-
Notifications
You must be signed in to change notification settings - Fork 7
/
Copy pathCargo.toml
131 lines (97 loc) · 3.31 KB
/
Cargo.toml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
[package]
name = "gsearch"
version = "0.1.5"
authors = ["[email protected]", "[email protected]"]
repository = "https://github.com/jean-pierreBoth/gsearch"
keywords = ["hnsw", "probminhash", "bacteria"]
edition = "2021"
license = "MIT OR Apache-2.0"
description = "genome classification, probminhash hnsw, genome search"
[[bin]]
name = "gsearch"
path = "src/bin/gsearch.rs"
[[bin]]
name = "reformat"
path = "src/bin/reformat.rs"
[[bin]]
name = "superani"
path = "src/bin/superani.rs"
[[bin]]
name = "FragGeneScanRs"
path = "src/bin/FragGeneScanRs.rs"
[[bin]]
name = "superaai"
path = "src/bin/superaai.rs"
[[bin]]
name = "bigsig"
path = "src/bin/bigsig.rs"
[[bin]]
name = "hnsw2knn"
path = "src/bin/hnsw2knn.rs"
[lib]
path = "src/lib.rs"
[dependencies]
# default is version spec is ^ meaning can update up to max non null version number
# cargo doc --no-deps avoid dependencies doc generation
#
serde = { version = "1.0", features = ["derive"] }
serde_json = { version = "1.0" }
num = { version = "0.4" }
chrono = { version = "0.4" }
memory-stats = { version = "1.1", features = ["always_use_statm"] }
# for //
crossbeam-utils = { version = "0.8" }
crossbeam-channel = { version = "0.5" }
crossbeam = { version = "0.8" }
concurrent-queue = { version = "2.5" }
parking_lot = { version = "0.12" }
rayon = { version = "1.10" }
num_cpus = { version = "1.13.0" }
cpu-time = { version = "1.0" }
needletail = { version = "0.5" }
clap = { version = "4.5" }
fxhash = { version = "0.2" }
##
seq_io = "0.3.1"
thiserror = "1.0.25"
strum = "0.21.0"
strum_macros = "0.21.0"
#frag_gene_scan_rs = "1.1.0"
frag_gene_scan_rs = { git = "https://gitlab.com/Jianshu_Zhao/fraggenescanrs" }
skani = "0.1.0"
sourmash = "0.15.1"
bigsig = "0.1.0"
#hmmer-rs-2 = "0.2.1"
probminhash = { version = "0.1.11" }
# probminhash = {git = "https://github.com/jean-pierreBoth/probminhash"}
# probminhash = {path = "../probminhash"}
hnsw_rs = { version = "=0.3.1" }
# hnsw_rs = { git = "https://github.com/jean-pierreBoth/hnswlib-rs" }
# hnsw_rs = {git = "https://gitlab.com/jpboth/hnswlib-rs.git"}
# hnsw_rs = { path = "../hnswlib-rs" }
# kmerutils = { path = "../kmerutils" }
# kmerutils = { git = "https://github.com/jean-pierreBoth/kmerutils" }
# kmerutils = {git = "https://gitlab.com/jpboth/kmerutils.git"}
kmerutils = { version = "=0.0.12" }
lazy_static = { version = "1.4" }
# decreasing order of log for debug build : (max_level_)trace debug info warn error off
# decreasing order of log for release build (release_max_level_) .. idem
#log = { version = "0.4", features = ["max_level_trace", "release_max_level_trace"] }
log = { version = "0.4" }
env_logger = { version = "0.11" }
# optional dependency to embed hnsw graph
annembed = { version = "=0.1.4", optional = true }
# annembed = { git = "https://github.com/jean-pierreBoth/annembed", optional = true }
#annembed = { path = "../annembed", optional = true }
# no more pb with between anyhow intel-mkl-src
anyhow = { version = "1.0.58" }
csv = { version = "1.1" }
num-traits = "0.2.19"
[features]
default = []
annembed_openblas-static = ["annembed/openblas-static"]
annembed_openblas-system = ["annembed/openblas-system"]
annembed_intel-mkl = ["annembed/intel-mkl-static"]
annembed_accelerate = ["annembed/macos-accelerate"]
withzmq = ["kmerutils/withzmq"]
simdeez_f = ["hnsw_rs/simdeez_f", "kmerutils/simdeez_f"]