Quick update on pysam - it needs FAI_FASTA declared which only comes with libhts-dev 1.9.
I have uploaded it to experimental. Cheers, Steffen On 7/29/18 5:28 PM, Steffen Möller wrote: > ;) Well spotted. Done. > > I also tested pysam in its _very_ new version 1.5.0.1 which built > flawlessly against htslib 1.9. There are quite some additional > rdependencies, though: > > $ apt-cache rdepends libhts2 > Reverse Depends: > bio-eagle > samtools > trinityrnaseq > stacks > sambamba > rsem > rna-star > reapr > qtltools > python3-pysam > python-pysam > pbdagcon > pbbamtools > libpbbam > nanopolish > libvcflib-tools > libtabixpp0 > freebayes > fastqtl > crac > blasr > bcftools > augustus > > My plan was to rebuild pysam 1.5.0.1 with version 1.7 of htslib which > they officially (so the readme says) support and upload that to main. > Nanopolish also has a new upstream version, so I will test that against > 1.9, too. Should that also pass tests then I tend to think we should > move htslib 1.9 from experimental to unstable. We should then possibly > block its transition to testing until all (most) its reverse > dependencies test successfully against it. > > Best, > > Steffen > > > On 7/29/18 1:13 AM, Andreas Tille wrote: >> Thanks. Please push your changes, Andreas. > > On Sat, Jul 28, 2018 at >> 06:49:14PM +0000, Debian FTP Masters wrote: >>>>>>> Accepted: >> >> Format: 1.8 >> Date: Thu, 26 Jul 2018 18:54:12 +0200 >> Source: htslib >> Binary: libhts2 libhts-dev libhts-private-dev htslib-test tabix >> Architecture: source all amd64 >> Version: 1.9-1 >> Distribution: experimental >> Urgency: medium >> Maintainer: Debian Med Packaging Team >> <[email protected]> >> Changed-By: Steffen Moeller <[email protected]> >> Description: >> htslib-test - Test data for HTSlib >> libhts-dev - development files for the HTSlib >> libhts-private-dev - private development files for the HTSlib (use >> with care) >> libhts2 - C library for high-throughput sequencing data formats >> tabix - generic indexer for TAB-delimited genome position files >> Changes: >> htslib (1.9-1) experimental; urgency=medium >> . >> * Team upload. >> . >> * New upstream version. Some symbols were added, others were removed: >> - cram_to_bam was removed >> - fai_build_core was removed >> * Updated symbols list >> * Introduced -flto >> Checksums-Sha1: >> b6836603611fa12f7f4f3d49f94ff7efd75be22e 2308 htslib_1.9-1.dsc >> 0bf3cb05883a38ea4da10711e833b007df723cc1 1285580 htslib_1.9.orig.tar.gz >> cac4c952709f984a1883cb46801164810b7966f3 13664 htslib_1.9-1.debian.tar.xz >> 0308c4a4b208732c16cf3fd2bfbc7b46e6657a5a 915596 htslib-test_1.9-1_all.deb >> aac61634077426e2e82ea26cddc3900feb27eaee 8287 >> htslib_1.9-1_amd64.buildinfo >> b3a2526b8cd55f04f31355de9d50b7174661d2a1 4295748 >> libhts-dev_1.9-1_amd64.deb >> bb8ca6d00fbd9e6626450da5f4bc2e78bfe8bc7a 41272 >> libhts-private-dev_1.9-1_all.deb >> 394dad423f318720fe9d0f690178c2b0c920cd33 216280 >> libhts2-dbgsym_1.9-1_amd64.deb >> a5c34245493dfcbb22a3be829fc1dec6cee758b2 305372 libhts2_1.9-1_amd64.deb >> dac0c156812eeb80928607ab157565ad84a91453 509288 >> tabix-dbgsym_1.9-1_amd64.deb >> 39114cde924723c28521cd87b27065a92deed5cf 295764 tabix_1.9-1_amd64.deb >> Checksums-Sha256: >> 6a0bd8be0403549734bd3caec0ddeb656aa7ddf085d227417dafdb9ba3a9ed02 2308 >> htslib_1.9-1.dsc >> d2e3cde77b8f874b37453c63390cd992901266336e9f70e871ef42402510467f >> 1285580 htslib_1.9.orig.tar.gz >> 1404fcd3edb1e2d3e45909e4a79a9442724c1d0c3186f77845181f5b36ba6b0c >> 13664 htslib_1.9-1.debian.tar.xz >> 1494fead8f0dd92200b44e79a558a841a68e21051c935cfb6079ecf313bd4549 >> 915596 htslib-test_1.9-1_all.deb >> 8497faa7840b427f2797dc0210785c7a5afd8f11c12327fef32d7839d93e1941 8287 >> htslib_1.9-1_amd64.buildinfo >> d1f2651d900d3f619f99f804144ba4bbde3833239086c0b81a709398539e0dc7 >> 4295748 libhts-dev_1.9-1_amd64.deb >> d02f2a8f764cb2a3d2fed21faa88ff540258cc646c793a15e58830a9eefa0970 >> 41272 libhts-private-dev_1.9-1_all.deb >> bd3df9e69b840cb9fb4321aa84c909a979b1fec8ac1fd90a48e6455bf497e4eb >> 216280 libhts2-dbgsym_1.9-1_amd64.deb >> 106afc805850075e2463ffb1d201accf1e775b4fa0c49073c672efaa0104a24f >> 305372 libhts2_1.9-1_amd64.deb >> b174f4844aaa65cf462176fea691950af8a3cb40774824c32f493c717a7d3a46 >> 509288 tabix-dbgsym_1.9-1_amd64.deb >> 6475264cd40ca6e5495a983460ccf42c488e4e332eaa1bf2e86b10858408b9e0 >> 295764 tabix_1.9-1_amd64.deb >> Files: >> afeb3aaae8e52b288834bdf5e13885b9 2308 science optional htslib_1.9-1.dsc >> deca473ddbf6227de3734fcf4e18f82f 1285580 science optional >> htslib_1.9.orig.tar.gz >> 39422ff3a617d1f86fec4fa7008c0b9c 13664 science optional >> htslib_1.9-1.debian.tar.xz >> e21552808286a07a9ab1a832557a0375 915596 science optional >> htslib-test_1.9-1_all.deb >> e852bcdc6f7424a1a8c31468e0c24043 8287 science optional >> htslib_1.9-1_amd64.buildinfo >> fe4750ebdb01aa1c53b65d795fb9619f 4295748 libdevel optional >> libhts-dev_1.9-1_amd64.deb >> 71447abc33630cf39fc7c40e458d2752 41272 libdevel optional >> libhts-private-dev_1.9-1_all.deb >> c3d685cf66bafdace6dd48bdc5488e29 216280 debug optional >> libhts2-dbgsym_1.9-1_amd64.deb >> aef13da00d69ba9f22a515de772979ef 305372 libs optional >> libhts2_1.9-1_amd64.deb >> afc2e9e6bc3160e58144d1b14b341ad3 509288 debug optional >> tabix-dbgsym_1.9-1_amd64.deb >> 9d1bda0d5f7b9fce2fffa33677371cb9 295764 science optional >> tabix_1.9-1_amd64.deb >> >>>>>>> Thank you for your contribution to Debian. >> >> > _______________________________________________ >> Debian-med-packaging > mailing list >> [email protected] >> > https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-packaging
