annotate README.rst @ 2:e618ab1c78d9 draft

"Release v0.8.4"
author althonos
date Sun, 21 Nov 2021 17:40:58 +0000
parents 0699939e6dd6
children 359232b58f6a
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
1 Hi, I’m GECCO!
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
2 ==============
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
3
1
0699939e6dd6 "Release v0.8.4"
althonos
parents: 0
diff changeset
4 .. image:: https://raw.githubusercontent.com/zellerlab/GECCO/v0.6.2/static/gecco-square.png
0699939e6dd6 "Release v0.8.4"
althonos
parents: 0
diff changeset
5 :target: https://github.com/zellerlab/GECCO/
0699939e6dd6 "Release v0.8.4"
althonos
parents: 0
diff changeset
6
0699939e6dd6 "Release v0.8.4"
althonos
parents: 0
diff changeset
7
0
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
8 🦎 ️Overview
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
9 ---------------
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
10
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
11 GECCO (Gene Cluster prediction with Conditional Random Fields) is a fast
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
12 and scalable method for identifying putative novel Biosynthetic Gene
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
13 Clusters (BGCs) in genomic and metagenomic data using Conditional Random
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
14 Fields (CRFs).
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
15
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
16 |GitLabCI| |License| |Coverage| |Docs| |Source| |Mirror| |Changelog|
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
17 |Issues| |Preprint| |PyPI| |Bioconda| |Versions| |Wheel|
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
18
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
19 🔧 Installing GECCO
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
20 -------------------
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
21
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
22 GECCO is implemented in `Python <https://www.python.org/>`__, and
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
23 supports `all versions <https://endoflife.date/python>`__ from Python
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
24 3.6. It requires additional libraries that can be installed directly
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
25 from `PyPI <https://pypi.org>`__, the Python Package Index.
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
26
1
0699939e6dd6 "Release v0.8.4"
althonos
parents: 0
diff changeset
27 Use `pip <https://pip.pypa.io/en/stable/>`__ to install GECCO on
0699939e6dd6 "Release v0.8.4"
althonos
parents: 0
diff changeset
28 your machine::
0
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
29
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
30 $ pip install gecco-tool
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
31
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
32 If you’d rather use `Conda <https://conda.io>`__, a package is available
1
0699939e6dd6 "Release v0.8.4"
althonos
parents: 0
diff changeset
33 in the `bioconda <https://bioconda.github.io/>`__ channel. You can
0699939e6dd6 "Release v0.8.4"
althonos
parents: 0
diff changeset
34 install with::
0
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
35
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
36 $ conda install -c bioconda gecco
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
37
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
38 This will install GECCO, its dependencies, and the data needed to run
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
39 predictions. This requires around 100MB of data to be downloaded, so it
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
40 could take some time depending on your Internet connection. Once done,
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
41 you will have a ``gecco`` command available in your $PATH.
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
42
1
0699939e6dd6 "Release v0.8.4"
althonos
parents: 0
diff changeset
43 *Note that GECCO uses* `HMMER3 <http://hmmer.org/>`__, *which can
0
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
44 only run on PowerPC and recent x86-64 machines running a POSIX operating
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
45 system. Therefore, Linux and OSX are supported platforms, but GECCO will
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
46 not be able to run on Windows.*
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
47
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
48 🧬 Running GECCO
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
49 -----------------
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
50
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
51 Once ``gecco`` is installed, you can run it from the terminal by giving
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
52 it a FASTA or GenBank file with the genomic sequence you want to
1
0699939e6dd6 "Release v0.8.4"
althonos
parents: 0
diff changeset
53 analyze, as well as an output directory::
0
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
54
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
55 $ gecco run --genome some_genome.fna -o some_output_dir
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
56
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
57 Additional parameters of interest are:
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
58
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
59 - ``--jobs``, which controls the number of threads that will be spawned
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
60 by GECCO whenever a step can be parallelized. The default, *0*, will
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
61 autodetect the number of CPUs on the machine using
1
0699939e6dd6 "Release v0.8.4"
althonos
parents: 0
diff changeset
62 `os.cpu_count <https://docs.python.org/3/library/os.html#os.cpu_count>`__.
0
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
63 - ``--cds``, controlling the minimum number of consecutive genes a BGC
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
64 region must have to be detected by GECCO (default is 3).
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
65 - ``--threshold``, controlling the minimum probability for a gene to be
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
66 considered part of a BGC region. Using a lower number will increase
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
67 the number (and possibly length) of predictions, but reduce accuracy.
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
68
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
69 🔖 Reference
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
70 -------------
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
71
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
72 GECCO can be cited using the following preprint:
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
73
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
74 **Accurate de novo identification of biosynthetic gene clusters with
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
75 GECCO**. Laura M Carroll, Martin Larralde, Jonas Simon Fleck, Ruby
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
76 Ponnudurai, Alessio Milanese, Elisa Cappio Barazzone, Georg Zeller.
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
77 bioRxiv 2021.05.03.442509;
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
78 `doi:10.1101/2021.05.03.442509 <https://doi.org/10.1101/2021.05.03.442509>`__
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
79
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
80 💭 Feedback
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
81 ------------
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
82
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
83 ⚠️ Issue Tracker
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
84 ~~~~~~~~~~~~~~~~
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
85
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
86 Found a bug ? Have an enhancement request ? Head over to the `GitHub
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
87 issue tracker <https://github.com/zellerlab/GECCO/issues>`__ if you need
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
88 to report or ask something. If you are filing in on a bug, please
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
89 include as much information as you can about the issue, and try to
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
90 recreate the same bug in a simple, easily reproducible situation.
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
91
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
92 🏗️ Contributing
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
93 ~~~~~~~~~~~~~~~~
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
94
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
95 Contributions are more than welcome! See
2
e618ab1c78d9 "Release v0.8.4"
althonos
parents: 1
diff changeset
96 `CONTRIBUTING.md <https://github.com/zellerlab/GECCO/blob/master/CONTRIBUTING.md>`__
0
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
97 for more details.
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
98
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
99 ⚖️ License
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
100 ----------
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
101
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
102 This software is provided under the `GNU General Public License v3.0 or
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
103 later <https://choosealicense.com/licenses/gpl-3.0/>`__. GECCO is
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
104 developped by the `Zeller
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
105 Team <https://www.embl.de/research/units/scb/zeller/index.html>`__ at
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
106 the `European Molecular Biology Laboratory <https://www.embl.de/>`__ in
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
107 Heidelberg.
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
108
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
109 .. |GitLabCI| image:: https://img.shields.io/gitlab/pipeline/grp-zeller/GECCO/master?gitlab_url=https%3A%2F%2Fgit.embl.de&style=flat-square&maxAge=600
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
110 :target: https://git.embl.de/grp-zeller/GECCO/-/pipelines/
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
111 .. |License| image:: https://img.shields.io/badge/license-GPLv3-blue.svg?style=flat-square&maxAge=2678400
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
112 :target: https://choosealicense.com/licenses/gpl-3.0/
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
113 .. |Coverage| image:: https://img.shields.io/codecov/c/gh/zellerlab/GECCO?style=flat-square&maxAge=600
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
114 :target: https://codecov.io/gh/zellerlab/GECCO/
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
115 .. |Docs| image:: https://img.shields.io/badge/docs-gecco.embl.de-green.svg?maxAge=2678400&style=flat-square
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
116 :target: https://gecco.embl.de
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
117 .. |Source| image:: https://img.shields.io/badge/source-GitHub-303030.svg?maxAge=2678400&style=flat-square
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
118 :target: https://github.com/zellerlab/GECCO/
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
119 .. |Mirror| image:: https://img.shields.io/badge/mirror-EMBL-009f4d?style=flat-square&maxAge=2678400
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
120 :target: https://git.embl.de/grp-zeller/GECCO/
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
121 .. |Changelog| image:: https://img.shields.io/badge/keep%20a-changelog-8A0707.svg?maxAge=2678400&style=flat-square
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
122 :target: https://github.com/zellerlab/GECCO/blob/master/CHANGELOG.md
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
123 .. |Issues| image:: https://img.shields.io/github/issues/zellerlab/GECCO.svg?style=flat-square&maxAge=600
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
124 :target: https://github.com/zellerlab/GECCO/issues
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
125 .. |Preprint| image:: https://img.shields.io/badge/preprint-bioRxiv-darkblue?style=flat-square&maxAge=2678400
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
126 :target: https://www.biorxiv.org/content/10.1101/2021.05.03.442509v1
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
127 .. |PyPI| image:: https://img.shields.io/pypi/v/gecco-tool.svg?style=flat-square&maxAge=3600
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
128 :target: https://pypi.python.org/pypi/gecco-tool
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
129 .. |Bioconda| image:: https://img.shields.io/conda/vn/bioconda/gecco?style=flat-square&maxAge=3600
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
130 :target: https://anaconda.org/bioconda/gecco
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
131 .. |Versions| image:: https://img.shields.io/pypi/pyversions/gecco-tool.svg?style=flat-square&maxAge=3600
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
132 :target: https://pypi.org/project/gecco-tool/#files
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
133 .. |Wheel| image:: https://img.shields.io/pypi/wheel/gecco-tool?style=flat-square&maxAge=3600
1625927fc16f "Release v0.8.4"
althonos
parents:
diff changeset
134 :target: https://pypi.org/project/gecco-tool/#files