Re: Hmmer2 fork / enhancements (Was: Is my post making it to the mailing list?)
I'm aware. I only really have time to touch this on weekends, sorry. Right now, I'm working on changes with squid to make things easier on Arch. This weekend is a tad busy, so I'll likely get time to touch this again on the 26th. I'm thinking to hold off on the upload until you or I run the build in test suite to make sure no surprises happened. On Thu, Jan 17, 2019 at 2:25 PM Andreas Tille wrote: > Hi again, > > I just want to repeat that I will not upload until you become more > verbose what exactly should be tested. I understood your last mail that > I should not upload before something is tested - but what exactly? > > Kind regards > > Andreas. > > On Mon, Jan 14, 2019 at 03:27:13PM +0100, Andreas Tille wrote: > > On Mon, Jan 14, 2019 at 06:41:32AM -0500, jrmarsha wrote: > > > There is no question in that message. > > > > > > On 1/13/19 11:35 PM, Andreas Tille wrote: > > > > On Sun, Jan 13, 2019 at 09:22:13PM -0500, jrmarsha wrote: > > > > > I've thought I've answered questions a few times. Are messages > getting > > > > > dropped? I didn't get the one just before from Steffen. > > > > I did not received any answer to > > > > > > > > https://lists.debian.org/debian-med/2019/01/msg00046.html > > > > Syntactically you are correct but I would have expected some response to > > "I'm not fully sure what you want me to test." > > > > I assumed you wanted me to test something before uploading. If this > > is not the case I can upload the current packaging status and users > > should test later (beyond the autopkgtest). > > > > Is this OK? > > > > Kind regards > > > > Andreas. > > > > -- > > http://fam-tille.de > > > > > > -- > http://fam-tille.de > >
Re: Hmmer2 fork / enhancements (Was: Is my post making it to the mailing list?)
Andreas: Both uploads are identical, but I'd defer to the Michigan Tech one as the reference since it is tied to the institution. Andrius: 3.0 and 3.1 are a different development line and are oddly different so that wouldn't help here. Thanks for the thought, though. On Fri, Jan 11, 2019 at 4:09 AM Andrius Merkys wrote: > Hello, > > On 2019-01-11 04:42, Joshua Marshall wrote: > > Does anyone on this list have an interest or use case for Hmmer2? I'd > like to put a pin in this. > > I have been using programs from hmmer Debian packages (3.0 and 3.1, I > guess) in a pipeline for protein structure prediction some three years ago. > I could share my pipeline (Makefile + some scripts, ultimately feeding > multiple alignment to 'modeller') if needed. > > Best, > Andrius > > -- > Andrius Merkys > Vilnius University Institute of Biotechnology, Saulėtekio al. 7, room V325 > LT-10257 Vilnius, Lithuania > >
Re: Hmmer2 fork / enhancements (Was: Is my post making it to the mailing list?)
Does anyone on this list have an interest or use case for Hmmer2? I'd like to put a pin in this. On Fri, Jan 4, 2019 at 12:42 PM Joshua Marshall wrote: > PVM is no longer maintained, and hasn't been for quite some time. The use > case for when PVM is relevant is when RAM on individual machines was closer > to 16M. Given that we have $5 computers with 256MB, I find it reasonable > to tell such users to upgrade. > > As for interpro-scan, most of the documents got updated for the project > and it is easier to set up locally. However, there is still a large amount > of work that goes into updates every few days to a few weeks and users > should rely on the service rather than a package. If you do want to have > the package, you need a employee charged with it's regular updates and > development because of how involved and federated that particular program > set is. > > On Fri, Jan 4, 2019 at 10:41 AM Steffen Möller > wrote: > >> Hello Joshua, >> >> I would be much of a fan to see interpro-scan redistributed with Debian. >> Andreas' concern is that nobody understands what happened. We have >> Hammer2 in our distribution https://packages.debian.org/sid/hmmer2 and >> if your work is plain compatible then I don't see why it should not >> substitute it. Is there a way to keep hmmer2-pvm? There are not too >> many on https://qa.debian.org/popcon.php?package=hmmer2 using it but I >> would not want to ruin established services anywhere with an apt-get >> update. >> >> Best, >> >> Steffen >> >> On 04.01.19 16:25, Joshua Marshall wrote: >> > Hello all, >> > >> > In Spring 2018 I was working on packaging interpro-scan for some >> > work. There were a number of packages which has some build or test >> > failures which I worked on. Of these, Hmmer needed some more >> > attention. Originally, this was an upstream request to tweak their >> > autoconf but that went bizarrely bad. At that point, I went in to fix >> > up a decade's worth of technical debt. Of these were removal of >> > Parallel Virtual Machine support, adjusting buffer sizes upwards for >> > memory found on modern systems, hard code enabling of pthreads, >> > renaming executable to hmmer2 in the build to not conflict with hmmer >> > or hmmer3 to allow for parallel installation, and simplification of >> > the configuration header. All unit tests pass. There is a need for >> > parallel installation of hmmer2 and hmmer3 because hmmer2 works on a >> > global genome scale, while hmmer3 is build to only operate on parts of >> > the genome. >> > >> > This should have do change in behavior or output in any way except for >> > removal of PVM support and minor runtime changes. This change set >> > should be viewed strictly as a technical debt clean up. >> > >> > On Fri, Jan 4, 2019 at 1:11 AM Andreas Tille > > <mailto:andr...@fam-tille.de>> wrote: >> > >> > Hi Joshua, >> > >> > On Thu, Jan 03, 2019 at 04:45:33PM -0500, Joshua Marshall wrote: >> > > Is now a better time to bring up my Hmmer 2 fork? >> > >> > Please shortly describe the purpose of your fork the changes you >> > did on the list and than we can (probably/hopefully) replace the >> > existing hmmer2 package by your fork. I'm *not* a hmmer2 user >> > (nor do I have the slightest idea what hmmer2 is doing - I'm not >> > a biologist) so it makes no sense to discuss this just with me. >> > Thus I'm posting this on the list. >> > >> > For other readers here are some links to previous posts about >> > this issue: >> > >> > >> https://alioth-lists.debian.net/pipermail/debian-med-packaging/2018-October/066203.html >> > >> https://alioth-lists.debian.net/pipermail/debian-med-packaging/2018-October/066757.html >> > >> https://alioth-lists.debian.net/pipermail/debian-med-packaging/2018-October/066762.html >> > >> https://alioth-lists.debian.net/pipermail/debian-med-packaging/2018-November/066997.html >> > >> > My prefered way to deal with this would be to point the debian/watch >> > file of hmmer2 to >> > >> > https://github.com/anadon/hmmer2/releases >> > >> > and package the latest release from there (instead of applying huge >> > patches that nobody can read or maintain) but please document the >> > relation to the official
Re: Hmmer2 fork / enhancements (Was: Is my post making it to the mailing list?)
PVM is no longer maintained, and hasn't been for quite some time. The use case for when PVM is relevant is when RAM on individual machines was closer to 16M. Given that we have $5 computers with 256MB, I find it reasonable to tell such users to upgrade. As for interpro-scan, most of the documents got updated for the project and it is easier to set up locally. However, there is still a large amount of work that goes into updates every few days to a few weeks and users should rely on the service rather than a package. If you do want to have the package, you need a employee charged with it's regular updates and development because of how involved and federated that particular program set is. On Fri, Jan 4, 2019 at 10:41 AM Steffen Möller wrote: > Hello Joshua, > > I would be much of a fan to see interpro-scan redistributed with Debian. > Andreas' concern is that nobody understands what happened. We have > Hammer2 in our distribution https://packages.debian.org/sid/hmmer2 and > if your work is plain compatible then I don't see why it should not > substitute it. Is there a way to keep hmmer2-pvm? There are not too > many on https://qa.debian.org/popcon.php?package=hmmer2 using it but I > would not want to ruin established services anywhere with an apt-get > update. > > Best, > > Steffen > > On 04.01.19 16:25, Joshua Marshall wrote: > > Hello all, > > > > In Spring 2018 I was working on packaging interpro-scan for some > > work. There were a number of packages which has some build or test > > failures which I worked on. Of these, Hmmer needed some more > > attention. Originally, this was an upstream request to tweak their > > autoconf but that went bizarrely bad. At that point, I went in to fix > > up a decade's worth of technical debt. Of these were removal of > > Parallel Virtual Machine support, adjusting buffer sizes upwards for > > memory found on modern systems, hard code enabling of pthreads, > > renaming executable to hmmer2 in the build to not conflict with hmmer > > or hmmer3 to allow for parallel installation, and simplification of > > the configuration header. All unit tests pass. There is a need for > > parallel installation of hmmer2 and hmmer3 because hmmer2 works on a > > global genome scale, while hmmer3 is build to only operate on parts of > > the genome. > > > > This should have do change in behavior or output in any way except for > > removal of PVM support and minor runtime changes. This change set > > should be viewed strictly as a technical debt clean up. > > > > On Fri, Jan 4, 2019 at 1:11 AM Andreas Tille > <mailto:andr...@fam-tille.de>> wrote: > > > > Hi Joshua, > > > > On Thu, Jan 03, 2019 at 04:45:33PM -0500, Joshua Marshall wrote: > > > Is now a better time to bring up my Hmmer 2 fork? > > > > Please shortly describe the purpose of your fork the changes you > > did on the list and than we can (probably/hopefully) replace the > > existing hmmer2 package by your fork. I'm *not* a hmmer2 user > > (nor do I have the slightest idea what hmmer2 is doing - I'm not > > a biologist) so it makes no sense to discuss this just with me. > > Thus I'm posting this on the list. > > > > For other readers here are some links to previous posts about > > this issue: > > > > > https://alioth-lists.debian.net/pipermail/debian-med-packaging/2018-October/066203.html > > > https://alioth-lists.debian.net/pipermail/debian-med-packaging/2018-October/066757.html > > > https://alioth-lists.debian.net/pipermail/debian-med-packaging/2018-October/066762.html > > > https://alioth-lists.debian.net/pipermail/debian-med-packaging/2018-November/066997.html > > > > My prefered way to deal with this would be to point the debian/watch > > file of hmmer2 to > > > > https://github.com/anadon/hmmer2/releases > > > > and package the latest release from there (instead of applying huge > > patches that nobody can read or maintain) but please document the > > relation to the official hmmer2, your fork/continuation and hmmer3 > > at an easily accessible place. > > > > Kind regards > > > > Andreas. > > > > > On Sun, Oct 28, 2018 at 4:47 PM jrmarsha > <mailto:jrmar...@mtu.edu>> wrote: > > > > > > > I'm sorry. > > > > > > > > On 10/28/18 4:15 PM, Andreas Tille wrote: > > > > > Hi, > > > > > > > > > > the list is archived: >
Re: Hmmer2 fork / enhancements (Was: Is my post making it to the mailing list?)
Hello all, In Spring 2018 I was working on packaging interpro-scan for some work. There were a number of packages which has some build or test failures which I worked on. Of these, Hmmer needed some more attention. Originally, this was an upstream request to tweak their autoconf but that went bizarrely bad. At that point, I went in to fix up a decade's worth of technical debt. Of these were removal of Parallel Virtual Machine support, adjusting buffer sizes upwards for memory found on modern systems, hard code enabling of pthreads, renaming executable to hmmer2 in the build to not conflict with hmmer or hmmer3 to allow for parallel installation, and simplification of the configuration header. All unit tests pass. There is a need for parallel installation of hmmer2 and hmmer3 because hmmer2 works on a global genome scale, while hmmer3 is build to only operate on parts of the genome. This should have do change in behavior or output in any way except for removal of PVM support and minor runtime changes. This change set should be viewed strictly as a technical debt clean up. On Fri, Jan 4, 2019 at 1:11 AM Andreas Tille wrote: > Hi Joshua, > > On Thu, Jan 03, 2019 at 04:45:33PM -0500, Joshua Marshall wrote: > > Is now a better time to bring up my Hmmer 2 fork? > > Please shortly describe the purpose of your fork the changes you > did on the list and than we can (probably/hopefully) replace the > existing hmmer2 package by your fork. I'm *not* a hmmer2 user > (nor do I have the slightest idea what hmmer2 is doing - I'm not > a biologist) so it makes no sense to discuss this just with me. > Thus I'm posting this on the list. > > For other readers here are some links to previous posts about > this issue: > > > https://alioth-lists.debian.net/pipermail/debian-med-packaging/2018-October/066203.html > > https://alioth-lists.debian.net/pipermail/debian-med-packaging/2018-October/066757.html > > https://alioth-lists.debian.net/pipermail/debian-med-packaging/2018-October/066762.html > > https://alioth-lists.debian.net/pipermail/debian-med-packaging/2018-November/066997.html > > My prefered way to deal with this would be to point the debian/watch > file of hmmer2 to > > https://github.com/anadon/hmmer2/releases > > and package the latest release from there (instead of applying huge > patches that nobody can read or maintain) but please document the > relation to the official hmmer2, your fork/continuation and hmmer3 > at an easily accessible place. > > Kind regards > > Andreas. > > > On Sun, Oct 28, 2018 at 4:47 PM jrmarsha wrote: > > > > > I'm sorry. > > > > > > On 10/28/18 4:15 PM, Andreas Tille wrote: > > > > Hi, > > > > > > > > the list is archived: > > > > > > > > https://lists.debian.org/debian-med/2018/10/threads.html > > > > > > > > Please do not expect always prompt responses - sometimes volunteers > > > > have other things to do. > > > > > > > > Kind regards > > > > > > > > Andreas. > > > > > > > > On Sun, Oct 28, 2018 at 09:03:27AM -0400, jrmarsha wrote: > > > >> Hello, > > > >> > > > >> > > > >> I've tried sending a few messages but I've gotten no response. Are > they > > > >> making it to the debian-med mailing list. > > > >> > > > >> > > > > > -- > http://fam-tille.de >
