blob: e32a15a70ab731386363f2152978ccad0ba49dde (
plain)
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
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
|
%global _empty_manifest_terminate_build 0
Name: python-minFQ
Version: 1.4.7
Release: 1
Summary: Command line interface for uploading fastq files and monitoring minKNOW for minotour.
License: MIT
URL: https://github.com/LooseLab/minotourcli
Source0: https://mirrors.aliyun.com/pypi/web/packages/f1/d3/a2087265819052338ccba9457caae60a7c12fe1589443c5d301dafaa71e8/minFQ-1.4.7.tar.gz
BuildArch: noarch
Requires: python3-tqdm
Requires: python3-dateutil
Requires: python3-requests
Requires: python3-numpy
Requires: python3-watchdog
Requires: python3-configargparse
Requires: python3-grpcio
Requires: python3-google
Requires: python3-protobuf
Requires: python3-pandas
Requires: python3-ont-fast5-api
Requires: python3-minknow-api
Requires: python3-validators
Requires: python3-grpcio-tools
Requires: python3-toml
%description
A command line client for uploading sequencing metrics from Oxford Nanopore Technologies MinKNOW to a LooseLab minoTour
server instance.
MinFQ only supports minknow core 4.X.X as it uses ONT's minknow-api, which is only compatible with said version of MinKNOW.
However, base called data can be uploaded from any version of MinKNOW/Guppy.
**To install -**
pip install minFQ
**Example Commands**
In the example commands below example parameters are:
- your_user_key: is the long string found in the profile section of your minoTour account.
- url_to_your_minotour_server: Probably 127.0.0.1, could be a remote address like minotour.nottingham.ac.uk
- port_for_your_server: Probably 8000
To monitor both live and fastq data.
minFQ -k [your_user_key] -w /path/to/your/fastq/files -ip 127.0.0.1 -hn
[url_to_your_minotour_server] -p [port_for_your_server]
To monitor just live data from minKNOW.
minFQ -k [your_user_key] -ip 127.0.0.1 -hn [url_to_your_minotour_server]
-p [port_for_your_server] -nf
To monitor live data and enable limited remote control of minKNOW.
minFQ -k [your_user_key] -ip 127.0.0.1 -hn [url_to_your_minotour_server]
-p [port_for_your_server] -nf -rc
To monitor just fastq data.
minFQ -k [your_user_key] -w /path/to/your/fastq/files -hn [url_to_your_minotour_server]
-p [port_for_your_server] -nm
To monitor fastq statistics only. (Note you will not be able to run subsequent analysis on the server which requires sequence data).
minFQ -k [your_user_key] -w /path/to/your/fastq/files -hn [url_to_your_minotour_server]
-p [port_for_your_server] -nm -s
To start an analysis remotely whilst uploading data. Note reference Id may not be required.
minFQ -k [your_user_key] -w /path/to/your/fastq/files -hn [url_to_your_minotour_server]
-p [port_for_your_server] -nm -j [job_id] -r [reference_id]
**minFQ Gui**
We are in the process of rebuilding a minFQ gui. Watch this space.
%package -n python3-minFQ
Summary: Command line interface for uploading fastq files and monitoring minKNOW for minotour.
Provides: python-minFQ
BuildRequires: python3-devel
BuildRequires: python3-setuptools
BuildRequires: python3-pip
%description -n python3-minFQ
A command line client for uploading sequencing metrics from Oxford Nanopore Technologies MinKNOW to a LooseLab minoTour
server instance.
MinFQ only supports minknow core 4.X.X as it uses ONT's minknow-api, which is only compatible with said version of MinKNOW.
However, base called data can be uploaded from any version of MinKNOW/Guppy.
**To install -**
pip install minFQ
**Example Commands**
In the example commands below example parameters are:
- your_user_key: is the long string found in the profile section of your minoTour account.
- url_to_your_minotour_server: Probably 127.0.0.1, could be a remote address like minotour.nottingham.ac.uk
- port_for_your_server: Probably 8000
To monitor both live and fastq data.
minFQ -k [your_user_key] -w /path/to/your/fastq/files -ip 127.0.0.1 -hn
[url_to_your_minotour_server] -p [port_for_your_server]
To monitor just live data from minKNOW.
minFQ -k [your_user_key] -ip 127.0.0.1 -hn [url_to_your_minotour_server]
-p [port_for_your_server] -nf
To monitor live data and enable limited remote control of minKNOW.
minFQ -k [your_user_key] -ip 127.0.0.1 -hn [url_to_your_minotour_server]
-p [port_for_your_server] -nf -rc
To monitor just fastq data.
minFQ -k [your_user_key] -w /path/to/your/fastq/files -hn [url_to_your_minotour_server]
-p [port_for_your_server] -nm
To monitor fastq statistics only. (Note you will not be able to run subsequent analysis on the server which requires sequence data).
minFQ -k [your_user_key] -w /path/to/your/fastq/files -hn [url_to_your_minotour_server]
-p [port_for_your_server] -nm -s
To start an analysis remotely whilst uploading data. Note reference Id may not be required.
minFQ -k [your_user_key] -w /path/to/your/fastq/files -hn [url_to_your_minotour_server]
-p [port_for_your_server] -nm -j [job_id] -r [reference_id]
**minFQ Gui**
We are in the process of rebuilding a minFQ gui. Watch this space.
%package help
Summary: Development documents and examples for minFQ
Provides: python3-minFQ-doc
%description help
A command line client for uploading sequencing metrics from Oxford Nanopore Technologies MinKNOW to a LooseLab minoTour
server instance.
MinFQ only supports minknow core 4.X.X as it uses ONT's minknow-api, which is only compatible with said version of MinKNOW.
However, base called data can be uploaded from any version of MinKNOW/Guppy.
**To install -**
pip install minFQ
**Example Commands**
In the example commands below example parameters are:
- your_user_key: is the long string found in the profile section of your minoTour account.
- url_to_your_minotour_server: Probably 127.0.0.1, could be a remote address like minotour.nottingham.ac.uk
- port_for_your_server: Probably 8000
To monitor both live and fastq data.
minFQ -k [your_user_key] -w /path/to/your/fastq/files -ip 127.0.0.1 -hn
[url_to_your_minotour_server] -p [port_for_your_server]
To monitor just live data from minKNOW.
minFQ -k [your_user_key] -ip 127.0.0.1 -hn [url_to_your_minotour_server]
-p [port_for_your_server] -nf
To monitor live data and enable limited remote control of minKNOW.
minFQ -k [your_user_key] -ip 127.0.0.1 -hn [url_to_your_minotour_server]
-p [port_for_your_server] -nf -rc
To monitor just fastq data.
minFQ -k [your_user_key] -w /path/to/your/fastq/files -hn [url_to_your_minotour_server]
-p [port_for_your_server] -nm
To monitor fastq statistics only. (Note you will not be able to run subsequent analysis on the server which requires sequence data).
minFQ -k [your_user_key] -w /path/to/your/fastq/files -hn [url_to_your_minotour_server]
-p [port_for_your_server] -nm -s
To start an analysis remotely whilst uploading data. Note reference Id may not be required.
minFQ -k [your_user_key] -w /path/to/your/fastq/files -hn [url_to_your_minotour_server]
-p [port_for_your_server] -nm -j [job_id] -r [reference_id]
**minFQ Gui**
We are in the process of rebuilding a minFQ gui. Watch this space.
%prep
%autosetup -n minFQ-1.4.7
%build
%py3_build
%install
%py3_install
install -d -m755 %{buildroot}/%{_pkgdocdir}
if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi
if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi
if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi
if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi
pushd %{buildroot}
if [ -d usr/lib ]; then
find usr/lib -type f -printf "\"/%h/%f\"\n" >> filelist.lst
fi
if [ -d usr/lib64 ]; then
find usr/lib64 -type f -printf "\"/%h/%f\"\n" >> filelist.lst
fi
if [ -d usr/bin ]; then
find usr/bin -type f -printf "\"/%h/%f\"\n" >> filelist.lst
fi
if [ -d usr/sbin ]; then
find usr/sbin -type f -printf "\"/%h/%f\"\n" >> filelist.lst
fi
touch doclist.lst
if [ -d usr/share/man ]; then
find usr/share/man -type f -printf "\"/%h/%f.gz\"\n" >> doclist.lst
fi
popd
mv %{buildroot}/filelist.lst .
mv %{buildroot}/doclist.lst .
%files -n python3-minFQ -f filelist.lst
%dir %{python3_sitelib}/*
%files help -f doclist.lst
%{_docdir}/*
%changelog
* Tue Jun 20 2023 Python_Bot <Python_Bot@openeuler.org> - 1.4.7-1
- Package Spec generated
|
