Help needed for discosnp
Hi Olivier, I've thought I'm so close to get at least discosnp[1] linked against gatb-core but there is a final thing missing: ... cd /build/discosnp-2.3.0/obj-x86_64-linux-gnu/tools/kissnp2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/kissnp2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/discosnp-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/kissnp2.dir/src/Bubble.cpp.o CMakeFiles/kissnp2.dir/src/Filter.cpp.o CMakeFiles/kissnp2.dir/src/Kissnp2.cpp.o CMakeFiles/kissnp2.dir/src/main.cpp.o -o ../../bin/kissnp2 -lgatbcore -lhdf5 /usr/bin/ld: cannot find -lhdf5 collect2: error: ld returned 1 exit status My attempt[2] to sneak in some -L/usr/lib/x86_64-linux-gnu/hdf5/serial/ which is obviously missing (if I add it to the '/usr/bin/c++ ' line it works) just failed. Any last tiny hint to get this done? Kind regards Andreas. [1] https://salsa.debian.org/med-team/discosnp [2] https://salsa.debian.org/med-team/discosnp/commit/6b87aec1e8d587e750fd1dd25d419269fc66ed7c -- http://fam-tille.de
Re: bali-phy: version 3.4.1
Hi Benjamin, uploaded, thanks a lot for your contribution, Andreas. On Tue, Jan 22, 2019 at 02:28:51PM -0500, Benjamin Redelings wrote: > Hi Andreas, > > I pushed bali-phy version 3.4.1 to the salsa repo. (This version fixes some > bugs in version 3.4.0 that are important for usability, but is not a major > update.) In any case, can you please upload it for me? > > Thank you! > > -BenRI > > -- http://fam-tille.de
bali-phy: version 3.4.1
Hi Andreas, I pushed bali-phy version 3.4.1 to the salsa repo. (This version fixes some bugs in version 3.4.0 that are important for usability, but is not a major update.) In any case, can you please upload it for me? Thank you! -BenRI
Do we need python-seqcluster (Python2) or is python3-seqcluster sufficient
Hi Steffen, I was a bit scared that we have a non-installable package inside Debian and thought it would be a good idea to have python-seqcluster quickly. I realised that some of the (Build-)Depends are only available for Python3. Do we really need python-seqcluster for Python2 or can we just drop that package (and the Python2 Build-Depends)? Kind regards Andreas. -- http://fam-tille.de
Re: Do we benefit from a Debian Med machine to run our workflows?
On Tue, Jan 22, 2019 at 10:32:30AM +0100, Steffen Möller wrote: > Hello, > > bcbio just arrived in the New Queue. Somewhat embarrassingly it does not > install, yet, since python3-seqcluster is still missing who have their > Python3 fixes in their devel branch. I am hoping for an upcoming official > release or will package that branch. We should use git mode in watch file if HEAD works for our purpose. BTW, I do not think its a good idea to upload a package before its pre-depends are fulfilled. > Either way, we are about to have our first workflow package in our > distribution. Now, I would like to test a bunch of research directions bcbio > supports. And tests shall be executed "continuously" (repeatedly) as we > update our packages. We have Debian's CI infrastructure - but tests run for > several hours and our CI infrastructure may not be perfectly suited for > that? Very much so since we are likely to desire access to the machine to > inspect what is going wrong? And not everyone with a genuine interest is a > DD? > > Admittedly, what I am more after than "integration testing" is "knowledge > integration". A imagine a site to which Debian Med can log in and adjust > parameters (maybe even in some automated fashion) to have the same dataset > analysed again and again as the reference databases/software underneath > matures/develops, preferably with some gold standard as a reference or some > easy access to the same material for labs around the world to prove stuff - > this may turn out to be interesting. And when there alternative workflows > arriving in our distro, like with GATK, this may become even more > interesting. Setup and maintenance would need to be completely automated - > we just don't have time for anything else. > > I was offered a 2x6-core 64GB (I know) server with rack space. It has a 2TB > drive and slots to add more. That we could play with. > > Comments? Just do it. Kind regards Andreas. -- http://fam-tille.de
Re: Where can I find igdiscover (Was: Updated bio for sqt python lib and igdiscover)
On Tue, Jan 22, 2019 at 03:51:17PM +0100, Steffen Möller wrote: > > On 22.01.19 09:11, Andreas Tille wrote: > > > Recommends: idba > > > +Recommends: igdiscover > > > + > > I seeked the package pool and salsa but can not find this package. > > Did you forgot to push some packaging? > Yes. Now I know why the "new project" window was open. You now find it on > > https://salsa.debian.org/med-team/igdiscover > > Thank you for spotting that. You are welcome. :-) > The package would not be prepared to receive some peer review. I'll > otherwise > leave it for a few days and then look at it again. Common deviations from policy you are usually doing are: 1. Not setting Maintainer to Debian Med team? 2. Not using UNRELEASED for unreleased packages 3. Not using `cme fix dpkg-control` on your package Please, pretty please do this - it makes team work way more simple and I can only repeat (how often did I before) that the package template[1] will prevent you from doing those deviation. It also does not create watch files that are more complex than necessary (and spoil my routine-upgrade script which smoothens most of the issues above automatically). > > BTW, I realised that you started to spread packages over different teams > > (airr and presto to Python team, vdjtools to Java team). We know that > > in many cases there are two options in what team to maintain some > > software. It can be based on the topic (than it is Debian Med, Debian > > Science, etc.) or on the programming language (Python, Java, etc.) > Hm. Yes. Vdjtools in particular belongs more to Debian Med since it is meant > for end users. > > I'd recommend if you find some relevant publication or some typical > > registry entries its a good idea to stick to the Debian Med team. > > Let us put something like that in the Debian Policy. Can **you** please put this into the Debian Med team policy. This would be really welcome and I invite everybody to simply not suggest something which is good but rather *do* implement the good ideas. Thank you Andreas. [1] https://salsa.debian.org/med-team/community/package_template -- http://fam-tille.de
Re: Where can I find igdiscover (Was: Updated bio for sqt python lib and igdiscover)
On 22.01.19 09:11, Andreas Tille wrote: Hi Steffen, you recently commited an entry to the Debian Med tasks: On Fri, Jan 18, 2019 at 11:57:15PM +, Steffen Möller wrote: Steffen Möller pushed to branch master at Debian Blends Team / med Commits: 2b2fb43c by Steffen Möller at 2019-01-18T23:57:13Z Updated bio for sqt python lib and igdiscover - - - - - 1 changed file: - tasks/bio Changes: = tasks/bio = @@ -643,6 +643,8 @@ Recommends: htqc Recommends: idba +Recommends: igdiscover + I seeked the package pool and salsa but can not find this package. Did you forgot to push some packaging? Yes. Now I know why the "new project" window was open. You now find it on https://salsa.debian.org/med-team/igdiscover Thank you for spotting that. The package would not be prepared to receive some peer review. I'll otherwise leave it for a few days and then look at it again. BTW, I realised that you started to spread packages over different teams (airr and presto to Python team, vdjtools to Java team). We know that in many cases there are two options in what team to maintain some software. It can be based on the topic (than it is Debian Med, Debian Science, etc.) or on the programming language (Python, Java, etc.) Hm. Yes. Vdjtools in particular belongs more to Debian Med since it is meant for end users. I'd recommend if you find some relevant publication or some typical registry entries its a good idea to stick to the Debian Med team. Let us put something like that in the Debian Policy. Best, Steffen
Do we benefit from a Debian Med machine to run our workflows?
Hello, bcbio just arrived in the New Queue. Somewhat embarrassingly it does not install, yet, since python3-seqcluster is still missing who have their Python3 fixes in their devel branch. I am hoping for an upcoming official release or will package that branch. Either way, we are about to have our first workflow package in our distribution. Now, I would like to test a bunch of research directions bcbio supports. And tests shall be executed "continuously" (repeatedly) as we update our packages. We have Debian's CI infrastructure - but tests run for several hours and our CI infrastructure may not be perfectly suited for that? Very much so since we are likely to desire access to the machine to inspect what is going wrong? And not everyone with a genuine interest is a DD? Admittedly, what I am more after than "integration testing" is "knowledge integration". A imagine a site to which Debian Med can log in and adjust parameters (maybe even in some automated fashion) to have the same dataset analysed again and again as the reference databases/software underneath matures/develops, preferably with some gold standard as a reference or some easy access to the same material for labs around the world to prove stuff - this may turn out to be interesting. And when there alternative workflows arriving in our distro, like with GATK, this may become even more interesting. Setup and maintenance would need to be completely automated - we just don't have time for anything else. I was offered a 2x6-core 64GB (I know) server with rack space. It has a 2TB drive and slots to add more. That we could play with. Comments? Best, Steffen Forwarded Message Subject:bcbio_1.1.2-2_amd64.changes is NEW Date: Mon, 21 Jan 2019 23:19:26 + From: Debian FTP Masters To: Steffen Moeller , Debian Med Packaging Team binary:bcbio is NEW. binary:python3-bcbio is NEW. binary:bcbio is NEW. binary:python3-bcbio is NEW. source:bcbio is NEW. bcbio_1.1.2.orig.tar.gz is only available in NEW. bcbio_1.1.2.orig.tar.gz is only available in NEW. Your package has been put into the NEW queue, which requires manual action from the ftpteam to process. The upload was otherwise valid (it had a good OpenPGP signature and file hashes are valid), so please be patient. Packages are routinely processed through to the archive, and do feel free to browse the NEW queue[1]. If there is an issue with the upload, you will receive an email from a member of the ftpteam. If you have any questions, you may reply to this email. [1]: https://ftp-master.debian.org/new.html or https://ftp-master.debian.org/backports-new.html for *-backports
Where can I find igdiscover (Was: Updated bio for sqt python lib and igdiscover)
Hi Steffen, you recently commited an entry to the Debian Med tasks: On Fri, Jan 18, 2019 at 11:57:15PM +, Steffen Möller wrote: > Steffen Möller pushed to branch master at Debian Blends Team / med > > > Commits: > 2b2fb43c by Steffen Möller at 2019-01-18T23:57:13Z > Updated bio for sqt python lib and igdiscover > - - - - - > > > 1 changed file: > > - tasks/bio > > > Changes: > > = > tasks/bio > = > @@ -643,6 +643,8 @@ Recommends: htqc > > Recommends: idba > > +Recommends: igdiscover > + I seeked the package pool and salsa but can not find this package. Did you forgot to push some packaging? BTW, I realised that you started to spread packages over different teams (airr and presto to Python team, vdjtools to Java team). We know that in many cases there are two options in what team to maintain some software. It can be based on the topic (than it is Debian Med, Debian Science, etc.) or on the programming language (Python, Java, etc.) I'd recommend if you find some relevant publication or some typical registry entries its a good idea to stick to the Debian Med team. Kind regards Andreas. -- http://fam-tille.de
