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 <directory name> 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 <[email protected]>: > 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
