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
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
|
%global _empty_manifest_terminate_build 0
Name: python-biobb-pmx
Version: 3.8.1
Release: 1
Summary: Biobb_pmx is the Biobb module collection to perform PMX (http://pmx.mpibpc.mpg.de) executions.
License: Apache Software License
URL: https://github.com/bioexcel/biobb_pmx
Source0: https://mirrors.aliyun.com/pypi/web/packages/4c/bf/0cd5c2f2adf3995be6e0df092e2db4a06fae039756be1c076d734d249409/biobb_pmx-3.8.1.tar.gz
BuildArch: noarch
Requires: python3-biobb-common
%description
[](https://biobb-pmx.readthedocs.io/en/latest/?badge=latest)
[](https://anaconda.org/bioconda/biobb_pmx)
[](https://quay.io/repository/biocontainers/biobb_pmx)
[](https://opensource.org/licenses/Apache-2.0)
# biobb_pmx
### Introduction
Biobb_pmx is the Biobb module collection to perform PMX (http://pmx.mpibpc.mpg.de) executions.
Biobb (BioExcel building blocks) packages are Python building blocks that
create new layer of compatibility and interoperability over popular
bioinformatics tools.
The latest documentation of this package can be found in our readthedocs site:
[latest API documentation](http://biobb_pmx.readthedocs.io/en/latest/).
### Version
v3.8.1 2022.3
### Installation
Using PIP:
> **Important:** PIP only installs the package. All the dependencies must be installed separately. To perform a complete installation, please use ANACONDA or DOCKER.
* Installation:
pip install "biobb_pmx>=3.8.1"
* Usage: [Python API documentation](https://biobb-pmx.readthedocs.io/en/latest/modules.html)
Using ANACONDA:
* Installation:
conda install -c bioconda "biobb_pmx>=3.8.1"
* Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-pmx.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-pmx.readthedocs.io/en/latest/command_line.html)
Using DOCKER:
* Installation:
docker pull quay.io/biocontainers/biobb_pmx:3.8.1--pyhdfd78af_0
* Usage:
docker run quay.io/biocontainers/biobb_pmx:3.8.1--pyhdfd78af_0 <command>
[//]: # (Using SINGULARITY:)
[//]: # (**MacOS users**: it's strongly recommended to avoid Singularity and use **Docker** as containerization system.)
[//]: # (* Installation:)
[//]: # (singularity pull --name biobb_pmx.sif shub://bioexcel/biobb_pmx)
[//]: # (* Usage:)
[//]: # (singularity exec biobb_pmx.sif <command>)
The command list and specification can be found at the [Command Line documentation](https://biobb-pmx.readthedocs.io/en/latest/command_line.html).
### Copyright & Licensing
This software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)).
* (c) 2015-2021 [Barcelona Supercomputing Center](https://www.bsc.es/)
* (c) 2015-2021 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)
Licensed under the
[Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details.
%package -n python3-biobb-pmx
Summary: Biobb_pmx is the Biobb module collection to perform PMX (http://pmx.mpibpc.mpg.de) executions.
Provides: python-biobb-pmx
BuildRequires: python3-devel
BuildRequires: python3-setuptools
BuildRequires: python3-pip
%description -n python3-biobb-pmx
[](https://biobb-pmx.readthedocs.io/en/latest/?badge=latest)
[](https://anaconda.org/bioconda/biobb_pmx)
[](https://quay.io/repository/biocontainers/biobb_pmx)
[](https://opensource.org/licenses/Apache-2.0)
# biobb_pmx
### Introduction
Biobb_pmx is the Biobb module collection to perform PMX (http://pmx.mpibpc.mpg.de) executions.
Biobb (BioExcel building blocks) packages are Python building blocks that
create new layer of compatibility and interoperability over popular
bioinformatics tools.
The latest documentation of this package can be found in our readthedocs site:
[latest API documentation](http://biobb_pmx.readthedocs.io/en/latest/).
### Version
v3.8.1 2022.3
### Installation
Using PIP:
> **Important:** PIP only installs the package. All the dependencies must be installed separately. To perform a complete installation, please use ANACONDA or DOCKER.
* Installation:
pip install "biobb_pmx>=3.8.1"
* Usage: [Python API documentation](https://biobb-pmx.readthedocs.io/en/latest/modules.html)
Using ANACONDA:
* Installation:
conda install -c bioconda "biobb_pmx>=3.8.1"
* Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-pmx.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-pmx.readthedocs.io/en/latest/command_line.html)
Using DOCKER:
* Installation:
docker pull quay.io/biocontainers/biobb_pmx:3.8.1--pyhdfd78af_0
* Usage:
docker run quay.io/biocontainers/biobb_pmx:3.8.1--pyhdfd78af_0 <command>
[//]: # (Using SINGULARITY:)
[//]: # (**MacOS users**: it's strongly recommended to avoid Singularity and use **Docker** as containerization system.)
[//]: # (* Installation:)
[//]: # (singularity pull --name biobb_pmx.sif shub://bioexcel/biobb_pmx)
[//]: # (* Usage:)
[//]: # (singularity exec biobb_pmx.sif <command>)
The command list and specification can be found at the [Command Line documentation](https://biobb-pmx.readthedocs.io/en/latest/command_line.html).
### Copyright & Licensing
This software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)).
* (c) 2015-2021 [Barcelona Supercomputing Center](https://www.bsc.es/)
* (c) 2015-2021 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)
Licensed under the
[Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details.
%package help
Summary: Development documents and examples for biobb-pmx
Provides: python3-biobb-pmx-doc
%description help
[](https://biobb-pmx.readthedocs.io/en/latest/?badge=latest)
[](https://anaconda.org/bioconda/biobb_pmx)
[](https://quay.io/repository/biocontainers/biobb_pmx)
[](https://opensource.org/licenses/Apache-2.0)
# biobb_pmx
### Introduction
Biobb_pmx is the Biobb module collection to perform PMX (http://pmx.mpibpc.mpg.de) executions.
Biobb (BioExcel building blocks) packages are Python building blocks that
create new layer of compatibility and interoperability over popular
bioinformatics tools.
The latest documentation of this package can be found in our readthedocs site:
[latest API documentation](http://biobb_pmx.readthedocs.io/en/latest/).
### Version
v3.8.1 2022.3
### Installation
Using PIP:
> **Important:** PIP only installs the package. All the dependencies must be installed separately. To perform a complete installation, please use ANACONDA or DOCKER.
* Installation:
pip install "biobb_pmx>=3.8.1"
* Usage: [Python API documentation](https://biobb-pmx.readthedocs.io/en/latest/modules.html)
Using ANACONDA:
* Installation:
conda install -c bioconda "biobb_pmx>=3.8.1"
* Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-pmx.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-pmx.readthedocs.io/en/latest/command_line.html)
Using DOCKER:
* Installation:
docker pull quay.io/biocontainers/biobb_pmx:3.8.1--pyhdfd78af_0
* Usage:
docker run quay.io/biocontainers/biobb_pmx:3.8.1--pyhdfd78af_0 <command>
[//]: # (Using SINGULARITY:)
[//]: # (**MacOS users**: it's strongly recommended to avoid Singularity and use **Docker** as containerization system.)
[//]: # (* Installation:)
[//]: # (singularity pull --name biobb_pmx.sif shub://bioexcel/biobb_pmx)
[//]: # (* Usage:)
[//]: # (singularity exec biobb_pmx.sif <command>)
The command list and specification can be found at the [Command Line documentation](https://biobb-pmx.readthedocs.io/en/latest/command_line.html).
### Copyright & Licensing
This software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)).
* (c) 2015-2021 [Barcelona Supercomputing Center](https://www.bsc.es/)
* (c) 2015-2021 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)
Licensed under the
[Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details.
%prep
%autosetup -n biobb_pmx-3.8.1
%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-biobb-pmx -f filelist.lst
%dir %{python3_sitelib}/*
%files help -f doclist.lst
%{_docdir}/*
%changelog
* Tue Jun 20 2023 Python_Bot <Python_Bot@openeuler.org> - 3.8.1-1
- Package Spec generated
|
