-
Notifications
You must be signed in to change notification settings - Fork 7
/
Cargo.toml
125 lines (92 loc) · 3.21 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
[package]
name = "gsearch"
version = "0.1.5"
authors = ["jeanpierre.both@gmail.com", "jianshu.zhao@gatech.edu"]
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 = "gsearchbin"
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"
[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" }
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 = "0.0.11" }
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 = "0.1.3", 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" }
[features]
default = ["annembed_openblas-system"]
annembed_openblas-static = ["annembed/openblas-static"]
annembed_openblas-system = ["annembed/openblas-system"]
annembed_intel-mkl = ["annembed/intel-mkl-static"]
withzmq = ["kmerutils/withzmq"]
simdeez_f = ["hnsw_rs/simdeez_f", "kmerutils/simdeez_f"]