Bug#996993: marked as done (ITP: biojava5-live -- Java API to biological data and applications (version 5))
Your message dated Sat, 19 Feb 2022 10:00:09 + with message-id and subject line Bug#996993: fixed in biojava5-live 5.4.0+dfsg-1 has caused the Debian Bug report #996993, regarding ITP: biojava5-live -- Java API to biological data and applications (version 5) 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.) -- 996993: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=996993 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems --- Begin Message --- Package: wnpp Severity: wishlist Owner: Debian-med team X-Debbugs-Cc: debian-de...@lists.debian.org, debian-med@lists.debian.org * Package name: biojava5-live Version : 5.4.0 Upstream Author : BioJava Developers * URL : https://www.biojava.org/ * License : LGPL-2.1 Programming Lang: Java Description : Java API to biological data and applications (version 5) This package presents the Open Source Java API to biological databases and a series of mostly sequence-based algorithms. BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It includes objects for manipulating sequences, file parsers, server support, access to BioSQL and Ensembl databases, and powerful analysis and statistical routines including a dynamic programming toolkit. This is the version 5 of biojava, which brings several changes compared to version 4, packaged in biojava4-live. It will be maintained by the Debian-med team. --- End Message --- --- Begin Message --- Source: biojava5-live Source-Version: 5.4.0+dfsg-1 Done: Pierre Gruet We believe that the bug you reported is fixed in the latest version of biojava5-live, 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 996...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Pierre Gruet (supplier of updated biojava5-live 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: Wed, 27 Oct 2021 09:53:27 +0200 Source: biojava5-live Binary: libbiojava5-java libbiojava5-java-doc Architecture: source all Version: 5.4.0+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Pierre Gruet Description: libbiojava5-java - Java API to biological data and applications (version 5) libbiojava5-java-doc - [Biology] Documentation for BioJava 5 Closes: 996993 Changes: biojava5-live (5.4.0+dfsg-1) unstable; urgency=medium . * Initial release (Closes: #996993) Checksums-Sha1: 45f265fd1a9ac06b1c9cfab33cccacf89c9e943b 3311 biojava5-live_5.4.0+dfsg-1.dsc d195c3376714253129449642cdd69faa1e4ae5f0 689571 biojava5-live_5.4.0+dfsg.orig-forester.tar.gz 4427e5c181727f232d704b3fb431a5031b86707f 11524 biojava5-live_5.4.0+dfsg.orig-jcolorbrewer.tar.gz 2974d2511c56be2ba09e4a845f86a2837cde11a8 18607769 biojava5-live_5.4.0+dfsg.orig.tar.gz 333bbc44a70b5fd3534eec056f0566b0d0ad7692 27004 biojava5-live_5.4.0+dfsg-1.debian.tar.xz b3a9f193699695df33c6011b23dd234ba2e8113c 17239 biojava5-live_5.4.0+dfsg-1_amd64.buildinfo 0c6f48638d4a2dfc5d83288216b9db1a35d3f744 2744372 libbiojava5-java-doc_5.4.0+dfsg-1_all.deb b1229bf3c7682a14cb0d83fc2f0f1d14a44f4d11 5510576 libbiojava5-java_5.4.0+dfsg-1_all.deb Checksums-Sha256: 1664374a62107135d68bd497092a744290e565a7ba05a39442e1779f3417ddd5 3311 biojava5-live_5.4.0+dfsg-1.dsc 0df0a935a1aac7cd8c404e81ff51794a2f63f6f8479a7ff91bf898610aeb13a3 689571 biojava5-live_5.4.0+dfsg.orig-forester.tar.gz 0d6c5b0e955e5f785bc5ee96fa682158e4692cb776dd1f342fdc8de97e211fdb 11524 biojava5-live_5.4.0+dfsg.orig-jcolorbrewer.tar.gz 6c6c6d12a0abe2d0087e923cea09a8746d02b594a43005a04dbfb5fc6c84060c 18607769 biojava5-live_5.4.0+dfsg.orig.tar.gz 47da24f69f1ca73581e9764054b90d2aab1f00a9f7397f396071f9e36acbf351 27004 biojava5-live_5.4.0+dfsg-1.debian.tar.xz 0e9d7490e51f5f649d02999b1cdaa72d9174f7b9750211e94c3b0e4803147286 17239 biojava5-live_5.4.0+dfsg-1_amd64.buildinfo cd7853badda5af6b72432e93a1acdf0b56ea0ad9ec382ace4677e68d960e2174 2744372 libbiojava5-java-doc_5.4.0+dfsg-1_all.deb 2c0f085aa30a672cdbbc444ca2c30d02be4d5b0e70a01afa4a55ce6e30abb028 5510576 libbiojava5-java_5.4.0+dfsg-1_all.deb Files: ae5ebbd0826b3d897416d0e61ee
Bug#1004152: marked as done (ITP: malt -- sequence alignment and analysis tool to process sequencing data)
Your message dated Sat, 19 Feb 2022 11:00:10 + with message-id and subject line Bug#1004152: fixed in malt 0.5.2-1 has caused the Debian Bug report #1004152, regarding ITP: malt -- sequence alignment and analysis tool to process sequencing data 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.) -- 1004152: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1004152 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems --- Begin Message --- Package: wnpp Severity: wishlist Owner: Debian-med team X-Debbugs-Cc: debian-de...@lists.debian.org, debian-med@lists.debian.org * Package name: malt Version : 0.5.2 Upstream Author : Daniel Huson * URL : https://github.com/danielhuson/malt * License : GPL-3+ Programming Lang: Java Description : sequence alignment and analysis tool to process sequencing data MALT, an acronym for MEGAN alignment tool, is a sequence alignment and analysis tool designed for processing high-throughput sequencing data, especially in the context of metagenomics. It is an extension of MEGAN6, the MEGenome Analyzer and is designed to provide the input for MEGAN6, but can also be used independently of MEGAN6. The core of the program is a sequence alignment engine that aligns DNA or protein sequences to a DNA or protein reference database in either BLASTN (DNA queries and DNA references), BLASTX (DNA queries and protein references) or BLASTP (protein queries and protein references) mode. The engine uses a banded-alignment algorithm with ane gap scores and BLOSUM substitution matrices (in the case of protein alignments). The program can compute both local alignments (Smith-Waterman) or semi-global alignments (in which reads are aligned end-to-end into reference sequences), the latter being more appropriate for aligning metagenomic reads to references. The package will be team-maintained in Debian-med team. --- End Message --- --- Begin Message --- Source: malt Source-Version: 0.5.2-1 Done: Pierre Gruet We believe that the bug you reported is fixed in the latest version of malt, 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 1004...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Pierre Gruet (supplier of updated malt 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: Fri, 18 Feb 2022 14:29:48 +0100 Source: malt Binary: malt Architecture: source all Version: 0.5.2-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Pierre Gruet Description: malt - sequence alignment and analysis tool to process sequencing data Closes: 1004152 Changes: malt (0.5.2-1) unstable; urgency=medium . * Initial release (Closes: #1004152) Checksums-Sha1: bcc7f0a89aa22f50f2fcf13e0085fa62f444e5ef 1975 malt_0.5.2-1.dsc 97f954c9dd87bdd8f1cfe04c75a79a7f175892ec 437746 malt_0.5.2.orig.tar.gz 3207a6ddc0ab6c769100c43e8090b137cba34f9f 6404 malt_0.5.2-1.debian.tar.xz c5d952f6d1131cfa37b02dd7b978d2f0d50088ff 416000 malt_0.5.2-1_all.deb 1a5cdd3f118c3ce2221828dd9219bf3812760ff0 15237 malt_0.5.2-1_amd64.buildinfo Checksums-Sha256: 41d760b2ab7824dbeb528e3b2690c6bf41abf61c4791d14c188f34b62bfee20c 1975 malt_0.5.2-1.dsc 904eb781aa0c7369bd7bccb88a3e8696fa83513e073988f0d76f09faea2dc1a1 437746 malt_0.5.2.orig.tar.gz 558b8949f84600d3df011d351c2bbc6fce1ae8feadbda2dd06b05b1b734879b8 6404 malt_0.5.2-1.debian.tar.xz c019ccff247efb961218f562e5a979247f68d2ef161bd830c52f03f0a4045a6f 416000 malt_0.5.2-1_all.deb a988e17536754cae269c1dfd14cd3a287fcd3f39ac816d8a11c3c42eda327066 15237 malt_0.5.2-1_amd64.buildinfo Files: f2876c2c18f5e80a485c111f7151c1d7 1975 science optional malt_0.5.2-1.dsc 1a9cc3c4cd75b2f13ea2bb5a76b5da57 437746 science optional malt_0.5.2.orig.tar.gz d6845786637e4eda46bb0030dc00db4d 6404 science optional malt_0.5.2-1.debian.tar.xz 4718b3f1390612628def9126eab478f7 416000 science optional malt_0.5.2-1_all.deb c4325ff56180d98e0f125f269e89701c 15237 science optional malt_0.5.2-1_amd64.buildinfo -BEGIN PGP SIGNATURE- iQIzBAEBCgAdFiEEM8soQxPpC9J9y0UjYAMWptwndHYFAmIPvSAACgkQYAMWptwn dHbIqQ//cMMBra+9rLCl22ZIBb7OllugBa5/oE7Exkq15
Is snakemake using drmaa?
Hi Rebecca, I've checked the situation of python3-drmaa: Autopkgtest of python3-drmaa fails with: OSError: /usr/lib/x86_64-linux-gnu/libjemalloc.so.2: cannot allocate memory in static TLS block which is caused by bug #951704 (tagged wontfix). Drmaa does not seem to be maintained upstream any more. Nilesh confirmed its a mess. The question is: Is it recommended by snakemake just for historic reasons or is it really profiting from it. I'm considering the consequences of just removing drmaa. What do you think? Kind regards Andreas. -- http://fam-tille.de
Can we remove probabel?
Hi, probabel fails its test suite for some architectures[1]. I reported this upstream and got the response[2] @lckarssen Shall we ask if they remove Probabel from the Debian project as a package? Since there is no workforce to maintain the software, it is better not to use it. ( so also distribution and installing is not a good idea) Popcon is low[3] - but that's not unusual for our packages. I see two options: 1. Remove probabel for the failing architectures only 2. Remove probabel completely from Debian What do you think? Kind regards Andreas. [1] https://buildd.debian.org/status/package.php?p=probabel [2] https://github.com/GenABEL-Project/ProbABEL/issues/47#issuecomment-939993369 [3] https://qa.debian.org/popcon-graph.php?packages=probabel&show_vote=on&want_legend=on&want_ticks=on&from_date=&to_date=&hlght_date=&date_fmt=%25Y-%25m&beenhere=1 -- http://fam-tille.de
Re: Is snakemake using drmaa?
The documentation says: https://github.com/snakemake/snakemake/blob/main/docs/tutorial/additional_features.rst#cluster-execution https://github.com/snakemake/snakemake/blob/main/docs/executing/cluster.rst I don't know how up to date this is, but the code to use drmaa is still there. snakemake already has several other options that only work with not-in-Debian packages, so I wouldn't consider adding another one to be a big deal, but I don't know how often this one is used.
Re: Datasets to design autopkgtests for our packages
Andrius Merkys writes: > It depends whether you need simple protein FASTA sequences or > alignments. You may find simple sequences in PDB, for example [1], go to > "Download Files" and FASTA format is just there. AFAIR, PDB data is > freely distributable. Likewise for everything in GenBank/GenPept, ENA, and DDBJ per [2] and everything in UniProt per [3]. > [1] https://www.rcsb.org/structure/6fti [2] https://www.insdc.org/policy.html [3] https://www.uniprot.org/help/license -- Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org) http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?a...@monk.mit.edu
FastQTL seems to be removed from sourceforge - where can we find it now?
Hi Olivier, I'm writing you on behalf of the Debian Med team which is maintaining FastQTL for Debian. I just realised that the original homepage at sourceforge[1] does not work any more. While I've found modified forks on Github I would like to hear your opinion what might be the best source to download the source code of FastQTL. Kind regards Andreas. [1] https://sourceforge.net/projects/fastqtl/ [2] https://github.com/hall-lab/fastqtl https://github.com/francois-a/fastqtl -- http://fam-tille.de
Re: Is snakemake using drmaa?
Am Sat, Feb 19, 2022 at 09:23:16PM + schrieb Rebecca N. Palmer: > The documentation says: > https://github.com/snakemake/snakemake/blob/main/docs/tutorial/additional_features.rst#cluster-execution > https://github.com/snakemake/snakemake/blob/main/docs/executing/cluster.rst > I don't know how up to date this is, but the code to use drmaa is still > there. > > snakemake already has several other options that only work with > not-in-Debian packages, so I wouldn't consider adding another one to be a > big deal, but I don't know how often this one is used. Feel free to name one or two alternatives we might package together to sensibly get rid of drmaa. Kind regards Andreas. -- http://fam-tille.de
Cmake help needed for ncbi-vdb
Hi, I think I need some cmake help for ncbi-vdb. In former versions ncbi-vdb came with a hand-crafted build system. Now cmake is provided alternatively which is a great progress IMHO since that hand-crafted system always created issues for every new version. I started using cmake but its not finished yet[1]. The point is that the linker flags to libmbedtls-dev, zlib and others need to be set. Excluding references to code copies was easy[2] ... but now we need the according -l options and my cmake knowledge is to weak. Any help would be welcome Andreas. [1] https://salsa.debian.org/med-team/ncbi-vdb/-/jobs/2489631 [2] https://salsa.debian.org/med-team/ncbi-vdb/-/blob/master/debian/patches/fix_cmake.patch#L30 -- http://fam-tille.de
Autodocksuite not available at Sourceforge any more
Hi Steffen, I realised that https://sourceforge.net/projects/autodocksuite/files/ has no files any more. Could you shade some light into what we should package and what we should rather drop? Does it help to keep the current autodocksuite code inside Debian (but provide a fake watch file to reduce noise about failed uscan)? Kind regards Andreas. -- http://fam-tille.de
Re: Autodocksuite not available at Sourceforge any more
Hello, On Sun, 20 Feb 2022, 09:40 Andreas Tille, wrote: > I realised that > >https://sourceforge.net/projects/autodocksuite/files/ > > has no files any more. Could you shade some light into what we should > package and what we should rather drop? Does it help to keep the > current autodocksuite code inside Debian (but provide a fake watch file > to reduce noise about failed uscan)? > Quick search lead me to: https://autodock.scripps.edu/download-autodock4/ Maybe the upstream migrated away from SourceForge? Best, Andrius
