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687 commits

Author SHA1 Message Date
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
Justin Bedő 4e83abb0cb
Merge pull request #142199 from jbedo/picard 
picard-tools: 2.26.2 -> 2.26.3
 2021-10-22 14:36:28 +11:00
Justin Bedo f120d4daf4
picard-tools: 2.26.2 -> 2.26.3 2021-10-19 21:24:56 +11:00
Justin Bedo 08489c40ab
fastp: 0.22.0 -> 0.23.1 2021-10-19 21:09:05 +11:00
Justin Bedo f7414542d0
last: 1179 -> 1256 2021-10-19 13:23:14 +11:00
Justin Bedo 02a1a2b3c8
samtools: 1.11 -> 1.13 2021-10-12 10:19:36 +11:00
figsoda 3109ff5765 treewide: avoid use of lib.optional with list in inputs 2021-10-04 13:02:42 -04:00
R. RyanTM 5becb56f71
star: 2.7.8a -> 2.7.9a 2021-09-24 10:37:28 +08:00
Bobby Rong c25465873c
Merge pull request #138022 from natsukium/blast/update 
blast: 2.11.0 -> 2.12.0
 2021-09-23 14:48:35 +08:00
Guillaume Girol 4bc83aaffa
Merge pull request #136489 from ehmry/nimPackages 
nimpackages / buildNimPackage
 2021-09-22 18:35:38 +00:00
figsoda 0e575a459e
Merge pull request #137974 from r-ryantm/auto-update/bowtie 
bowtie: 1.3.0 -> 1.3.1
 2021-09-17 22:52:43 -04:00
Bobby Rong 12d38c57c3
Merge pull request #134133 from Kranzes/auto-update/SPAdes 
SPAdes: 3.15.2 -> 3.15.3
 2021-09-16 17:09:24 +08:00
Tomoya Otabi 1e9bd43214 blast: 2.11.0 -> 2.12.0 2021-09-15 15:33:44 +00:00
R. RyanTM 7bf7c9b92b bowtie: 1.3.0 -> 1.3.1 2021-09-15 07:35:44 +00:00
R. RyanTM e676fdcb90 picard-tools: 2.26.0 -> 2.26.2 2021-09-14 19:53:25 +00:00