1002 Commits

Author	SHA1	Message	Date
R. Ryantm	fc65d6e66e	star: 2.7.10a -> 2.7.10b	2023-01-14 06:06:52 +00:00
github-actions[bot]	33aa224777	Merge master into staging-next	2023-01-09 18:01:24 +00:00
R. Ryantm	e0db41ab1a	ants: 2.4.2 -> 2.4.3	2023-01-09 09:48:53 -06:00
Robert Schütz	b3241be75d	python310Packages.levenshtein: don't use alias	2023-01-09 06:09:31 -08:00
R. Ryantm	605d013aac	igv: 2.15.1 -> 2.15.4	2023-01-03 14:36:54 +08:00
Ben Darwin	9c748218f2	itk: unstable -> 5.3.0	2022-12-27 09:06:37 +01:00
Sandro	b20fb264cc	Merge pull request #197575 from thyol/sratoolkit-init	2022-12-24 02:58:47 +01:00
amesgen	d499bc2447	tandem-aligner: init at unstable-2022-09-17	2022-12-15 20:48:53 +01:00
Weijia Wang	fa19b16e93	ecopcr: 0.8.0 -> 1.0.1	2022-12-08 04:35:53 +01:00
Jonas Heinrich	20193b6d86	Merge pull request #202395 from thyol/muscle ... muscle: 3.8.31 -> 5.1.0	2022-11-24 15:47:12 +01:00
Jonas Heinrich	57728b51cf	Merge pull request #202404 from thyol/veryfasttree ... veryfasttree: init at 3.1.1	2022-11-24 15:14:13 +01:00
thyol	cdcb7946ba	veryfasttree: init at 3.1.1	2022-11-22 20:45:45 +01:00
thyol	35d3a6fa79	muscle: add myself to maintainers	2022-11-22 20:19:17 +01:00
thyol	d7c8595f62	muscle: 3.8.31 -> 5.1.0	2022-11-22 20:19:17 +01:00
thyol	81d6f1c7dc	sratoolkit: init at 2.11.3	2022-11-21 20:27:28 +01:00
R. Ryantm	6ba0d20487	igv: 2.14.1 -> 2.15.1	2022-11-20 14:06:29 +08:00
Jiajie Chen	fc2812a1f8	nest: init at 3.3	2022-11-10 09:20:41 +08:00
R. Ryantm	c7ba9b459c	delly: 1.1.5 -> 1.1.6	2022-11-08 18:21:37 +00:00
Justin Bedő	3a90ab68e6	Merge pull request #197631 from jbedo/octopus ... octopus-caller: backport patch to fix build	2022-11-07 21:26:21 +00:00
Bruno Bzeznik	9243a44c9c	seqkit: init at 2.3.1	2022-11-04 08:51:32 +01:00
Stanisław Pitucha	9ed8ce7ff3	Merge pull request #198609 from natsukium/mmseqs2/init ... mmseqs2: init at 14-7e284	2022-11-01 21:47:20 +11:00
natsukium	ed7511ad02	mmseqs2: init at 14-7e284	2022-10-31 23:49:10 +09:00
Justin Bedo	5f5bb45093	octopus-caller: backport patch to fix build	2022-10-25 09:52:28 +11:00
OPNA2608	982a1bfd80	sambamba: fix compilation on Darwin, cleanup installPhase	2022-10-23 16:12:47 +02:00
Jan Tojnar	457f28f6f8	Merge branch 'master' into staging-next ... ; Conflicts: ; pkgs/development/tools/codespell/default.nix codespell 2.2.2 switched to pyproject & setuptools_scm: https://github.com/codespell-project/codespell/pull/2523	2022-10-19 05:24:28 +02:00
R. Ryantm	4ab06e3223	ants: 2.4.1 -> 2.4.2	2022-10-19 09:19:31 +08:00
github-actions[bot]	f52955a521	Merge master into staging-next	2022-10-16 18:01:42 +00:00
R. Ryantm	00b3b4ee24	gatk: 4.2.6.1 -> 4.3.0.0	2022-10-16 21:48:30 +08:00
Martin Weinelt	51fcbf5bb7	Merge remote-tracking branch 'origin/master' into staging-next	2022-10-16 00:18:40 +02:00
Jonas Heinrich	9259c4b841	Merge pull request #195990 from r-ryantm/auto-update/angsd ... angsd: 0.938 -> 0.940	2022-10-15 09:33:23 +02:00
github-actions[bot]	886633ba43	Merge master into staging-next	2022-10-15 00:04:00 +00:00
R. Ryantm	4cee9b9ddb	angsd: 0.938 -> 0.940	2022-10-14 14:50:26 +00:00
Artturi	e66d2fd89d	Merge pull request #194256 from Artturin/treewides2	2022-10-13 00:08:01 +03:00
Markus S. Wamser	c9d167f174	pkgs.applications: remove unused args	2022-10-12 16:00:16 +02:00
Martin Weinelt	cf7f4393f3	Merge pull request #193494 from NixOS/staging-next	2022-10-11 01:12:59 +02:00
Alexis Praga	2ce78bd571	gatk: add java and python to PATH ... gatk is actually a python script that starts either the local or spark .jar file according to a fixed setup. In the initial commit, neither java nor python were present in PATH.	2022-10-10 23:06:01 +02:00
Artturin	7e49471316	treewide: optional -> optionals where the argument is a list ... the argument to optional should not be list	2022-10-10 15:40:21 +03:00
R. Ryantm	92bc5dbbae	picard-tools: 2.27.4 -> 2.27.5	2022-10-08 00:09:59 +00:00
github-actions[bot]	f18d801779	Merge staging-next into staging	2022-09-28 18:05:53 +00:00
R. Ryantm	ddf9f1800a	delly: 1.1.3 -> 1.1.5	2022-09-27 11:26:09 +00:00
Artturin	0734f54ef2	treewide: move pkg-config, autoreconfHook, intltool to nativeBuildInputs ... found with nixpkgs-lint	2022-09-26 17:53:26 +03:00
Justin Bedő	d21b5ac044	Merge pull request #192211 from r-ryantm/auto-update/last ... last: 1409 -> 1411	2022-09-26 11:49:30 +10:00
Brad Langhorst	2beb26b45b	seqtk: init at 1.3 ... Co-authored-by: Anderson Torres <torres.anderson.85@protonmail.com>	2022-09-25 19:55:58 -04:00
R. Ryantm	1008651931	last: 1409 -> 1411	2022-09-21 08:24:01 +00:00
Christian Kögler	e06e88d003	Merge pull request #189923 from r-ryantm/auto-update/igv ... igv: 2.14.0 -> 2.14.1	2022-09-18 15:59:16 +02:00
R. Ryantm	9da745bfaf	messer-slim: 4.0 -> 4.0.1	2022-09-15 22:25:51 +00:00
Sandro	785031e430	Merge pull request #185819 from apraga/gatk-4.2.6.1	2022-09-10 21:31:42 +02:00
natsukium	9e65d09e3d	mafft: 7.505 -> 7.508 ... changed to fetch from new gitlab repository	2022-09-09 13:26:38 +09:00
R. Ryantm	c7832514ef	igv: 2.14.0 -> 2.14.1	2022-09-05 22:29:15 +00:00
Sandro	ef987a9604	Merge pull request #189329 from bcdarwin/itk4-removal	2022-09-05 16:05:51 +02:00
Sandro	73bf7a0ca0	Merge pull request #181954 from bzizou/treemix	2022-09-05 15:57:48 +02:00
Bruno Bzeznik	7c09cfdc1a	treemix: init at 1.13	2022-09-05 06:55:03 +02:00
Jonas Heinrich	eb3d3b2e90	Merge pull request #175449 from bzizou/iqtree ... iqtree: init at 2.2.0.4	2022-09-04 23:58:04 +02:00
Ben Darwin	1280129aab	EZminc: itk4 -> itk (formally; package is broken)	2022-09-04 13:36:24 -04:00
Ben Darwin	961b308fe1	ants: 2.2.0 -> 2.4.1	2022-09-04 13:36:24 -04:00
Alexis Praga	95da303902	gatk : init at 4.2.6.1 ... GATK is the industry standard for genetics analysis, more precisely for identifying SNPs and indels in germline DNA and RNAseq data . This package does not ship the Spark version. Apply suggestions from code review Co-authored-by: Sandro <sandro.jaeckel@gmail.com>	2022-09-04 15:34:30 +02:00
Jonas Heinrich	3b3a01e3f9	Merge pull request #188785 from jbedo/last ... last: 1406 -> 1409	2022-09-04 12:40:30 +02:00
Justin Bedo	d9acf90371	last: 1406 -> 1409	2022-09-04 10:36:01 +10:00
Sandro	9b214e6dad	Merge pull request #177830 from r-ryantm/auto-update/eggnog-mapper	2022-09-03 22:43:11 +02:00
Jonas Heinrich	ed227dc9fb	Merge pull request #168109 from r-ryantm/auto-update/bcftools ... bcftools: 1.15 -> 1.16	2022-08-27 08:51:34 +02:00
Jonas Heinrich	21ba29f226	Merge pull request #181338 from thyol/diamond ... diamond: 0.8.36 -> 2.0.15	2022-08-25 15:25:03 +02:00
Jonas Heinrich	b8e0c9b652	Merge pull request #183253 from r-ryantm/auto-update/angsd ... angsd: 0.937 -> 0.938	2022-08-24 10:35:05 +02:00
Jonas Heinrich	c199cfabff	Merge pull request #184694 from r-ryantm/auto-update/SPAdes ... SPAdes: 3.15.4 -> 3.15.5	2022-08-23 20:21:42 +02:00
Jonas Heinrich	5cb64f6046	Merge pull request #186958 from r-ryantm/auto-update/igv ... igv: 2.13.2 -> 2.14.0	2022-08-21 21:11:49 +02:00
R. Ryantm	49f4071f30	eggnog-mapper: 2.1.7 -> 2.1.9	2022-08-21 12:45:21 +00:00
Jonas Heinrich	8508d5decf	Merge pull request #183724 from r-ryantm/auto-update/picard-tools ... picard-tools: 2.26.11 -> 2.27.4	2022-08-21 10:03:42 +02:00
R. Ryantm	98d1f4c35d	bcftools: 1.15 -> 1.16	2022-08-18 18:44:42 +00:00
R. Ryantm	f4c3ff2d7f	igv: 2.13.2 -> 2.14.0	2022-08-16 13:24:02 +00:00
R. Ryantm	c37112d2d0	messer-slim: 3.7.1 -> 4.0	2022-08-14 14:11:37 +00:00
Mario Rodas	0cab4c8f8a	Merge pull request #183012 from bcdarwin/update-mni-autoreg ... mni_autoreg: unstable-2017-09-22 -> unstable-2022-05-20	2022-08-13 01:05:26 -05:00
Mario Rodas	6aeb44c32e	Merge pull request #185211 from r-ryantm/auto-update/delly ... delly: 1.0.3 -> 1.1.3	2022-08-13 00:41:48 -05:00
kilianar	0442ab82e0	igv: 2.8.13 -> 2.13.2 ... - https://software.broadinstitute.org/software/igv/2.9.x - https://software.broadinstitute.org/software/igv/2.10.x - https://software.broadinstitute.org/software/igv/2.11.x - https://software.broadinstitute.org/software/igv/2.12.x - https://software.broadinstitute.org/software/igv/2.13.x	2022-08-07 17:53:06 +02:00
Bobby Rong	934c6c9a95	Merge pull request #184334 from r-ryantm/auto-update/mafft ... mafft: 7.490 -> 7.505	2022-08-07 16:18:05 +08:00
R. Ryantm	8b7c09d0e6	delly: 1.0.3 -> 1.1.3	2022-08-05 08:58:15 +00:00
Sandro	e9984bc607	Merge pull request #182705 from luispedro/no_test_samtools_on_cross_compile	2022-08-02 23:20:38 +02:00
Luis Pedro Coelho	5877d8e072	samtools: Fix cross-compilation ... Tests require bgzip which comes from the htslib package. This did not cause problems prior to 41485e7337 as tests were not run in cross-compilation.	2022-08-02 17:52:50 +02:00
Sandro	e76aa82431	Merge pull request #184598 from wegank/treewide-fix-platforms	2022-08-02 15:57:56 +02:00
R. Ryantm	921b81745d	SPAdes: 3.15.4 -> 3.15.5	2022-08-02 02:26:56 +00:00
Weijia Wang	278086eddb	treewide: fix platforms	2022-08-01 18:33:27 +02:00
R. Ryantm	b2bbba02ba	mafft: 7.490 -> 7.505	2022-07-31 20:32:57 +00:00
R. Ryantm	e0a9011556	last: 1268 -> 1406	2022-07-31 16:58:20 +00:00
R. Ryantm	9338d8c9b7	picard-tools: 2.26.11 -> 2.27.4	2022-07-29 16:12:10 +00:00
R. Ryantm	8c0e56fc14	angsd: 0.937 -> 0.938	2022-07-28 07:50:11 +00:00
Justin Bedő	9e80da74b0	Merge pull request #182028 from jbedo/bedops ... bedops: 2.4.40 -> 2.4.41	2022-07-28 09:14:23 +10:00
Ben Darwin	125da19866	mni_autoreg: unstable-2017-02-22 -> unstable-2022-05-20	2022-07-26 16:03:12 -04:00
natsukium	cf0dc604a6	dssp: init at 4.0.5	2022-07-19 12:17:34 +09:00
Justin Bedo	99fb9abfaa	bedops: 2.4.40 -> 2.4.41	2022-07-19 09:09:52 +10:00
Lassulus	01853c3bcc	Merge pull request #174547 from r-ryantm/auto-update/delly ... delly: 0.9.1 -> 1.0.3	2022-07-16 10:49:50 +02:00
Pascal Wittmann	26ddf3454a	Merge pull request #138255 from natsukium/mafft/init ... mafft: init at 7.487	2022-07-16 00:54:59 +02:00
thyol	0d6e3afdba	diamond: update metadata	2022-07-13 12:33:33 +02:00
thyol	55853ae096	maintainers: add thyol	2022-07-13 12:30:44 +02:00
thyol	4e79b5e370	diamond: remove patch	2022-07-13 11:58:39 +02:00
thyol	5e765ecc68	diamond: 0.8.36 -> 2.0.15	2022-07-13 11:58:02 +02:00
R. Ryantm	5ea1c721e1	delly: 0.9.1 -> 1.0.3	2022-07-07 22:10:48 +00:00
ajs124	3b5f125515	maintainers: remove metabar ... no github account + only commit is 78c052e91a	2022-06-29 00:52:13 +02:00
Robert Scott	466c2e342a	treewide/applications: add sourceType binaryNativeCode for many packages	2022-06-23 18:38:19 +01:00
Robert Scott	444d3a825a	treewide/python-modules: add sourceProvenance for several packages	2022-06-20 09:43:10 +02:00
Sandro Jäckel	0f14467d44	MACS2: mark broken	2022-06-06 11:46:22 -07:00
Robert Scott	3b6bc4b69c	treewide: set sourceProvenance for packages containing downloaded jars ... these are the easily identifiable cases and will not be comprehensive	2022-06-04 19:47:57 +01:00
Sergei Trofimovich	fd48676596	Merge pull request #175259 from trofi/workaround-fno-common-for-svaba ... svaba: add -fcommon workaround	2022-06-03 05:59:16 +00:00
ckie	958fcfb4fa	Merge pull request #175477 from bzizou/astral ... astral: init at 5.7.1	2022-05-31 14:55:37 +03:00
Bruno Bzeznik	376897ced3	astral: init at 5.7.1	2022-05-31 09:03:24 +02:00
Rick van Schijndel	433701147a	treewide: pkgs/applications: mark broken for aarch64-linux	2022-05-30 13:42:58 +02:00
Bruno Bzeznik	c15d568d0b	iqtree: init at 2.2.0.4	2022-05-30 10:53:40 +02:00
Rick van Schijndel	37c633f7ae	treewide: pkgs/applications: mark broken for darwin	2022-05-29 10:56:04 +02:00
Sergei Trofimovich	2f60be03bb	svaba: add -fcommon workaround ... Workaround build failure on -fno-common toolchains like upstream gcc-10. Otherwise build fails as: ld: ./libfml.a(rle.o):/build/source/SeqLib/fermi-lite/rle.h:33: multiple definition of `rle_auxtab'; ./libfml.a(misc.o):/build/source/SeqLib/fermi-lite/rle.h:33: first defined here	2022-05-29 08:07:23 +01:00
Rick van Schijndel	331e26b6ec	Merge pull request #173867 from trofi/fix-fno-common-for-kssd ... kssd: pull upstream fix for -fno-common tollchains	2022-05-28 20:39:38 +02:00
Sandro	3b9985498d	Merge pull request #174036 from trofi/workaround-fno-common-for-paml ... paml: add -fcommon workaround	2022-05-25 00:35:00 +02:00
Sergei Trofimovich	8cba3775d8	paml: add -fcommon workaround ... Workaround build failure on -fno-common toolchains like upstream gcc-10. Otherwise build fails as: ld: /build/ccKomtcd.o:(.bss+0x4544): multiple definition of `SeqTypes'; /build/ccx7EsgU.o:(.bss+0x2a0dfdc): first defined here	2022-05-22 20:23:12 +01:00
Sergei Trofimovich	94a5ae4f91	mni_autoreg: pull upstream workaround for -fno-common toolchains ... Without the change build fails on upstream gcc-10 as: ld: lib_minctracc.a(minctracclib.c.o):(.bss+0x78): multiple definition of `prog_name'; CMakeFiles/xfm2param.dir/Extra_progs/xfm2param.c.o:(.bss+0x18): first defined here	2022-05-22 14:37:30 +01:00
Bobby Rong	3b468e68b7	Merge pull request #173017 from trofi/workaround-fno-common-for-freebayes ... freebayes: add -fcommon workaround	2022-05-22 13:39:14 +08:00
Sergei Trofimovich	eb0590ec3d	kssd: pull upstream fix for -fno-common tollchains ... Without the change build fails on upstream gcc-10 as: ld: ccD2iWhk.o:(.bss+0x8): multiple definition of `domain'; ccgA4lYl.o:(.bss+0x8): first defined here ld: ccD2iWhk.o:(.bss+0x0): multiple definition of `long_domain'; ccgA4lYl.o:(.bss+0x0): first defined here	2022-05-21 11:22:53 +01:00
Ben Darwin	5cf446f41b	ezminc: mark broken ... Package refuses to build with current GCC (11), but building with older GCC causes error linking libminc and I don't want to pin a bunch of deps. A newer version is available upstream but it only works with ITK 5.0 (see https://github.com/BIC-MNI/EZminc/issues/15), but we have 4.x and 5.2.x in tree and I'm reluctant to add 5.0 just for one package (even ITK 4.x is only used by ants and ezminc and should be removed as soon as ants is upgraded).	2022-05-17 10:24:07 -07:00
Sergei Trofimovich	deaab56289	freebayes: add -fcommon workaround ... Workaround build failure on -fno-common toolchains like upstream gcc-10. Otherwise build fails as: ld: foomatic_rip-options.o:/build/foomatic-filters-4.0.17/options.c:49: multiple definition of `cupsfilter'; foomatic_rip-foomaticrip.o:/build/foomatic-filters-4.0.17/foomaticrip.c:158: first defined here	2022-05-14 13:19:17 +01:00
Thomas Gerbet	44c1590f1f	bayescan: fix the build ... Moved back to C++14 to avoid the new errors and warnings introduced with C++17.	2022-05-13 12:00:08 +02:00
Theodore Ni	81046b393b	bowtie: fix build on case insensitive file systems ... Add a patch that removes the current source directory from the include search path during compilation so that #include <version> does not end up picking the VERSION source code file.	2022-05-11 03:20:03 -05:00
Theodore Ni	802a8416b6	bowtie: add arm64 patch to build on M1 Macs ... This does not fix the build on Macs, but it brings the build on M1 Macs to parity with non-M1 Macs.	2022-05-11 02:36:56 -05:00
Sergei Trofimovich	428045f39b	bwa: pull upstream fix for -fno-common tollchains ... Without the change build fails on -fno-common toolchains like upstream gcc-10 as: $ nix build -L --impure --expr 'with import ./. {}; bwa.overrideAttrs (oa: { NIX_CFLAGS_COMPILE = (oa.NIX_CFLAGS_COMPILE or "") + "-fno-common"; })' ... ld: ./libbwa.a(rope.o):/build/bwa-0.7.17/rle.h:33: multiple definition of `rle_auxtab'; ./libbwa.a(bwtindex.o):/build/bwa-0.7.17/rle.h:33: first defined here ld: ./libbwa.a(rle.o):/build/bwa-0.7.17/rle.h:33: multiple definition of `rle_auxtab'; ./libbwa.a(bwtindex.o):/build/bwa-0.7.17/rle.h:33: first defined here	2022-05-08 08:56:43 +01:00
Luis Pedro Coelho	596c5e7ea2	Static bwa ... AR needs to be passed specifically on the command line	2022-05-04 02:20:50 +02:00
Luis Pedro Coelho	4758873378	Static build for samtools ... Curses is not supported (it may be possible to support it)	2022-05-04 02:16:17 +02:00
Luis Pedro Coelho	0b1c28d5a1	Static build for megahit	2022-05-04 02:13:31 +02:00
Vladimír Čunát	c480cc2895	Merge branch 'master' into staging-next-2022-04-23	2022-04-30 23:02:28 +02:00
R. Ryantm	a82b1b63c3	blast: 2.12.0 -> 2.13.0	2022-04-29 09:39:10 -05:00
github-actions[bot]	073cad8fd6	Merge master into staging-next	2022-04-25 12:04:02 +00:00
Sandro	2f517412c4	Merge pull request #165477 from rbreslow/dcm2niix-optional-modules	2022-04-25 11:59:49 +02:00
Rocky Breslow	d1c3fea7ec	dcm2niix: support usage of suggested Cloudflare zlib	2022-04-18 15:00:45 -04:00
Rocky Breslow	9019ce0106	dcm2niix: add maintainer ... Also, fix grammatical error in long description.	2022-04-18 15:00:16 -04:00
Ben Siraphob	259fa13d53	treewide: remove nativeBuildInputs that are in stdenv	2022-04-16 21:46:46 +03:00
Fabián Heredia Montiel	8a9d5e296b	cmtk: add -std=c++11 to fix build on gcc11	2022-04-15 11:15:30 -05:00
Malo Bourgon	0e802eafad	treewide: add meta.mainProgram to many packages	2022-04-14 10:24:01 -07:00
Artturi	ebf6f84ea2	Merge pull request #164722 from armeenm/bump-eggnog-mapper ... eggnog-mapper: 1.0.3 -> 2.1.7	2022-04-10 14:37:21 +03:00
Rocky Breslow	09b7444b82	dcm2niix: add support for configuring optional compile-time modules ... Right now, the dcm2niix package produces a single binary without support for dcm2niibatch, JPEG-LS, OpenJPEG, or an alternative zlib library. The official build process for dcm2niix configures all these options (minus batch support). I was motivated to make these changes so my organization could process JPEG 2000 imagery using the Nix binary.	2022-04-04 10:41:27 -04:00
ajs124	60f1e6ffe2	ncbi_tools: remove after being marked broken for over two years ... It was marked in commit b9948fedc6 by Robin Gloster on 2017-03-30 (commited on 2017-03-30)	2022-04-03 16:14:18 +01:00
Ben Siraphob	5187709ff7	Merge pull request #166508 from siraben/automake-buildinputs	2022-03-31 03:15:41 -05:00
Ben Siraphob	21faf9fc29	treewide: move autoconf, automake to nativeBuildInputs	2022-03-30 20:17:24 -05:00
Sandro	1f6bdf4d93	Merge pull request #165458 from rbreslow/add-flywheel-cli	2022-03-29 13:33:54 +02:00
Rocky Breslow	603e9d7b64	flywheel-cli: init at 16.2.0	2022-03-28 15:54:39 -04:00
Felix Buehler	3bc5196252	treewide: rename name to pname&version	2022-03-23 22:55:50 +01:00
Armeen Mahdian	6cfaf0a464	eggnog-mapper: 1.0.3 -> 2.1.7 ... https://github.com/eggnogdb/eggnog-mapper/releases	2022-03-18 10:26:47 -05:00
Bruno Bzeznik	7d62054650	angsd: init at 0.937	2022-03-04 09:17:35 -06:00
Matthew Wakefield	e85b65f986	minimap2: enable aarch64 builds (#161169) ... Co-authored-by: Bobby Rong <rjl931189261@126.com> Co-authored-by: Sandro <sandro.jaeckel@gmail.com>	2022-03-04 12:27:29 +01:00
Justin Bedo	89eff15f31	last: 1260 -> 1268	2022-03-02 13:35:56 +11:00
Felix Buehler	fe7678ca81	raxml-mpi: remove appendToName to have a consistent package name for repology	2022-02-28 12:46:15 +01:00
Felix Buehler	13dca33cdc	neuron-mpi: remove appendToName to have a consistent package name for repology	2022-02-28 12:46:15 +01:00
R. Ryantm	1e7c64aae1	bcftools: 1.14 -> 1.15	2022-02-25 11:12:05 -08:00
R. Ryantm	ce9d28cc49	picard-tools: 2.26.10 -> 2.26.11	2022-02-24 17:34:18 +00:00
natsukium	0524e8856b	mafft: 7.487 -> 7.490	2022-02-22 21:35:45 +09:00
Scriptkiddi	4e60a4823b	febio-studio: init at 1.6.1	2022-02-21 16:43:36 +01:00
R. RyanTM	94f61e4c82	SPAdes: 3.15.3 -> 3.15.4 ... (#158938)	2022-02-18 00:55:34 +01:00
R. Ryantm	240262f564	messer-slim: 3.7 -> 3.7.1	2022-02-14 00:46:29 +00:00
Justin Bedő	2759d6f8d8	Merge pull request #159675 from r-ryantm/auto-update/picard-tools ... picard-tools: 2.26.9 -> 2.26.10	2022-02-13 09:53:20 +11:00
Justin Bedő	7ff9c00c4b	Merge pull request #159562 from r-ryantm/auto-update/mosdepth ... mosdepth: 0.3.2 -> 0.3.3	2022-02-13 09:27:54 +11:00
R. Ryantm	8a4946df2d	picard-tools: 2.26.9 -> 2.26.10	2022-02-12 22:20:29 +00:00
R. Ryantm	8bb7bc766f	mosdepth: 0.3.2 -> 0.3.3	2022-02-12 14:31:47 +00:00
R. Ryantm	6ca5bb6e20	last: 1256 -> 1260	2022-02-12 02:52:18 +00:00
Renaud	2ddcc2b369	hisat2: update homepage ... and use SPDX 3.0 license identifier	2022-02-06 15:10:53 +01:00
R. Ryantm	d44e044d84	kallisto: 0.46.2 -> 0.48.0	2022-01-31 09:53:54 -08:00
Bruno Bzeznik	b6fa4975cf	repseek: init at 9Sep2014 (#148017) ... Co-authored-by: Sandro <sandro.jaeckel@gmail.com>	2022-01-31 14:59:32 +01:00
markuskowa	01f1b41a7d	Merge pull request #156381 from r-ryantm/auto-update/bowtie2 ... bowtie2: 2.4.4 -> 2.4.5	2022-01-29 14:56:23 +01:00
R. RyanTM	8bd7d6d6e0	star: 2.7.9a -> 2.7.10a ... (#155868)	2022-01-24 19:51:44 +01:00
R. Ryantm	ebb9e86bf9	bowtie2: 2.4.4 -> 2.4.5	2022-01-23 22:45:59 +00:00
Mario Rodas	111d7dc831	Merge pull request #156014 from r-ryantm/auto-update/deeptools ... deeptools: 3.5.0 -> 3.5.1	2022-01-22 23:45:09 -05:00
Justin Bedő	c24af4642c	sambamba: 0.8.1 -> 0.8.2 (#155972) ... Co-authored-by: Sandro <sandro.jaeckel@gmail.com>	2022-01-23 04:51:46 +01:00
R. Ryantm	227011af59	deeptools: 3.5.0 -> 3.5.1	2022-01-21 05:36:24 +00:00
Frederik Rietdijk	afef6d0e81	Merge pull request #154687 from dotlambda/python-alias ... python,pythonPackages: make aliases	2022-01-17 09:37:49 +01:00
R. RyanTM	4fa7c297f2	minimap2: 2.23 -> 2.24 ... * minimap2: 2.23 -> 2.24 (#153189) * minimap2: no support for aarch64 Co-authored-by: Renaud <c0bw3b@users.noreply.github.com>	2022-01-17 08:49:35 +01:00
Robert Schütz	d5cceedbd1	python,pythonPackages: make aliases ... Since aliases are disallowed in nixpkgs, this makes usage of Python 2 which is EOL more explicit.	2022-01-16 18:39:59 +00:00
Robert Schütz	65e959eb9a	tebreak: also use python3 for tests	2022-01-16 18:00:59 +00:00
Martin Weinelt	492e5e07c9	lumpy: drop ... Removed because it requires python2 and the upstream repository looks undermaintained.	2022-01-16 02:36:23 +01:00
markuskowa	09819d7eff	Merge pull request #152801 from r-ryantm/auto-update/messer-slim ... messer-slim: 3.6 -> 3.7	2022-01-03 10:50:18 +01:00
R. RyanTM	e4992cdd65	stacks: 2.59 -> 2.60 ... (#149101)	2022-01-02 19:23:58 +01:00
Martin Weinelt	4beaf5301d	python3Packages.xenomapper: move to top-level	2022-01-01 02:09:11 +01:00
R. Ryantm	37d2f5cbb4	messer-slim: 3.6 -> 3.7	2021-12-30 20:32:56 +00:00
Bobby Rong	4fdcad0d6b	Merge pull request #149379 from r-ryantm/auto-update/minimap2 ... minimap2: 2.22 -> 2.23	2021-12-27 18:05:04 +08:00
Felix Buehler	e578d45c10	diamond: switch to fetchFromGitHub	2021-12-23 19:11:17 +01:00
Felix Buehler	865eee2b26	kssd: switch to fetchFromGitHub	2021-12-23 19:11:17 +01:00
Felix Buehler	2f4a86e7d7	messer-slim: switch to fetchFromGitHub	2021-12-23 19:11:17 +01:00
Felix Buehler	e1bd890fb0	niftyseg: switch to fetchFromGitHub	2021-12-23 19:11:17 +01:00
Justin Bedo	fa6244b712	picard-tools: 2.26.6 -> 2.26.9	2021-12-22 22:20:36 +11:00
Justin Bedő	f6e14b6ada	Merge pull request #150628 from jbedo/subread ... subread: init 2.0.3	2021-12-15 13:46:45 +11:00
Justin Bedo	6a1f4a51eb	subread: init 2.0.3	2021-12-14 13:30:23 +11:00
R. Ryantm	d4a5bdc264	seaview: 5.0.4 -> 5.0.5	2021-12-12 15:59:16 +00:00
R. Ryantm	d337b164d6	minimap2: 2.22 -> 2.23	2021-12-07 15:04:36 +00:00
Justin Bedő	711ef56370	Merge pull request #148514 from jbedo/picard ... picard-tools: 2.26.4 -> 2.26.6	2021-12-05 06:56:25 +11:00
Justin Bedo	17e3b75414	picard-tools: 2.26.4 -> 2.26.6	2021-12-04 07:51:31 +11:00
Justin Bedo	1a768ef4da	genmap: init 1.3.0	2021-12-04 06:51:16 +11:00
Justin Bedo	82aef7957d	fastp: 0.23.1 -> 0.23.2	2021-12-02 08:03:17 +11:00
Vikram Narayanan	b1d95dca56	mrtrix: 3.0.2 -> unstable-2021-11-25 ... The latest stable version fails to build with latest eigen (> 3). https://github.com/MRtrix3/mrtrix3/pull/2368	2021-11-30 21:03:53 -08:00
Sergei Trofimovich	8147fb683c	samtools: pull upstream fix for ncurses-6.3 ... Without the fix build on ncurses-6.3 fails as: bam_tview_curses.c:88:5: error: format not a string literal and no format arguments [-Werror=format-security] 88 | mvprintw(y,x,str); | ^~~~~~~~	2021-11-26 13:02:05 +00:00
Justin Bedo	c1eb0dddea	delly: 0.8.7 -> 0.9.1	2021-11-25 21:19:48 +11:00
Robert Scott	ec24bab90e	hmmer: restrict platforms to x86_64 ... technically big-endian powerpc with VMX is also supported, but on x86, SSE is apparently *required* which means we can't build a pure i686 version	2021-11-20 19:17:57 +00:00
Mario Rodas	c8fb7191ad	Merge pull request #143541 from r-ryantm/auto-update/bcftools ... bcftools: 1.13 -> 1.14	2021-11-14 21:14:30 -05:00
Bruno Bzeznik	4e5a245894	obitools3: removed useless python restriction	2021-11-08 07:51:48 +01:00
Felix Buehler	b52ab3b712	pkgs/applications: rename name to pname&version part 2	2021-11-07 14:53:06 +01:00
Justin Bedő	a5ac0a33a7	Merge pull request #144529 from r-ryantm/auto-update/picard-tools ... picard-tools: 2.26.3 -> 2.26.4	2021-11-04 07:19:02 +11:00
R. Ryantm	509a8c298f	picard-tools: 2.26.3 -> 2.26.4	2021-11-03 19:57:00 +00:00
Bruno Bzeznik	0d9ec2d3f0	obitools3: fix build on aarch64 + formatting	2021-11-03 11:59:05 +02:00
R. Ryantm	6282512ef7	dcm2niix: 1.0.20210317 -> 1.0.20211006	2021-10-29 09:34:20 +00:00
R. Ryantm	5f6bd8187b	bcftools: 1.13 -> 1.14	2021-10-29 02:49:14 +00:00
Artturi	493094366b	Merge pull request #142164 from jbedo/last ... last: 1179 -> 1256	2021-10-22 08:37:19 +03:00