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Processing commands for cont...@bugs.debian.org: owner 787977 debian-med-packag...@lists.alioth.debian.org Bug #787977 [wnpp] ITP: smrtanalysis -- software suite for single molecule, real-time sequencing Owner changed from Debian Med Packaging Team debian-med@lists.debian.org to debian-med-packag...@lists.alioth.debian.org. owner 787982 debian-med-packag...@lists.alioth.debian.org Bug #787982 [wnpp] ITP: python-pbh5tools -- tools for manipulating HDF5 files produced by, Pacific Biosciences sequencing instruments Owner changed from Debian Med Packaging Team debian-med@lists.debian.org to debian-med-packag...@lists.alioth.debian.org. -- Stopping processing here. Please contact me if you need assistance. -- 787977: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=787977 787982: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=787982 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems -- 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/handler.s.c.14380695928589.transcr...@bugs.debian.org
pbcore post-upload changelog
Hi, Andreas, Can you push your changelog update and tag from after your upload for python-pbcore? The DDPO page wrongly shows version mismatch between unstable and git; thinking it's still unreleased. Thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name -- 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/55b83c78.1040...@ghraoui.name
Re: Sponsering libdivsufsort?
On Tue, Jul 28, 2015 at 05:40:57PM +0200, Fabian Klötzl wrote: list and not private e-mail communication. ... and I already did it wrong. Sorry for the duplicate, Andreas. I just realised that Thunderbird has a handy *Reply to List* button! Will be using that in the future. Ahh, Thunderbird as well. We should stress this option in addition to the mutt feature. The package is uploaded to NEW - thanks for your work on this I'd like to thank you and the whole Debian Med Team for your awesome work! ☺ You are welcome ... and part of the team :-) Andreas. -- http://fam-tille.de -- 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/20150728161323.gy16...@an3as.eu
Re: Sponsering libdivsufsort?
Hi, you have injected libdivsufsort into Debian Med Git. If you confirm that the package is ready I could sponsor the package. As far as I can tell, the package is ready. But as this is my first Debian package, I might be wrong. If you would sponsor libdivsufsort that would be great. Steffen has also volunteered to sponsor the package, once he is done recovering his laptop. PS: The fact that I keep you in CC is exception since usually people are expected to be subscribed to this list. I will probably forget to CC you in the future - so please make sure you subscribed this list and communicate the status of your packages here. Done. Best, Fabian -- 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/55b7963f.9080...@evolbio.mpg.de
Re: Sponsering libdivsufsort?
Hi, On 28.07.2015 17:08, Andreas Tille wrote: I did two aditional commits: One removing an unusued get-orig-source template and more importantly I fixed the clean target that tried to remove not existing files (please test such things using pbuilder and `gbp buildpackage` next time). Oh yeah, I missed those things. Thanks for the fix! If you would sponsor libdivsufsort that would be great. Steffen has also volunteered to sponsor the package, once he is done recovering his laptop. I tried to give all Debian Med protagonists the feeling that we are a team and not a 1:1 releation of individual members. If somebody is unable to do the sponsoring (in this case because of a broken laptop) somebody else will step in. The place of coordination is this mailing list and not private e-mail communication. ... and I already did it wrong. Sorry for the duplicate, Andreas. I just realised that Thunderbird has a handy *Reply to List* button! Will be using that in the future. The package is uploaded to NEW - thanks for your work on this I'd like to thank you and the whole Debian Med Team for your awesome work! ☺ Fabian -- 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/55b7a289.8060...@evolbio.mpg.de
Re: mips/mipsel in samtools and pysam
Hi Afif, regarding bug #749367 of htslib I inspected the upstream discussion about the proposed patch[4]. I need to admit that I can not make any safe conclusion whether the mips issue is solved or not. The fact that the build problem remains (OK, according to #749367 there were 5 failures in the beginning the build log [3] now has only 4 failures) seems to me that upstream does not found a final solution. However, this is not release critical since htslib was never available for mips. However, as far as I can see there in tracker[5] are more important problems in samtools affecting several architectures. According to Charles[6] this might be fixed upstream in the next release. I'm not sure how promissing the suggested action (=waiting for upstream) might be. Does anybody have contact to upstream and would find out whether a new release can be expected soon or whether we should try to backport the changes (and would volunteer to do the backporting ;-)). Kind regards Andreas. On Mon, Jul 27, 2015 at 11:30:37PM -0700, Afif Elghraoui wrote: The build logs for the current versions of samtools and pysam (without contributed patches provided for the older release) show that building was successful on mipsel [1-2]. Building on mips has not been attempted for these two packages since htslib has apparently failed to [3] build there. Perhaps mips will work as well if htslib becomes available there. At least for pysam, the provided patches no longer apply cleanly, but maybe they will not be needed anymore.. Regards Afif 1. https://buildd.debian.org/status/package.php?p=python-pysam 2. https://buildd.debian.org/status/package.php?p=samtoolssuite=sid 3. https://buildd.debian.org/status/logs.php?pkg=htslibver=1.2.1-1arch=mips [4] https://github.com/samtools/htslib/pull/99 [5] https://tracker.debian.org/pkg/samtools [6] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=762647#39 -- http://fam-tille.de -- 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/20150728105243.gq16...@an3as.eu
Re: Git repository of htslib is lacking pristine-tar
On 28/07/15 11:19, Andreas Tille wrote: Hi Charles, $ gbp clone ssh://git.debian.org/git/debian-med/htslib.git $ cd htslib $ gbp buildpackage gbp:info: Orig tarball 'htslib_1.2.1.orig.tar.gz' not found at '../tarballs/' gbp:error: Pristine-tar couldn't checkout htslib_1.2.1.orig.tar.gz: fatal: Path 'htslib_1.2.1.orig.tar.gz.delta' does not exist in 'refs/heads/pristine-tar' pristine-tar: git show refs/heads/pristine-tar:htslib_1.2.1.orig.tar.gz.delta failed I tried: $ pristine-tar commit ../htslib_1.2.1.orig.tar.gz v1.2.1 pristine-tar: failed to find ref using: git show-ref v1.2.1 which I took from bedtools debian/README.source. It seems that the 'v' in front of the version number in the end needs to be left our here. I commited an according README.source. I admit I'm not yet convinced that the chance to enable upstream pull requests are worth the drawback that other team members have trouble to follow an undocumented workflow. Kind regards Andreas. You can normally do: gbp buildpackage --git-upstream-tag=v1.2.1 \ --git-debian-branch=debian/unstable \ --git-no-pristine-tar \ --git-pristine-tar-commit The last 2 options explicitly tell gbp that a pristine-tar commit does not exist yet for this tag and that is should generate a tarball and commit one. In case the tarball for the current tag already exist in pristine-tar, these options are simply ignored. This is a beginning of a documented workflow following DEP-14: http://blog.mycre.ws/articles/git-packaging-workflow-for-py-lmdb/ Ghis -- 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/55b75f3c.1000...@gmail.com
Sponsering libdivsufsort?
Hi Fabian, you have injected libdivsufsort into Debian Med Git. If you confirm that the package is ready I could sponsor the package. Kind regards Andreas. PS: The fact that I keep you in CC is exception since usually people are expected to be subscribed to this list. I will probably forget to CC you in the future - so please make sure you subscribed this list and communicate the status of your packages here. [1] git://anonscm.debian.org/debian-med/libdivsufsort.git -- http://fam-tille.de -- 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/20150728114938.gt16...@an3as.eu
Re: pbcore post-upload changelog
On Tue, Jul 28, 2015 at 07:37:44PM -0700, Afif Elghraoui wrote: Hi, Andreas, Can you push your changelog update and tag from after your upload for python-pbcore? The DDPO page wrongly shows version mismatch between unstable and git; thinking it's still unreleased. Done. Should I reupload to unstable now since python-pysam is there? Kind regards Andreas. -- http://fam-tille.de -- 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/20150729044005.gg16...@an3as.eu
Re: pbcore post-upload changelog
On الثلاثاء 28 تـمـوز 2015 21:40, Andreas Tille wrote: Done. Thanks :) Should I reupload to unstable now since python-pysam is there? Maybe it's not worth it since I need to update for the new upstream release. Thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name -- 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/55b85c3a.6050...@ghraoui.name
Bug#793907: ITP: tantan -- low complexity and tandem repeat masker for biosequences
Package: wnpp Severity: wishlist Owner: Sascha Steinbiss sa...@tetrinetsucht.de * Package name: tantan Version : 13 Upstream Author : Martin Frith tan...@cbrc.jp * URL : http://www.cbrc.jp/tantan/ * License : GPL Programming Lang: C Description : low complexity and tandem repeat masker for biosequences tantan is a tool to mask simple regions (low complexity and short-period tandem repeats) in DNA, RNA, and protein sequences. The aim of tantan is to prevent false predictions when searching for homologous regions between two sequences. Simple repeats often align strongly to each other, causing false homology predictions. This tool is very useful in conjunction with fast aligners like LAST. See http://www.ncbi.nlm.nih.gov/pubmed/25172925 for a good use case example. The tantan package will be maintained by the Debian Med Packaging Team. -- 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/20150728192230.29965.57314.report...@jessie64.vagrantup.com
Re: mips/mipsel in samtools and pysam
Hi, Andreas, The build logs for the current versions of samtools and pysam (without contributed patches provided for the older release) show that building was successful on mipsel [1-2]. Building on mips has not been attempted for these two packages since htslib has apparently failed to [3] build there. Perhaps mips will work as well if htslib becomes available there. At least for pysam, the provided patches no longer apply cleanly, but maybe they will not be needed anymore.. Regards Afif 1. https://buildd.debian.org/status/package.php?p=python-pysam 2. https://buildd.debian.org/status/package.php?p=samtoolssuite=sid 3. https://buildd.debian.org/status/logs.php?pkg=htslibver=1.2.1-1arch=mips -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name -- 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/55b7218d.9090...@ghraoui.name
Re: mips/mipsel in samtools and pysam
On Wed, Jul 29, 2015 at 05:24:38AM +0900, Charles Plessy wrote: Why not just patiently waiting for the next upstream release ? The htlslib packages work very well on amd64, and this is where our work is used. Yes, but reverse dependencies are currently removed from testing. Bringing them back to testing is my main motivation. Thus specifying a positive list for samtools that should be revised for next upstream seems to be the most sensible thing to do for me if the effort of backporting is to high. An please do not take this comment negatively: if people can do more that is great, but at the moment, with my reduced free time and an intensely stressful job, I am not even in a position to participate to such an effort occasionally. Perfectly understood and no offense taken. Kind regards Andreas. -- http://fam-tille.de -- 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/20150728210312.ge16...@an3as.eu
Re: mips/mipsel in samtools and pysam
Le Tue, Jul 28, 2015 at 12:52:43PM +0200, Andreas Tille a écrit : However, as far as I can see there in tracker[5] are more important problems in samtools affecting several architectures. According to Charles[6] this might be fixed upstream in the next release. I'm not sure how promissing the suggested action (=waiting for upstream) might be. Does anybody have contact to upstream and would find out whether a new release can be expected soon or whether we should try to backport the changes (and would volunteer to do the backporting ;-)). Hi Andreas, life is short, time is precisous, and frankly speaking, MIPS, hurd, hppa, etc. are irrelevant to bioinformatics. Why not just patiently waiting for the next upstream release ? The htlslib packages work very well on amd64, and this is where our work is used. On my side, I do not have time and patience to deal with these porting issues with more than a best effort priority, because there are no users for htlslib on these platforms. If there are volunteers to backport changes in order to go faster than Upstream, please do so but please also remove my name from the Uploaders field. On my side I have no time for this wokflow that multiplies patch management and uploads. An please do not take this comment negatively: if people can do more that is great, but at the moment, with my reduced free time and an intensely stressful job, I am not even in a position to participate to such an effort occasionally. Making bioinformatics viable on alternative architectures is a huge task that is only doable with full dedication. Actually, this is really the kind of task that I think should be only done if hardware vendors or granting agencies would provide a strong support. I am not seeing myself as a pioneer to develop a new market for manufacturers, I am a researcher sharing the tools of today on the machines of today. Have a nice day, Charles -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan -- 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/20150728202354.gb19...@falafel.plessy.net
