Happy! Fwd: pigx-rnaseq_0.0.10+ds-1_amd64.changes ACCEPTED into unstable, unstable
Dear all, We got our first RNA-seq pipeline as a package in Debian. Many thanks go to all who contributed. I need to let this sink in for a while, which coincides with being distracted with what I am paid to do :o) And then let's use it to reanalyse a few datasets that are associated with COVID-19. Got some ideas already that need to somehow solidify themselves, still. Best, Steffen Forwarded Message Subject: pigx-rnaseq_0.0.10+ds-1_amd64.changes ACCEPTED into unstable, unstable Date: Thu, 22 Oct 2020 21:00:15 + From: Debian FTP Masters To: ti...@debian.org, Steffen Moeller , Debian Med Packaging Team Accepted: Format: 1.8 Date: Mon, 05 Aug 2019 14:48:15 +0200 Source: pigx-rnaseq Binary: pigx-rnaseq Architecture: source all Version: 0.0.10+ds-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Steffen Moeller Description: pigx-rnaseq - pipeline for checkpointed and distributed RNA-seq analyses Closes: 934041 Changes: pigx-rnaseq (0.0.10+ds-1) unstable; urgency=medium . * Initial release (Closes: #934041) Checksums-Sha1: f833af87aa580c07c829fbe93091bb6576342e7d 2832 pigx-rnaseq_0.0.10+ds-1.dsc 452bd436002f06fed63800408918e9b5bdb9d59e 7056584 pigx-rnaseq_0.0.10+ds.orig.tar.xz 74295ab103076ef2640ce154835fd2478d955ea6 5408 pigx-rnaseq_0.0.10+ds-1.debian.tar.xz 8b93c0f72d6d97da1444e7c36c20581fa78f5d66 54268 pigx-rnaseq_0.0.10+ds-1_all.deb 404ce1425a48110fee53eed828c7f09f6e6a9a4c 26070 pigx-rnaseq_0.0.10+ds-1_amd64.buildinfo Checksums-Sha256: 25f1ab95dbc2fa3bebb89e51243a0fe5caa40cc13a6ba6005ff5656716759b2f 2832 pigx-rnaseq_0.0.10+ds-1.dsc 720e19eadb3aeaa2ebe1e2ed61ea1d45bb98a2779ee75b958c3b6913774a 7056584 pigx-rnaseq_0.0.10+ds.orig.tar.xz 5e0ee44c3b5ca433f56b6adcc20b9d89271570c88cd8d45ca11f18a0dcf9e721 5408 pigx-rnaseq_0.0.10+ds-1.debian.tar.xz 948c5b95ad2db564fcefc55fb033755e8ce95110427ee273571e1792e4f6c835 54268 pigx-rnaseq_0.0.10+ds-1_all.deb 36fa400ef1ca2b870bf0cdb175abcd2feadb10c0ef445590166edd1ca672dd7c 26070 pigx-rnaseq_0.0.10+ds-1_amd64.buildinfo Files: 618f262f76f3819c3ec6bd01e989346a 2832 science optional pigx-rnaseq_0.0.10+ds-1.dsc 3ca602582a8a4ff3769023aaa2e29c07 7056584 science optional pigx-rnaseq_0.0.10+ds.orig.tar.xz c57a792531d28fbfc3270d7a434c80da 5408 science optional pigx-rnaseq_0.0.10+ds-1.debian.tar.xz 8048404e8102cad8ea3569b3559af024 54268 science optional pigx-rnaseq_0.0.10+ds-1_all.deb fe2b0d42d1dd636c992de11ad93eb5e7 26070 science optional pigx-rnaseq_0.0.10+ds-1_amd64.buildinfo Thank you for your contribution to Debian.
Re: Any idea how to create shared lobrary for libatomicqueue
Hi Andreas,
On Sat, 24 Oct 2020 at 02:17, Andreas Tille wrote:
> Hi,
>
> I checked libatomicqueue[1] and realised that only a static library is
> built. Any idea how to create a shared library in addition.
>
I tried something and was successful in making a shared library, however I
noticed that the debian/tmp directory does _not_ take in any of the
installed files - neither includes, not the static nor the .so lib. Hence
I'm not sure of using d-shlibs for the same.
I'm anyway, attaching my patche here - you'd probably know a way to setup
d-shlibs with this.
Kind Regards,
Nilesh
--- a/Makefile
+++ b/Makefile
@@ -10,6 +10,7 @@
TOOLSET := gcc
build_dir := ${CURDIR}/build/${BUILD}/${TOOLSET}
+build_dir_shared := ${CURDIR}/build_shared/${BUILD}/${TOOLSET}
cxx.gcc := g++
cc.gcc := gcc
@@ -66,13 +67,17 @@
all : ${exes}
-${exes} : % : ${build_dir}/%
+${exes} : % : ${build_dir}/% ${build_dir_shared}/libatomic_queue.so
ln -sf ${<:${CURDIR}/%=%}
${build_dir}/libatomic_queue.a : $(addprefix ${build_dir}/,cpu_base_frequency.o huge_pages.o)
-include ${build_dir}/cpu_base_frequency.d
-include ${build_dir}/huge_pages.d
+${build_dir_shared}/libatomic_queue.so : $(addprefix ${build_dir_shared}/,cpu_base_frequency.o huge_pages.o)
+-include ${build_dir_shared}/cpu_base_frequency.d
+-include ${build_dir_shared}/huge_pages.d
+
${build_dir}/benchmarks : cppflags += ${cppflags.tbb} ${cppflags.moodycamel} ${cppflags.xenium}
${build_dir}/benchmarks : ldlibs += ${ldlibs.tbb} ${ldlibs.moodycamel} ${ldlibs.xenium} -ldl
${build_dir}/benchmarks : ${build_dir}/benchmarks.o ${build_dir}/libatomic_queue.a Makefile | ${build_dir}
@@ -85,8 +90,8 @@
$(strip ${LINK.EXE})
-include ${build_dir}/tests.d
-${build_dir}/%.so : cxxflags += -fPIC
-${build_dir}/%.so : Makefile | ${build_dir}
+${build_dir_shared}/%.so : cxxflags += -fPIC
+${build_dir_shared}/%.so : Makefile | ${build_dir}
$(strip ${LINK.SO})
${build_dir}/%.a : Makefile | ${build_dir}
@@ -108,6 +113,13 @@
${build_dir}/%.o : src/%.c Makefile | ${build_dir}
$(strip ${COMPILE.C})
+${build_dir_shared}/%.o : src/%.cc Makefile | ${build_dir_shared}
+ $(strip ${COMPILE.CXX})
+
+${build_dir_shared}/%.o : src/%.c Makefile | ${build_dir_shared}
+ $(strip ${COMPILE.C})
+
+
%.S : cppflags += ${cppflags.tbb} ${cppflags.moodycamel} ${cppflags.xenium}
%.S : src/%.cc Makefile | ${build_dir}
$(strip ${COMPILE.S})
@@ -118,6 +130,9 @@
${build_dir} :
mkdir -p $@
+${build_dir_shared} :
+ mkdir -p $@
+
rtags : clean
${MAKE} -nk | rc -c -; true
Bug#971870: marked as done (ITP: sepp -- methods using ensembles of Hidden Markov Models (HMM))
Your message dated Fri, 23 Oct 2020 22:00:14 + with message-id and subject line Bug#971870: fixed in sepp 4.3.10+dfsg-1 has caused the Debian Bug report #971870, regarding ITP: sepp -- methods using ensembles of Hidden Markov Models (HMM) to be marked as done. This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact ow...@bugs.debian.org immediately.) -- 971870: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=971870 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems --- Begin Message --- Package: wnpp Severity: wishlist Owner: Debian-med project X-Debbugs-Cc: debian-de...@lists.debian.org, debian-med@lists.debian.org * Package name: sepp Version : 4.3.10 Upstream Author : Siavash Mirarab * URL : https://github.com/smirarab/sepp/ * License : GPL-3 Programming Lang: Python, Java Description : methods using ensembles of Hidden Markov Models (HMM) The tools SEPP and TIPP implementing these methods use ensembles of Hidden Markov Models (HMMs) in different ways, each focusing on a different problem. SEPP stands for "SATe-enabled Phylogenetic Placement", and addresses the problem of phylogenetic placement of short reads into reference alignments and trees. TIPP stands for "Taxonomic Identification and Phylogenetic Profiling", and addresses the problem of taxonomic identification and abundance profiling of metagenomic data. This package is useful to treat genomic data and will be maintained by Debian-med. --- End Message --- --- Begin Message --- Source: sepp Source-Version: 4.3.10+dfsg-1 Done: Pierre Gruet We believe that the bug you reported is fixed in the latest version of sepp, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to 971...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Pierre Gruet (supplier of updated sepp package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing ftpmas...@ftp-master.debian.org) -BEGIN PGP SIGNED MESSAGE- Hash: SHA512 Format: 1.8 Date: Thu, 08 Oct 2020 22:18:43 +0200 Source: sepp Binary: sepp Architecture: source amd64 Version: 4.3.10+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Pierre Gruet Description: sepp - methods use ensembles of Hidden Markov Models (HMM) Closes: 971870 Changes: sepp (4.3.10+dfsg-1) unstable; urgency=medium . * Initial release (Closes: #971870) Checksums-Sha1: 621ad66c6aaa92737e8fc104f53e654c0ddcbb48 2131 sepp_4.3.10+dfsg-1.dsc baf7d2cc04acac0a1869b6dca1e9d4fb995beb49 4287844 sepp_4.3.10+dfsg.orig.tar.xz 48f7822429fa0fdfe4f7fb69c057517867a80586 13428 sepp_4.3.10+dfsg-1.debian.tar.xz 5d5882cd7d64e8fc21545708db3d57ed2812934e 7930 sepp_4.3.10+dfsg-1_amd64.buildinfo 49355215c3ba665f454c0aee391885c0190b7f32 181084 sepp_4.3.10+dfsg-1_amd64.deb Checksums-Sha256: 76de4d9e5cf70274c920dbf9a1356a70da3d01b4e72b4127b36bf2292a9ceb4b 2131 sepp_4.3.10+dfsg-1.dsc d0840407c5387b7d4db0baf701c220580ecc0fcc88f91ef1f6295a9da0869c7e 4287844 sepp_4.3.10+dfsg.orig.tar.xz 4a80191a1ba7fefc9a104ed95488f9bc9bea65cc5566fcae8d95639fe84f6366 13428 sepp_4.3.10+dfsg-1.debian.tar.xz 68b7c52011cafcb7b48b7b437c831f9e207318bba547e38b69b9e39dabde8c7d 7930 sepp_4.3.10+dfsg-1_amd64.buildinfo cbceeff332861fab1d2f497c58a9bdad6af158ec446ff93698f34d826724cb5a 181084 sepp_4.3.10+dfsg-1_amd64.deb Files: 846306506b7186a748531896a23ab584 2131 science optional sepp_4.3.10+dfsg-1.dsc 46f9be63a75122114424d6b09eb5ba1f 4287844 science optional sepp_4.3.10+dfsg.orig.tar.xz e21102c9132b9ebf7e7b09228d0b306f 13428 science optional sepp_4.3.10+dfsg-1.debian.tar.xz 7e4877275fca0d17685204d225eea3d1 7930 science optional sepp_4.3.10+dfsg-1_amd64.buildinfo 23fe9305afe5f3bfef2b9653cc176c32 181084 science optional sepp_4.3.10+dfsg-1_amd64.deb -BEGIN PGP SIGNATURE- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl+AkF8RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtH4ng/+JoVwvZ+OsfE+QTzbl19C1GDaZVcae/hr vvL1VFcREp+d24dSjqnt7xjMCNzXjEBfPbyo4u5lEDxjpEnnUrhA39k+6jMf6Dhy 2hnaKXOzFvudNTlOL36C83eL9a0bj01NUTgtkhHeQb082/oZ7/GaWNEGgJXy3OQ3 MOs7fGxqE3J264vxSkvfRvtngoGxbA8q+8OJjkWIMUHUX7qPZq0IxcJjGx3BdsII PMTQkCEHcwAhoAPNmaO8KcR+tgUBiVYMGePddw5Rmkd/JbyKT9krBdb7uLL8ya1p lufW7plqs3DLM5DlR5pct/L9tG1M/Mgc6hwugCvBdIGCslj1x8NDTjjg2XlrYPHn
Any idea how to create shared lobrary for libatomicqueue
Hi, I checked libatomicqueue[1] and realised that only a static library is built. Any idea how to create a shared library in addition. Kind regards Andreas. [1] https://salsa.debian.org/med-team/libatomicqueue -- http://fam-tille.de
Re: Regarding LoRTIA Package
Hi Med Team I am working on LoRTIA I have installed all the dependencies as given in READ.md - [bedtools] (tested v. 2.28) Make sure that `bedtools> - [pandas] (tested v. 0.24.0 and up) - [Biopython] (tested Release 1.73) - [pysam] (tested v. 0.15.0) - [scipy] (tested v. 1.2.2) Not able to install LoRTIA package its showing following error ERROR: Could not find a version that satisfies the requirement LoRTIA (from versions: none) ERROR: No matching distribution found for LoRTIA Please suggest to me next steps what exactly I have to do in this package. Regards Shruti Gupta On Thu, Oct 22, 2020 at 10:41 PM shruti gupta wrote: > Hello Everyone > > I am working on LoRTIA > > I have installed all the dependencies as given in READ.md > - [bedtools] (tested v. 2.28) Make sure that `bedtools> > - [pandas] (tested v. 0.24.0 and up) > - [Biopython] (tested Release 1.73) > - [pysam] (tested v. 0.15.0) > - [scipy] (tested v. 1.2.2) > > Kindly suggest to me what I have to do in this package. > > Thanks to you all for your support. > > Regards > Shruti Gupta > > >
Re: Packaging "AGAT - Another Gff Analysis Toolkit "
Hi Andreas, On 10/22/20 3:29 PM, Andreas Tille wrote: Hi again, Ok. got it. I tried to fix pristine-tar. You should *not* manually add complete tarballs there. Also the tarball is *without* the Debian revision - so the name should be agat_0.5.0.orig.tar.gz (and not agat_0.5.0-1.orig.tar.gz) Please re-read the recommendations from MoM and the Debian Med policy. Its finally important that you can successfully do `gbp buildpackage` - if it works for you to recreate the tarball it works for others as well. I have removed d/tests. Regarding the packaging: It contains the unchanged autopkgtest boilerplate. Please either provide a sensible autopkgtest or remove the boilerplate debian/tests. They dont have a formal (paper) citation, only https://zenodo.org/record/4044553. I have added agat to conda - metadata. So you know some citation about agat? This would be great. There is also the Conda ID "agat" which you could specify in debian/upstream/metadata (see template). should be done. You should also provide a lintian override for script-with-language-extension lintian warning (there exist a proper example to do so in the Debian Med template!) should be done. I still get lintian issues "bad-whatis-entry" that I am now running out of options on how to fix them. However, man displays a ok page (in my eyes). Please also fix the incorrect-path-for-interpreter - just check the rules file of package sspace or vcftools for example. There are also some manpage errors mentioned by lintian. Please try to fix these. Kind regards Andreas. On Thu, Oct 22, 2020 at 02:06:47PM +0200, Andrei Rozanski wrote: Hi Andreas, Thanks for the replying even in "real life mode" :D On 10/21/20 10:53 PM, Andreas Tille wrote: Hi, Thanks for pointing that out. I have pushed it. very short notice (I'm in real life mode this week): The pristine-tar branch is missing agat_0.5.0.orig.tar.gz. Kind regards Andreas. On Wed, Oct 21, 2020 at 06:44:54PM +0200, Andrei Rozanski wrote: Hello, I have worked on AGAT (https://salsa.debian.org/med-team/agat). For the moment, lintian seems fine. The build also looks promising. I would like to request some help for checking/guidance on what I have done so far. Many thanks. Best, AndreiR On Fri, Oct 16, 2020 at 7:41 AM Andrei Rozanski wrote: Hi Andreas, Thanks for the answer! I will work on it. On October 16, 2020 07:39:23 Andreas Tille wrote: Hi Andrei, On Fri, Oct 16, 2020 at 07:30:11AM +0200, Andrei Rozanski wrote: More recently I have tried AGAT - Another Gff Analysis Toolkit (https://github.com/NBISweden/AGAT) and found it quite useful in general. I have failed to find a debian package for it. Would it be ok for me to try to package it or should I prioritize the COVID list and do AGAT later? The general rule is: We package what we use. So yes, just go for it. (May be those who assembled the COVID list did not had this on the radar?) Feel free to keep on asking here in case of trouble. Thanks a lot for your contribution Andreas. -- http://fam-tille.de Best AndreiR -- Andrei R Many thanks ! Best AndreiR Thanks! Best AndreiR
Re: Bug#937488: pynast: Python2 removal in sid/bullseye
On Wed, Oct 21, 2020 at 11:09:57PM +0200, Moritz Mühlenhoff wrote: > On Wed, Jan 08, 2020 at 03:03:57PM +0100, Andreas Tille wrote: > > Control: tags -1 upstream > > Control: forwarded -1 https://github.com/biocore/pynast/issues/20 > > > > I managed to create a patch using 2to3 but pynast depends python-cogent > > vesion <= 1.9 which is Python2. The python3-cogent3 package has a > > different API and is not compatible with pynast any more. If upstream > > might not be able to adapt to cogent3 we probably need to remove pynast > > from Debian. > > Given that there's been no upstream reaction for almost a year, let's > remove? > > Cheers, > Moritz > -- http://fam-tille.de
