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Author SHA1 Message Date
R. Ryantm d89c2af58a bowtie2: 2.5.1 -> 2.5.2 2023-10-14 10:06:32 +00:00
OTABI Tomoya e8f331680d
Merge pull request #259418 from natsukium/blast-bin/update 
blast-bin: 2.13.0 -> 2.14.1
 2023-10-12 23:49:59 +09:00
natsukium d60c85fb75
blast-bin: add sourceProvenance to meta 2023-10-07 10:12:24 +09:00
natsukium 3dc0f1e7b7
blast-bin: 2.13.0 -> 2.14.1 
Changelog: https://www.ncbi.nlm.nih.gov/books/NBK131777/#_Blast_ReleaseNotes_BLAST_2_14_1_August_2_
 2023-10-07 01:59:18 +09:00
natsukium 96178c29a4
truvari: 4.0.0 -> 4.1.0 
Diff: https://github.com/ACEnglish/truvari/compare/v4.0.0...v4.1.0

Changelog: https://github.com/ACEnglish/truvari/releases/tag/v4.1.0
 2023-10-07 01:30:27 +09:00
natsukium 776b2694a3
truvari: add meta.changelog 2023-10-07 01:30:27 +09:00
Justin Bedo e347cca9f8
delly: 1.1.6 -> 1.1.7 
Diff: https://github.com/dellytools/delly/compare/v1.1.6...1.1.7
 2023-10-06 14:12:05 +11:00
Weijia Wang 0396d3b0fb
Merge pull request #258254 from r-ryantm/auto-update/nest-mpi 
nest-mpi: 3.5 -> 3.6
 2023-10-01 03:53:05 +02:00
Weijia Wang d2f79d7443
Merge pull request #257369 from r-ryantm/auto-update/stacks 
stacks: 2.62 -> 2.65
 2023-10-01 03:20:19 +02:00
Weijia Wang 293062bbdb stacks: set platforms 2023-10-01 02:26:34 +02:00
Weijia Wang 00d57438ab
Merge pull request #256805 from r-ryantm/auto-update/neuron-mpi 
neuron-mpi: 8.2.2 -> 8.2.3
 2023-10-01 00:44:58 +02:00
R. Ryantm a78f4ed541 nest-mpi: 3.5 -> 3.6 2023-09-30 18:54:13 +00:00
natsukium c90607c5a7
dssp: 4.4.2 -> 4.4.3 
Diff: https://github.com/PDB-REDO/dssp/compare/refs/tags/v4.4.2...v4.4.3

Changelog: https://github.com/PDB-REDO/libcifpp/releases/tag/refs/tags/v4.4.3
 2023-09-28 15:38:55 +09:00
R. Ryantm 90361534b7 stacks: 2.62 -> 2.65 2023-09-26 03:03:04 +00:00
github-actions[bot] 3e52e5929d
Merge master into staging-next 2023-09-25 12:01:02 +00:00
Mario Rodas b289d79b8d hmmer: add changelog to meta 2023-09-24 04:24:00 +00:00
R. Ryantm 272a0e1edb hmmer: 3.3.2 -> 3.4 2023-09-24 04:23:47 +00:00
R. Ryantm d660b340ee neuron-mpi: 8.2.2 -> 8.2.3 2023-09-23 02:33:53 +00:00
github-actions[bot] 583877beb2
Merge master into staging-next 2023-09-22 18:01:00 +00:00
László Kupcsik c678bba28c trimmomatic: init at 0.39 
Co-authored-by: Anderson Torres <torres.anderson.85@protonmail.com>
 2023-09-22 13:50:18 -03:00
github-actions[bot] 3245a21e71
Merge master into staging-next 2023-09-19 06:01:00 +00:00
R. Ryantm 65033fea28 mosdepth: 0.3.4 -> 0.3.5 2023-09-19 00:55:31 +00:00
github-actions[bot] 9fd6a65a3a
Merge master into staging-next 2023-09-18 12:01:07 +00:00
R. Ryantm e567f85a64 blast: 2.14.0 -> 2.14.1 2023-09-16 03:10:11 +00:00
Alyssa Ross 4a027948f9
Merge remote-tracking branch 'origin/staging-next' into staging 
Conflicts:
	pkgs/applications/radio/soapysdr/default.nix
 2023-09-14 11:31:01 +00:00
Mario Rodas 48780fa239
Merge pull request #250309 from trofi/angsd-fix-parallel 
angsd: pull patch pending upstream inclusion for parallel build fix
 2023-09-13 06:24:00 -05:00
github-actions[bot] 564dc31f47
Merge staging-next into staging 2023-09-12 18:01:30 +00:00
R. Ryantm d5e6e8ac03 veryfasttree: 4.0.2 -> 4.0.3 2023-09-12 06:13:28 +00:00
github-actions[bot] 6d1f33a3ed
Merge staging-next into staging 2023-09-09 12:01:22 +00:00
R. Ryantm ac77a8f7d0 igv: 2.16.1 -> 2.16.2 2023-09-09 05:56:58 +00:00
Sandro Jäckel fccf04b620 treewide: replace -DCMAKE_BUILD_TYPE in cmakeFlags with cmakeBuildType 2023-09-08 14:18:26 +00:00
Ben Darwin 5bbcb4840b mrtrix: unstable-2021-11-25 -> 3.0.4 2023-09-06 12:11:38 -04:00
Pol Dellaiera 55b00aa1f7
ants: update postInstall attribute 2023-09-02 23:09:28 +02:00
Pol Dellaiera ad1e8a5b43
ants: update meta attributes 2023-09-02 23:08:44 +02:00
Pol Dellaiera d04a1a598e
ants: use finalAttrs pattern 2023-09-02 22:18:19 +02:00
Pol Dellaiera 35145f9df0
ants: reformat file using nixpkgs-fmt 2023-09-02 22:17:19 +02:00
R. Ryantm 875e737bfa ants: 2.4.4 -> 2.5.0 2023-09-02 11:57:30 +00:00
Justin Bedő f25f30b17a
Merge pull request #251304 from r-ryantm/auto-update/sambamba 
sambamba: 1.0.0 -> 1.0.1
 2023-09-01 15:30:29 +10:00
github-actions[bot] e79f8fd118
Merge master into staging-next 2023-08-25 18:00:58 +00:00
R. Ryantm e1b695a96f iqtree: 2.2.2.6 -> 2.2.2.7 2023-08-25 12:25:13 +00:00
R. Ryantm d564dfa4d0 sambamba: 1.0.0 -> 1.0.1 2023-08-25 06:20:00 +00:00
github-actions[bot] a451dcf514
Merge master into staging-next 2023-08-24 06:01:14 +00:00
OTABI Tomoya 21943b1829
Merge pull request #248172 from alxsimon/bwa 
bwa-mem2: init at version 2.2.1
 2023-08-24 09:28:34 +09:00
Alexis Simon 556dac0725 bwa-mem2: init at version 2.2.1 
Co-authored-by: OTABI Tomoya <tomoya.otabi@gmail.com>
 2023-08-23 15:02:06 -07:00
github-actions[bot] 56f5b9fafc
Merge staging-next into staging 2023-08-21 12:01:35 +00:00
OTABI Tomoya 325b09c1b5
Merge pull request #249878 from jbedo/last 
last: 1460 -> 1471
 2023-08-21 16:09:10 +09:00
Emery Hemingway ed353dc721 mosdepth: build with Nim-2 2023-08-21 07:32:46 +01:00
Emery Hemingway 9025a583b1 nimPackages.hts: 0.3.4 -> 0.3.23, rename from hts-nim 2023-08-21 07:32:46 +01:00
Sergei Trofimovich f434e83d62 angsd: pull patch pending upstream inclusion for parallel build fix 
Without the change rapallel builds fail occasionally as:

    $ make --shuffle -j
    ...
    g++ -c   -O3 -D__STDC_FORMAT_MACROS   argStruct.cpp
    g++ -c   -O3 -D__STDC_FORMAT_MACROS   ancestral_likes.cpp
    gcc -c   -O3 -D__STDC_FORMAT_MACROS   fet.c
    g++ -c   -O3 -D__STDC_FORMAT_MACROS   abcGL.cpp
    g++ -c   -O3 -D__STDC_FORMAT_MACROS   pop1_read.cpp
    g++ -c   -O3 -D__STDC_FORMAT_MACROS   angsd.cpp
    g++ -c   -O3 -D__STDC_FORMAT_MACROS   abcHWE_F.cpp
    gcc -c   -O3 -D__STDC_FORMAT_MACROS   kprobaln.c
    g++ -c   -O3 -D__STDC_FORMAT_MACROS   mpileup.cpp
    argStruct.cpp:3:10: fatal error: version.h: No such file or directory
        3 | #include "version.h"
          |          ^~~~~~~~~~~
    compilation terminated.
    angsd.cpp:11:10: fatal error: version.h: No such file or directory
       11 | #include "version.h"
          |          ^~~~~~~~~~~
 2023-08-20 08:50:53 +01:00
github-actions[bot] 9145b3fd81
Merge staging-next into staging 2023-08-19 18:01:22 +00:00