  Do you have
>> any specific reason for this suggestion?  I do not think that the fact
>> that calls to deepnano might take some time makes this suggestion
>> necessary specifically since some status update is given as output.
>>
>> One hint for your debug code in run-test.sh:  The sequence !! will be
>> interpreted by bash by he history function.  I wrapped your debug line
>> into '' to prevent this.
>>
>> > But when writing manpages, I realize that
>> > deepnano uses some files under nets_data/ in default arguments.
>> >
>> > in source code:
>> >
>> > parser.add_argument('--template_net', type=str,
>> default="nets_data/map6temp.
>> > npz")
>> > parser.add_argument('--complement_net', type=str, default=
>> > "nets_data/map6comp.npz")
>> > parser.add_argument('--big_net', type=str, default="nets_data/map6-2d-
>> > big.npz")
>> >
>> > these .npz files is python numpy saves. And I think, they use different
>> > reads
>> > according to this issue[1]. What can we do for this defaults? (Quilt
>> patch?)
>>
>> If upstream has a solution for [1] a quilt patch drawn from their
>> repository would be an apropriate solution.  As far as I can see there
>> is no solution for the issue yet so what we can do is giving a hint
>> for the users of the Debian package in README.Debian.
>>
>> In case you feel able to find a patch to solve this issue, yes, a quilt
>> patch would be an excelent solution and you should forward this patch to
>> the upstream tracker.  This will be recieved as a very welcome
>> distribution from Debian to upstream and might give a good motivation
>> for upstream in case of further issues.  Otherwise I do not think that
>> an open issue of upstream code should prevent us from releasing the
>> package since the test suite is running and seems to do something
>> sensible.
>>
>> BTW, when checking for fresh commits I realised that my versioning which
>> should have matched the last commit data was wrong.  I've fixed this.
>>
>> > Are there anything else I can do for this program until we get a
>> response
>> > from developer?
>>
>> I do not think so.  Usually new packages need to wait in the Debian new
>> queue for some time - if we are lucky upstream has fixed the issue
>> meanwhile and we can come up with a fix.  So I'm tempted to upload the
>> package (after commenting out the debug code in run-test.sh) and if you
>> clarified your motivation for watchdog suggestion.
>>
>> Please also inspect the latest changes I did:
>>
>>   1. Upstream does not provide a proper makefile and thus you added
>>  the compilation lines in d/rules which is fine.  I just added
>>  $(CFLAGS) which was missing.
>>   2. There was a lintian info about duplicated short description -
>>  thus I've added (data) to the data package.  Its a pretty minor
>>  issue but simple to fix.
>>   3. You ITPed the package (#844010)
>>
>> Kind regards and thanks for your work on this
>>
>>  Andreas.
>>
>> > [1] https://bitbucket.org/vboza/deepnano/issues/4/deepnano-with-
>> metrichor-bad-input-argument
>>
>> --
>> http://fam-tille.de
>>
>>
>
>
> --
> *Çağrı ULAŞ*
> about.me/cagriulas
>



-- 
*Çağrı ULAŞ*
about.me/cagriulas

Re: [MoM] deepnano getting info from maintainer

[Çağrı ULAŞ]

​​
Hi Andreas,

In README.md file they said:

If you want to watch a directory for new files, first install:
>
>- watchdog==0.8.3
>
> And then use (the output parameter has no effect, we output separate fasta
> files for each fast5 file):
> OMP_NUM_THREADS=1 python basecall_no_metrichor.py --watch 

watchdog version is fixed there but didn't test this feature with watchdog
package in sid

or version 0.8.3 though.

Regards.

2017-02-22 11:45 GMT+03:00 Andreas Tille :

> Hi Çağrı,
>
> On Wed, Feb 22, 2017 at 01:45:56AM +0300, Çağrı ULAŞ wrote:
> > I made some changes and will push them soon. Add manpages for scripts,
> > changes in testsuite etc.
>
> Sounds good.
>
> I checked this and noticed you added "Suggests: watchdog".  Do you have
> any specific reason for this suggestion?  I do not think that the fact
> that calls to deepnano might take some time makes this suggestion
> necessary specifically since some status update is given as output.
>
> One hint for your debug code in run-test.sh:  The sequence !! will be
> interpreted by bash by he history function.  I wrapped your debug line
> into '' to prevent this.
>
> > But when writing manpages, I realize that
> > deepnano uses some files under nets_data/ in default arguments.
> >
> > in source code:
> >
> > parser.add_argument('--template_net', type=str,
> default="nets_data/map6temp.
> > npz")
> > parser.add_argument('--complement_net', type=str, default=
> > "nets_data/map6comp.npz")
> > parser.add_argument('--big_net', type=str, default="nets_data/map6-2d-
> > big.npz")
> >
> > these .npz files is python numpy saves. And I think, they use different
> > reads
> > according to this issue[1]. What can we do for this defaults? (Quilt
> patch?)
>
> If upstream has a solution for [1] a quilt patch drawn from their
> repository would be an apropriate solution.  As far as I can see there
> is no solution for the issue yet so what we can do is giving a hint
> for the users of the Debian package in README.Debian.
>
> In case you feel able to find a patch to solve this issue, yes, a quilt
> patch would be an excelent solution and you should forward this patch to
> the upstream tracker.  This will be recieved as a very welcome
> distribution from Debian to upstream and might give a good motivation
> for upstream in case of further issues.  Otherwise I do not think that
> an open issue of upstream code should prevent us from releasing the
> package since the test suite is running and seems to do something
> sensible.
>
> BTW, when checking for fresh commits I realised that my versioning which
> should have matched the last commit data was wrong.  I've fixed this.
>
> > Are there anything else I can do for this program until we get a response
> > from developer?
>
> I do not think so.  Usually new packages need to wait in the Debian new
> queue for some time - if we are lucky upstream has fixed the issue
> meanwhile and we can come up with a fix.  So I'm tempted to upload the
> package (after commenting out the debug code in run-test.sh) and if you
> clarified your motivation for watchdog suggestion.
>
> Please also inspect the latest changes I did:
>
>   1. Upstream does not provide a proper makefile and thus you added
>  the compilation lines in d/rules which is fine.  I just added
>  $(CFLAGS) which was missing.
>   2. There was a lintian info about duplicated short description -
>  thus I've added (data) to the data package.  Its a pretty minor
>  issue but simple to fix.
>   3. You ITPed the package (#844010)
>
> Kind regards and thanks for your work on this
>
>  Andreas.
>
> > [1] https://bitbucket.org/vboza/deepnano/issues/4/deepnano-
> with-metrichor-bad-input-argument
>
> --
> http://fam-tille.de
>
>


-- 
*Çağrı ULAŞ*
about.me/cagriulas

Re: [MoM] deepnano getting info from maintainer

[Andreas Tille]

Hi Çağrı,

On Wed, Feb 22, 2017 at 01:45:56AM +0300, Çağrı ULAŞ wrote:
> I made some changes and will push them soon. Add manpages for scripts,
> changes in testsuite etc.

Sounds good.

I checked this and noticed you added "Suggests: watchdog".  Do you have
any specific reason for this suggestion?  I do not think that the fact
that calls to deepnano might take some time makes this suggestion
necessary specifically since some status update is given as output.

One hint for your debug code in run-test.sh:  The sequence !! will be
interpreted by bash by he history function.  I wrapped your debug line
into '' to prevent this.

> But when writing manpages, I realize that
> deepnano uses some files under nets_data/ in default arguments.
> 
> in source code:
> 
> parser.add_argument('--template_net', type=str, default="nets_data/map6temp.
> npz")
> parser.add_argument('--complement_net', type=str, default=
> "nets_data/map6comp.npz")
> parser.add_argument('--big_net', type=str, default="nets_data/map6-2d-
> big.npz")
> 
> these .npz files is python numpy saves. And I think, they use different
> reads
> according to this issue[1]. What can we do for this defaults? (Quilt patch?)

If upstream has a solution for [1] a quilt patch drawn from their
repository would be an apropriate solution.  As far as I can see there
is no solution for the issue yet so what we can do is giving a hint
for the users of the Debian package in README.Debian.

In case you feel able to find a patch to solve this issue, yes, a quilt
patch would be an excelent solution and you should forward this patch to
the upstream tracker.  This will be recieved as a very welcome
distribution from Debian to upstream and might give a good motivation
for upstream in case of further issues.  Otherwise I do not think that
an open issue of upstream code should prevent us from releasing the
package since the test suite is running and seems to do something
sensible.

BTW, when checking for fresh commits I realised that my versioning which
should have matched the last commit data was wrong.  I've fixed this.

> Are there anything else I can do for this program until we get a response
> from developer?

I do not think so.  Usually new packages need to wait in the Debian new
queue for some time - if we are lucky upstream has fixed the issue
meanwhile and we can come up with a fix.  So I'm tempted to upload the
package (after commenting out the debug code in run-test.sh) and if you
clarified your motivation for watchdog suggestion.

Please also inspect the latest changes I did:

  1. Upstream does not provide a proper makefile and thus you added
 the compilation lines in d/rules which is fine.  I just added
 $(CFLAGS) which was missing.
  2. There was a lintian info about duplicated short description -
 thus I've added (data) to the data package.  Its a pretty minor
 issue but simple to fix.
  3. You ITPed the package (#844010) 

Kind regards and thanks for your work on this

 Andreas.

> [1] 
> https://bitbucket.org/vboza/deepnano/issues/4/deepnano-with-metrichor-bad-input-argument

-- 
http://fam-tille.de

Re: [MoM] deepnano getting info from maintainer

[Çağrı ULAŞ]

Hi Andreas,

I made some changes and will push them soon. Add manpages for scripts,
changes in testsuite etc. But when writing manpages, I realize that
deepnano uses some files under nets_data/ in default arguments.

in source code:

parser.add_argument('--template_net', type=str, default="nets_data/map6temp.
npz")
parser.add_argument('--complement_net', type=str, default=
"nets_data/map6comp.npz")
parser.add_argument('--big_net', type=str, default="nets_data/map6-2d-
big.npz")

these .npz files is python numpy saves. And I think, they use different
reads
according to this issue[1]. What can we do for this defaults? (Quilt patch?)
Are there anything else I can do for this program until we get a response
from
developer?

Regards

[1] https://bitbucket.org/vboza/deepnano/issues/4/deepnano-
with-metrichor-bad-input-argument

2017-02-15 17:06 GMT+03:00 Andreas Tille :

> Hi,
>
> On Wed, Feb 15, 2017 at 04:36:36PM +0300, Çağrı ULAŞ wrote:
> > What exactly did you plan in connection with the poretools package?
>
> I do not plan anything with poretools.
>
> > In deepnano at debian/deepnano-data-files/test_data/ , there are 3 gz
> files.
> > These files are copied from poretools source. Thanks to Afif,
> poretools-data
> > package is currently present in sid. So we can remove these files from
> > deepnano-data and use poretools-data, deepnano-data for testing.
>
> So do you want to do this in Git?
>
> > deepnano-data will only contain nets_data/ .
>
> Sounds good.
>
> > > I have fixed the deepnano debian/control file a bit (see my last
> > > commits) and think a manpage could be written using help2man.
> >
> > ​Ok.
> >
> >
> > > How do we want to proceed to finalise the MoM project?
> >
> > ​I think, package is usable but still no version tag on it. I'm going to
> > create an issue
> > on bitbucket. Maybe get a response from there.
>
> Good.
>
> Please adapt the test of deepnano to avoid duplicated data files and
> write a manpage using help2man.  As a hint:  I've written a script[1]
> which you can put into the debian/ dir replace "" (if there
> are more binaries you need to copy the according paragraph).  Than
> install the preliminary package on your local machine and run
>
> debian/createmanpages
>
> May be you need to adapt --help-option to fit what the program expects.
>
> Hope this helps.
>
> Kind regards
>
>   Andreas.
>
>
> [1] https://anonscm.debian.org/viewvc/debian-med/trunk/helper-
> scripts/createmanpages?view=markup
>
> --
> http://fam-tille.de
>



-- 
*Çağrı ULAŞ*
about.me/cagriulas

Re: [MoM] deepnano getting info from maintainer

[Çağrı ULAŞ]

Hi Andreas,

What exactly did you plan in connection with the poretools package?


In deepnano at debian/deepnano-data-files/test_data/ , there are 3 gz files.
These files are copied from poretools source. Thanks to Afif, poretools-data
package is currently present in sid. So we can remove these files from
deepnano-data and use poretools-data, deepnano-data for testing.
deepnano-data will only contain nets_data/ .

I have fixed the deepnano debian/control file a bit (see my last
> commits) and think a manpage could be written using help2man.


​Ok.


> How do we want to proceed to finalise the MoM project?


​I think, package is usable but still no version tag on it. I'm going to
create an issue
on bitbucket. Maybe get a response from there.

Regards.

2017-02-12 22:06 GMT+03:00 Andreas Tille :

> Hi,
>
> sorry, left this project alone for close to three monthes despite
> promising to have a look.  The preparation of Squeeze got my full
> interest. but now I had a look.
>
> On Sat, Dec 17, 2016 at 12:55:35AM -0800, Afif Elghraoui wrote:
> > Hi, Çağrı,
> >
> > على الجمعـة 16 كانون الأول 2016 ‫21:06، كتب Çağrı ULAŞ:
> > > I push some changes for deepnano. Used a few poretools data for the
> > > deepnano-data because poretools use pybuild for packaging. When I
> create
> > > new package in control file (for split packaging) poretools package
> > > created with empty package. I dont want to change the way this package
> > > builded. Didn't find any useful example for python split packaging. Any
> > > ideas?
> >
> > I just made this change and will upload poretools with a data package
> > shortly.
>
> What exactly did you plan in connection with the poretools package?
>
> I have fixed the deepnano debian/control file a bit (see my last
> commits) and think a manpage could be written using help2man.
>
> The test debian/tests/run-test.sh runs in my local machine.
>
> How do we want to proceed to finalise the MoM project?
>
> Kind regards
>
>Andreas.
>
> --
> http://fam-tille.de
>



-- 
*Çağrı ULAŞ*
about.me/cagriulas

Re: [MoM] deepnano getting info from maintainer

[Andreas Tille]

Hi,

sorry, left this project alone for close to three monthes despite
promising to have a look.  The preparation of Squeeze got my full
interest. but now I had a look.

On Sat, Dec 17, 2016 at 12:55:35AM -0800, Afif Elghraoui wrote:
> Hi, Çağrı,
> 
> على الجمعـة 16 كانون الأول 2016 ‫21:06، كتب Çağrı ULAŞ:
> > I push some changes for deepnano. Used a few poretools data for the
> > deepnano-data because poretools use pybuild for packaging. When I create
> > new package in control file (for split packaging) poretools package
> > created with empty package. I dont want to change the way this package
> > builded. Didn't find any useful example for python split packaging. Any
> > ideas?
> 
> I just made this change and will upload poretools with a data package
> shortly.

What exactly did you plan in connection with the poretools package?

I have fixed the deepnano debian/control file a bit (see my last
commits) and think a manpage could be written using help2man. 

The test debian/tests/run-test.sh runs in my local machine.

How do we want to proceed to finalise the MoM project?

Kind regards

   Andreas.

-- 
http://fam-tille.de

Re: [MoM] deepnano getting info from maintainer

[Andreas Tille]

Hi Çağrı,

On Sat, Dec 17, 2016 at 08:06:00AM +0300, Çağrı ULAŞ wrote:
> 
> I push some changes for deepnano. Used a few poretools data for the
> deepnano-data because poretools use pybuild for packaging. When I create
> new package in control file (for split packaging) poretools package created
> with empty package. I dont want to change the way this package builded.
> Didn't find any useful example for python split packaging. Any ideas?
> Currently, this way test passed. I didn't use dch for now. What should I do
> next?

I'll have a look later.  As Afif wrote the data package is prepared and
there is no real need to duplicate those larger data sets.

Just a remerk: You commited a dir debian/deepnano to the Git repository.
These files should not be commited since these are results of a build
process.  Moreover I'm a bit worried that you are not using gbp +
pbuilder as recommended in the Debian policy document.  Please make sure
that you at least know how to do this since you should in any case once
in a while check building in a pbuilder chroot.

I'll report later once I checked the test using poretools data.

Kind regards

  Andreas.

-- 
http://fam-tille.de

Re: [MoM] deepnano getting info from maintainer

[Afif Elghraoui]

Hi, Çağrı,

على الجمعـة 16 كانون الأول 2016 ‫21:06، كتب Çağrı ULAŞ:
> I push some changes for deepnano. Used a few poretools data for the
> deepnano-data because poretools use pybuild for packaging. When I create
> new package in control file (for split packaging) poretools package
> created with empty package. I dont want to change the way this package
> builded. Didn't find any useful example for python split packaging. Any
> ideas?

I just made this change and will upload poretools with a data package
shortly.

regards
Afif

-- 
Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name

Re: [MoM] deepnano getting info from maintainer

[Çağrı ULAŞ]

Hi Andreas,

I push some changes for deepnano. Used a few poretools data for the
deepnano-data because poretools use pybuild for packaging. When I create
new package in control file (for split packaging) poretools package created
with empty package. I dont want to change the way this package builded.
Didn't find any useful example for python split packaging. Any ideas?
Currently, this way test passed. I didn't use dch for now. What should I do
next?

Regards

2016-12-14 11:40 GMT+03:00 Andreas Tille :

> Hi Çağrı,
>
> any news?
>
> Kind regards
>
>Andreas.
>
> On Fri, Dec 02, 2016 at 12:47:23AM +0300, Çağrı ULAŞ wrote:
> > Hi Andreas,
> >
> > I already started to make poretools-data package. Had to make some
> > practice on split packaging . It's almost done. When I finished
> > I will upload them both.
> >
> > Regards.
> >
> > 2016-12-01 16:00 GMT+03:00 Andreas Tille :
> >
> > > Hi Çağrı,
> > >
> > > I wonder whether Afif's hint how to get the example files might have
> > > been helpful for you.  I admit I'm not keen to stick to the monthly
> > > boundaries of the MoM projects but if deepnano should make it into
> > > stretch we need to hurry up a bit.
> > >
> > > Kind regards
> > >
> > >Andreas.
> > >
> > > On Wed, Nov 16, 2016 at 11:50:43AM +0200, Çağrı ULAŞ wrote:
> > > > Hi Andreas,
> > > >
> > > > I finally find fast5 files from poretools which is an utility for
> > > > converting fast5 to fasta/fastq file. There are fast5 examples on
> > > > poretools' github page. Is there any thing we need to specify for
> this
> > > data
> > > > in debian directory?
> > > >
> > > > Regards
> > > >
> > > > 2016-11-12 1:01 GMT+03:00 Andreas Tille :
> > > >
> > > > > Hi,
> > > > >
> > > > > On Fri, Nov 11, 2016 at 08:34:15PM +0200, Çağrı ULAŞ wrote:
> > > > > > Working on autopkgtest but I have issues with deepnano. There
> are no
> > > man
> > > > > > pages or example files I found.
> > > > >
> > > > > Did you tried -h/--help options that might be used with help2man?
> > > > >
> > > > > > Only bitbucket page have a basic usage but
> > > > > > this is more different from classic alignment tools.
> > > > >
> > > > > If there is no chance with help2man you might try to find some
> simple
> > > > > introduction how to write manpages (or check out a simple manpage
> on
> > > the
> > > > > Debian system) and feed in the content of the bitbucket page.
> > > > >
> > > > > > I try to run with some
> > > > > > .npz datas in nets_data directory. But give me an error 'Unable
> to
> > > open
> > > > > > file (File signature not found)'. Anyway, .npz datas are numpy's
> > > > > > uncompressed files according to scipy's docs. 'OMP_NUM_THREADS=1
> > > > > > deepnano_basecall' command uses fast5 files. Cant get any fast5
> file.
> > > > > Where
> > > > > > can I get them, any ideas?
> > > > >
> > > > >  * Asking upstream
> > > > >  * Asking Canberk how he found example files
> > > > >  * Hoping for hints of other readers here
> > > > >
> > > > > Sorry, I can not help myself since I'm not working as
> bioinformatican.
> > > > >
> > > > > > Nowadays, lots of work on me at university but I'll try to
> > > communicate
> > > > > more
> > > > > > often.
> > > > >
> > > > > OK.
> > > > >
> > > > > Kind regards
> > > > >
> > > > >   Andreas.
> > > > >
> > > > > --
> > > > > http://fam-tille.de
> > > > >
> > > > >
> > > >
> > > >
> > > > --
> > > > *Çağrı ULAŞ*
> > > > about.me/cagriulas
> > >
> > > --
> > > http://fam-tille.de
> > >
> > >
> >
> >
> > --
> > *Çağrı ULAŞ*
> > about.me/cagriulas
>
> --
> http://fam-tille.de
>
>


-- 
*Çağrı ULAŞ*
about.me/cagriulas

Re: [MoM] deepnano getting info from maintainer

[Andreas Tille]

Hi Çağrı,

any news?

Kind regards

   Andreas.

On Fri, Dec 02, 2016 at 12:47:23AM +0300, Çağrı ULAŞ wrote:
> Hi Andreas,
> 
> I already started to make poretools-data package. Had to make some
> practice on split packaging . It's almost done. When I finished
> I will upload them both.
> 
> Regards.
> 
> 2016-12-01 16:00 GMT+03:00 Andreas Tille :
> 
> > Hi Çağrı,
> >
> > I wonder whether Afif's hint how to get the example files might have
> > been helpful for you.  I admit I'm not keen to stick to the monthly
> > boundaries of the MoM projects but if deepnano should make it into
> > stretch we need to hurry up a bit.
> >
> > Kind regards
> >
> >Andreas.
> >
> > On Wed, Nov 16, 2016 at 11:50:43AM +0200, Çağrı ULAŞ wrote:
> > > Hi Andreas,
> > >
> > > I finally find fast5 files from poretools which is an utility for
> > > converting fast5 to fasta/fastq file. There are fast5 examples on
> > > poretools' github page. Is there any thing we need to specify for this
> > data
> > > in debian directory?
> > >
> > > Regards
> > >
> > > 2016-11-12 1:01 GMT+03:00 Andreas Tille :
> > >
> > > > Hi,
> > > >
> > > > On Fri, Nov 11, 2016 at 08:34:15PM +0200, Çağrı ULAŞ wrote:
> > > > > Working on autopkgtest but I have issues with deepnano. There are no
> > man
> > > > > pages or example files I found.
> > > >
> > > > Did you tried -h/--help options that might be used with help2man?
> > > >
> > > > > Only bitbucket page have a basic usage but
> > > > > this is more different from classic alignment tools.
> > > >
> > > > If there is no chance with help2man you might try to find some simple
> > > > introduction how to write manpages (or check out a simple manpage on
> > the
> > > > Debian system) and feed in the content of the bitbucket page.
> > > >
> > > > > I try to run with some
> > > > > .npz datas in nets_data directory. But give me an error 'Unable to
> > open
> > > > > file (File signature not found)'. Anyway, .npz datas are numpy's
> > > > > uncompressed files according to scipy's docs. 'OMP_NUM_THREADS=1
> > > > > deepnano_basecall' command uses fast5 files. Cant get any fast5 file.
> > > > Where
> > > > > can I get them, any ideas?
> > > >
> > > >  * Asking upstream
> > > >  * Asking Canberk how he found example files
> > > >  * Hoping for hints of other readers here
> > > >
> > > > Sorry, I can not help myself since I'm not working as bioinformatican.
> > > >
> > > > > Nowadays, lots of work on me at university but I'll try to
> > communicate
> > > > more
> > > > > often.
> > > >
> > > > OK.
> > > >
> > > > Kind regards
> > > >
> > > >   Andreas.
> > > >
> > > > --
> > > > http://fam-tille.de
> > > >
> > > >
> > >
> > >
> > > --
> > > *Çağrı ULAŞ*
> > > about.me/cagriulas
> >
> > --
> > http://fam-tille.de
> >
> >
> 
> 
> -- 
> *Çağrı ULAŞ*
> about.me/cagriulas

-- 
http://fam-tille.de

Re: [MoM] deepnano getting info from maintainer

[Çağrı ULAŞ]

Hi Andreas,

I already started to make poretools-data package. Had to make some
practice on split packaging . It's almost done. When I finished
I will upload them both.

Regards.

2016-12-01 16:00 GMT+03:00 Andreas Tille :

> Hi Çağrı,
>
> I wonder whether Afif's hint how to get the example files might have
> been helpful for you.  I admit I'm not keen to stick to the monthly
> boundaries of the MoM projects but if deepnano should make it into
> stretch we need to hurry up a bit.
>
> Kind regards
>
>Andreas.
>
> On Wed, Nov 16, 2016 at 11:50:43AM +0200, Çağrı ULAŞ wrote:
> > Hi Andreas,
> >
> > I finally find fast5 files from poretools which is an utility for
> > converting fast5 to fasta/fastq file. There are fast5 examples on
> > poretools' github page. Is there any thing we need to specify for this
> data
> > in debian directory?
> >
> > Regards
> >
> > 2016-11-12 1:01 GMT+03:00 Andreas Tille :
> >
> > > Hi,
> > >
> > > On Fri, Nov 11, 2016 at 08:34:15PM +0200, Çağrı ULAŞ wrote:
> > > > Working on autopkgtest but I have issues with deepnano. There are no
> man
> > > > pages or example files I found.
> > >
> > > Did you tried -h/--help options that might be used with help2man?
> > >
> > > > Only bitbucket page have a basic usage but
> > > > this is more different from classic alignment tools.
> > >
> > > If there is no chance with help2man you might try to find some simple
> > > introduction how to write manpages (or check out a simple manpage on
> the
> > > Debian system) and feed in the content of the bitbucket page.
> > >
> > > > I try to run with some
> > > > .npz datas in nets_data directory. But give me an error 'Unable to
> open
> > > > file (File signature not found)'. Anyway, .npz datas are numpy's
> > > > uncompressed files according to scipy's docs. 'OMP_NUM_THREADS=1
> > > > deepnano_basecall' command uses fast5 files. Cant get any fast5 file.
> > > Where
> > > > can I get them, any ideas?
> > >
> > >  * Asking upstream
> > >  * Asking Canberk how he found example files
> > >  * Hoping for hints of other readers here
> > >
> > > Sorry, I can not help myself since I'm not working as bioinformatican.
> > >
> > > > Nowadays, lots of work on me at university but I'll try to
> communicate
> > > more
> > > > often.
> > >
> > > OK.
> > >
> > > Kind regards
> > >
> > >   Andreas.
> > >
> > > --
> > > http://fam-tille.de
> > >
> > >
> >
> >
> > --
> > *Çağrı ULAŞ*
> > about.me/cagriulas
>
> --
> http://fam-tille.de
>
>


-- 
*Çağrı ULAŞ*
about.me/cagriulas

Re: [MoM] deepnano getting info from maintainer

[Andreas Tille]

Hi Çağrı,

I wonder whether Afif's hint how to get the example files might have
been helpful for you.  I admit I'm not keen to stick to the monthly
boundaries of the MoM projects but if deepnano should make it into
stretch we need to hurry up a bit.

Kind regards

   Andreas.

On Wed, Nov 16, 2016 at 11:50:43AM +0200, Çağrı ULAŞ wrote:
> Hi Andreas,
> 
> I finally find fast5 files from poretools which is an utility for
> converting fast5 to fasta/fastq file. There are fast5 examples on
> poretools' github page. Is there any thing we need to specify for this data
> in debian directory?
> 
> Regards
> 
> 2016-11-12 1:01 GMT+03:00 Andreas Tille :
> 
> > Hi,
> >
> > On Fri, Nov 11, 2016 at 08:34:15PM +0200, Çağrı ULAŞ wrote:
> > > Working on autopkgtest but I have issues with deepnano. There are no man
> > > pages or example files I found.
> >
> > Did you tried -h/--help options that might be used with help2man?
> >
> > > Only bitbucket page have a basic usage but
> > > this is more different from classic alignment tools.
> >
> > If there is no chance with help2man you might try to find some simple
> > introduction how to write manpages (or check out a simple manpage on the
> > Debian system) and feed in the content of the bitbucket page.
> >
> > > I try to run with some
> > > .npz datas in nets_data directory. But give me an error 'Unable to open
> > > file (File signature not found)'. Anyway, .npz datas are numpy's
> > > uncompressed files according to scipy's docs. 'OMP_NUM_THREADS=1
> > > deepnano_basecall' command uses fast5 files. Cant get any fast5 file.
> > Where
> > > can I get them, any ideas?
> >
> >  * Asking upstream
> >  * Asking Canberk how he found example files
> >  * Hoping for hints of other readers here
> >
> > Sorry, I can not help myself since I'm not working as bioinformatican.
> >
> > > Nowadays, lots of work on me at university but I'll try to communicate
> > more
> > > often.
> >
> > OK.
> >
> > Kind regards
> >
> >   Andreas.
> >
> > --
> > http://fam-tille.de
> >
> >
> 
> 
> -- 
> *Çağrı ULAŞ*
> about.me/cagriulas

-- 
http://fam-tille.de

Re: [MoM] deepnano getting info from maintainer

[Afif Elghraoui]

Hello,

على الأربعاء 16 تشرين الثاني 2016 ‫01:50، كتب Çağrı ULAŞ:
> 
> I finally find fast5 files from poretools which is an utility for
> converting fast5 to fasta/fastq file. There are fast5 examples on
> poretools' github page. Is there any thing we need to specify for this
> data in debian directory?

I created the poretools Debian package, but the data files are not part
of any binary package. Do you two think it would be a good idea to make
a poretools-data package? Then you could build-depend on it to get
access to these files.

Çağrı, perhaps you can see whether those files are useful for you. If
they are, we can arrange to get them packaged and you can pull it in as
a dependency.

regards
Afif

-- 
Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name

Re: [MoM] deepnano getting info from maintainer

[Çağrı ULAŞ]

Hi Andreas,

I finally find fast5 files from poretools which is an utility for
converting fast5 to fasta/fastq file. There are fast5 examples on
poretools' github page. Is there any thing we need to specify for this data
in debian directory?

Regards

2016-11-12 1:01 GMT+03:00 Andreas Tille :

> Hi,
>
> On Fri, Nov 11, 2016 at 08:34:15PM +0200, Çağrı ULAŞ wrote:
> > Working on autopkgtest but I have issues with deepnano. There are no man
> > pages or example files I found.
>
> Did you tried -h/--help options that might be used with help2man?
>
> > Only bitbucket page have a basic usage but
> > this is more different from classic alignment tools.
>
> If there is no chance with help2man you might try to find some simple
> introduction how to write manpages (or check out a simple manpage on the
> Debian system) and feed in the content of the bitbucket page.
>
> > I try to run with some
> > .npz datas in nets_data directory. But give me an error 'Unable to open
> > file (File signature not found)'. Anyway, .npz datas are numpy's
> > uncompressed files according to scipy's docs. 'OMP_NUM_THREADS=1
> > deepnano_basecall' command uses fast5 files. Cant get any fast5 file.
> Where
> > can I get them, any ideas?
>
>  * Asking upstream
>  * Asking Canberk how he found example files
>  * Hoping for hints of other readers here
>
> Sorry, I can not help myself since I'm not working as bioinformatican.
>
> > Nowadays, lots of work on me at university but I'll try to communicate
> more
> > often.
>
> OK.
>
> Kind regards
>
>   Andreas.
>
> --
> http://fam-tille.de
>
>


-- 
*Çağrı ULAŞ*
about.me/cagriulas

Re: [MoM] deepnano getting info from maintainer

[Andreas Tille]

Hi,

On Fri, Nov 11, 2016 at 08:34:15PM +0200, Çağrı ULAŞ wrote:
> Working on autopkgtest but I have issues with deepnano. There are no man
> pages or example files I found.

Did you tried -h/--help options that might be used with help2man?

> Only bitbucket page have a basic usage but
> this is more different from classic alignment tools.

If there is no chance with help2man you might try to find some simple
introduction how to write manpages (or check out a simple manpage on the
Debian system) and feed in the content of the bitbucket page.

> I try to run with some
> .npz datas in nets_data directory. But give me an error 'Unable to open
> file (File signature not found)'. Anyway, .npz datas are numpy's
> uncompressed files according to scipy's docs. 'OMP_NUM_THREADS=1
> deepnano_basecall' command uses fast5 files. Cant get any fast5 file. Where
> can I get them, any ideas?

 * Asking upstream
 * Asking Canberk how he found example files
 * Hoping for hints of other readers here

Sorry, I can not help myself since I'm not working as bioinformatican.

> Nowadays, lots of work on me at university but I'll try to communicate more
> often.

OK.
 
Kind regards

  Andreas.

-- 
http://fam-tille.de

Re: [MoM] deepnano getting info from maintainer

[Andreas Tille]

Ping?  Usually the mentor should require more frequents (at best daily
reports).  I failed in beeing that strict but to get the package ready
at the end of the month we should increase the frequency of
communication.

Kind regards

Andreas.

On Thu, Oct 27, 2016 at 08:23:24AM +0200, Andreas Tille wrote:
> Hi Çağrı,
> 
> On Thu, Oct 27, 2016 at 03:44:19AM +0300, Çağrı ULAŞ wrote:
> > Sorry for delayed reply. I filed an ITP but I cant get how to track it. It
> > said:
> > 
> > If you want to provide additional information, please wait to receive the
> > > bug tracking number via email, ...
> > >
> > 
> > but I did not get any email. Is this may take time? What should I do to
> > know is it worked?
> 
> Hmmm, did you used
> 
> reportbug wnpp
> 
> to file the bug?  Did you added the Debian Med list as additional
> receiver of the mail?  Since there was no any mail here it might be that
> your MTA is not configured properly and the mail created by reportbug
> never left your local computer.  You might like to try this by
> 
> mailx -s "test"   
> If you do not get any mail your mailer is brocken (you might like to
> check the logs for any hints).  If you do not manage to configure this
> properly you can manually copy the mail content which is created by
> reportbug to your gmail webmailer and send it to - hmmm, I think its
> cont...@bugs.debian.org - please check this on www.debian.org where the
> BTS interface is documented.
> 
> In any case you can check whether your ITP was successful by checking
> 
> https://bugs.debian.org/wnpp
> 
> Hope this helps
> 
>   Andreas.
> 
> 
> -- 
> http://fam-tille.de
> 
> 

-- 
http://fam-tille.de

Re: [MoM] deepnano getting info from maintainer

[Andreas Tille]

Hi Çağrı,

On Thu, Oct 27, 2016 at 03:44:19AM +0300, Çağrı ULAŞ wrote:
> Sorry for delayed reply. I filed an ITP but I cant get how to track it. It
> said:
> 
> If you want to provide additional information, please wait to receive the
> > bug tracking number via email, ...
> >
> 
> but I did not get any email. Is this may take time? What should I do to
> know is it worked?

Hmmm, did you used

reportbug wnpp

to file the bug?  Did you added the Debian Med list as additional
receiver of the mail?  Since there was no any mail here it might be that
your MTA is not configured properly and the mail created by reportbug
never left your local computer.  You might like to try this by

mailx -s "test"  https://bugs.debian.org/wnpp

Hope this helps

  Andreas.


-- 
http://fam-tille.de

Re: [MoM] deepnano getting info from maintainer

[Çağrı ULAŞ]

Hi Andreas,

Sorry for delayed reply. I filed an ITP but I cant get how to track it. It
said:

If you want to provide additional information, please wait to receive the
> bug tracking number via email, ...
>

but I did not get any email. Is this may take time? What should I do to
know is it worked?

Best Regards


2016-10-25 11:50 GMT+03:00 Andreas Tille :

> Hi,
>
> On Thu, Oct 20, 2016 at 03:55:02PM +0300, Çağrı ULAŞ wrote:
> > I cannot find any e-mail unfortunately. Try to contact via bitbucket but
> i
> > think bitbucket sends messages to email.
> > Yes, I successfully built it and run it. I'll try to write autopkgtest
> and
> > find out how can file an ITP.
>
> Did you found out how to ITP.  If yes make sure you CC this mailing list
> to keep people informed.  If not please tell so to receive some hints.
>
> Kind regards
>
>  Andreas.
>
> --
> http://fam-tille.de
>
>


-- 
*Çağrı ULAŞ*
about.me/cagriulas

Re: [MoM] deepnano getting info from maintainer

[Andreas Tille]

Hi Çağrı,

On Thu, Oct 20, 2016 at 03:17:22PM +0300, Çağrı ULAŞ wrote:
> I try to reach Vlado Boza (deepnano's maintainer) from bitbucket but he has
> not reply yet.

If you contacted the maintainer vie e-mail please always CC this list.
It would be nice to bounce your e-mail you've sent or send the content
of whatever interface you've used here to keep others informed.

> Are there another things i have to do on this package?

Could you please confirm that you were able to build and install the
package as well as running the program?

If yes, would you please try writing an autopkgtest?

Moreover you can file an ITP (if you have no idea how please fetch
this information from the other MoM thread ;-) ).

Kind regards

  Andreas.

-- 
http://fam-tille.de

[MoM] deepnano getting info from maintainer

[Çağrı ULAŞ]

Hi Andreas,

I try to reach Vlado Boza (deepnano's maintainer) from bitbucket but he 
has not reply yet. Are there another things i have to do on this 
package?


Çağrı ULAŞ
about.me/cagriulas