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).
2 years ago
Thomas Gerbet
44c1590f1f
bayescan: fix the build
...
Moved back to C++14 to avoid the new errors and warnings introduced with
C++17.
2 years ago
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.
2 years ago
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.
2 years ago
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
2 years ago
Luis Pedro Coelho
596c5e7ea2
Static bwa
...
AR needs to be passed specifically on the command line
2 years ago
Luis Pedro Coelho
4758873378
Static build for samtools
...
Curses is not supported (it may be possible to support it)
2 years ago
Luis Pedro Coelho
0b1c28d5a1
Static build for megahit
2 years ago
R. Ryantm
a82b1b63c3
blast: 2.12.0 -> 2.13.0
2 years ago
Rocky Breslow
d1c3fea7ec
dcm2niix: support usage of suggested Cloudflare zlib
2 years ago
Rocky Breslow
9019ce0106
dcm2niix: add maintainer
...
Also, fix grammatical error in long description.
2 years ago
Ben Siraphob
259fa13d53
treewide: remove nativeBuildInputs that are in stdenv
2 years ago
Fabián Heredia Montiel
8a9d5e296b
cmtk: add `-std=c++11` to fix build on gcc11
2 years ago
Malo Bourgon
0e802eafad
treewide: add meta.mainProgram to many packages
2 years ago
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.
2 years ago
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)
2 years ago
Ben Siraphob
21faf9fc29
treewide: move autoconf, automake to nativeBuildInputs
2 years ago
Rocky Breslow
603e9d7b64
flywheel-cli: init at 16.2.0
2 years ago
Felix Buehler
3bc5196252
treewide: rename name to pname&version
2 years ago
Armeen Mahdian
6cfaf0a464
eggnog-mapper: 1.0.3 -> 2.1.7
...
https://github.com/eggnogdb/eggnog-mapper/releases
2 years ago
Bruno Bzeznik
7d62054650
angsd: init at 0.937
2 years ago
Matthew Wakefield
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
Justin Bedo
89eff15f31
last: 1260 -> 1268
2 years ago
Felix Buehler
fe7678ca81
raxml-mpi: remove appendToName to have a consistent package name for repology
2 years ago
Felix Buehler
13dca33cdc
neuron-mpi: remove appendToName to have a consistent package name for repology
2 years ago
R. Ryantm
1e7c64aae1
bcftools: 1.14 -> 1.15
2 years ago
R. Ryantm
ce9d28cc49
picard-tools: 2.26.10 -> 2.26.11
2 years ago
Scriptkiddi
4e60a4823b
febio-studio: init at 1.6.1
2 years ago
R. RyanTM
94f61e4c82
SPAdes: 3.15.3 -> 3.15.4
...
(#158938 )
2 years ago
R. Ryantm
240262f564
messer-slim: 3.7 -> 3.7.1
2 years ago
R. Ryantm
8a4946df2d
picard-tools: 2.26.9 -> 2.26.10
2 years ago
R. Ryantm
8bb7bc766f
mosdepth: 0.3.2 -> 0.3.3
2 years ago
R. Ryantm
6ca5bb6e20
last: 1256 -> 1260
2 years ago
Renaud
2ddcc2b369
hisat2: update homepage
...
and use SPDX 3.0 license identifier
2 years ago
R. Ryantm
d44e044d84
kallisto: 0.46.2 -> 0.48.0
2 years ago
Bruno Bzeznik
b6fa4975cf
repseek: init at 9Sep2014 ( #148017 )
...
Co-authored-by: Sandro <sandro.jaeckel@gmail.com>
2 years ago
R. RyanTM
8bd7d6d6e0
star: 2.7.9a -> 2.7.10a
...
(#155868 )
2 years ago
R. Ryantm
ebb9e86bf9
bowtie2: 2.4.4 -> 2.4.5
2 years ago
Justin Bedő
c24af4642c
sambamba: 0.8.1 -> 0.8.2 ( #155972 )
...
Co-authored-by: Sandro <sandro.jaeckel@gmail.com>
2 years ago
R. Ryantm
227011af59
deeptools: 3.5.0 -> 3.5.1
2 years ago
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>
2 years ago
Robert Schütz
d5cceedbd1
python,pythonPackages: make aliases
...
Since aliases are disallowed in nixpkgs, this makes usage of Python 2
which is EOL more explicit.
2 years ago
Robert Schütz
65e959eb9a
tebreak: also use python3 for tests
2 years ago
Martin Weinelt
492e5e07c9
lumpy: drop
...
Removed because it requires python2 and the upstream repository looks
undermaintained.
2 years ago
R. RyanTM
e4992cdd65
stacks: 2.59 -> 2.60
...
(#149101 )
2 years ago
Martin Weinelt
4beaf5301d
python3Packages.xenomapper: move to top-level
2 years ago
R. Ryantm
37d2f5cbb4
messer-slim: 3.6 -> 3.7
2 years ago
Felix Buehler
e578d45c10
diamond: switch to fetchFromGitHub
2 years ago
Felix Buehler
865eee2b26
kssd: switch to fetchFromGitHub
2 years ago
Felix Buehler
2f4a86e7d7
messer-slim: switch to fetchFromGitHub
2 years ago