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.
2 years ago
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.
2 years ago
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
2 years ago
596c5e7ea2
Static bwa
...
AR needs to be passed specifically on the command line
2 years ago
4758873378
Static build for samtools
...
Curses is not supported (it may be possible to support it)
2 years ago
0b1c28d5a1
Static build for megahit
2 years ago
a82b1b63c3
blast: 2.12.0 -> 2.13.0
2 years ago
d1c3fea7ec
dcm2niix: support usage of suggested Cloudflare zlib
2 years ago
9019ce0106
dcm2niix: add maintainer
...
Also, fix grammatical error in long description.
2 years ago
259fa13d53
treewide: remove nativeBuildInputs that are in stdenv
2 years ago
8a9d5e296b
cmtk: add `-std=c++11` to fix build on gcc11
2 years ago
0e802eafad
treewide: add meta.mainProgram to many packages
2 years ago
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.
2 years ago
60f1e6ffe2
ncbi_tools: remove after being marked broken for over two years
...
It was marked in commit b9948fedc6
2 years ago
21faf9fc29
treewide: move autoconf, automake to nativeBuildInputs
2 years ago
603e9d7b64
flywheel-cli: init at 16.2.0
2 years ago
3bc5196252
treewide: rename name to pname&version
2 years ago
6cfaf0a464
eggnog-mapper: 1.0.3 -> 2.1.7
...
https://github.com/eggnogdb/eggnog-mapper/releases
2 years ago
7d62054650
angsd: init at 0.937
2 years ago
e85b65f986
minimap2: enable aarch64 builds ( #161169 )
...
Co-authored-by: Bobby Rong <rjl931189261@126.com>
Co-authored-by: Sandro <sandro.jaeckel@gmail.com>
2 years ago
89eff15f31
last: 1260 -> 1268
2 years ago
fe7678ca81
raxml-mpi: remove appendToName to have a consistent package name for repology
2 years ago
13dca33cdc
neuron-mpi: remove appendToName to have a consistent package name for repology
2 years ago
1e7c64aae1
bcftools: 1.14 -> 1.15
2 years ago
ce9d28cc49
picard-tools: 2.26.10 -> 2.26.11
2 years ago
4e60a4823b
febio-studio: init at 1.6.1
2 years ago
94f61e4c82
SPAdes: 3.15.3 -> 3.15.4
...
(#158938 )
2 years ago
240262f564
messer-slim: 3.7 -> 3.7.1
2 years ago
8a4946df2d
picard-tools: 2.26.9 -> 2.26.10
2 years ago
8bb7bc766f
mosdepth: 0.3.2 -> 0.3.3
2 years ago
6ca5bb6e20
last: 1256 -> 1260
2 years ago
2ddcc2b369
hisat2: update homepage
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and use SPDX 3.0 license identifier
2 years ago
d44e044d84
kallisto: 0.46.2 -> 0.48.0
2 years ago
b6fa4975cf
repseek: init at 9Sep2014 ( #148017 )
...
Co-authored-by: Sandro <sandro.jaeckel@gmail.com>
2 years ago
8bd7d6d6e0
star: 2.7.9a -> 2.7.10a
...
(#155868 )
2 years ago
ebb9e86bf9
bowtie2: 2.4.4 -> 2.4.5
2 years ago
c24af4642c
sambamba: 0.8.1 -> 0.8.2 ( #155972 )
...
Co-authored-by: Sandro <sandro.jaeckel@gmail.com>
2 years ago
227011af59
deeptools: 3.5.0 -> 3.5.1
2 years ago
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>
2 years ago
d5cceedbd1
python,pythonPackages: make aliases
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Since aliases are disallowed in nixpkgs, this makes usage of Python 2
which is EOL more explicit.
2 years ago
65e959eb9a
tebreak: also use python3 for tests
2 years ago
492e5e07c9
lumpy: drop
...
Removed because it requires python2 and the upstream repository looks
undermaintained.
2 years ago
e4992cdd65
stacks: 2.59 -> 2.60
...
(#149101 )
2 years ago
4beaf5301d
python3Packages.xenomapper: move to top-level
2 years ago
37d2f5cbb4
messer-slim: 3.6 -> 3.7
2 years ago
e578d45c10
diamond: switch to fetchFromGitHub
2 years ago
865eee2b26
kssd: switch to fetchFromGitHub
2 years ago
2f4a86e7d7
messer-slim: switch to fetchFromGitHub
2 years ago
e1bd890fb0
niftyseg: switch to fetchFromGitHub
2 years ago
fa6244b712
picard-tools: 2.26.6 -> 2.26.9
2 years ago
Theodore Ni