Mercurial > repos > althonos > gecco
annotate README.rst @ 11:40a525d0e1fe draft
"Release v0.9.1-alpha2"
| author | althonos |
|---|---|
| date | Wed, 23 Mar 2022 15:19:49 +0000 |
| parents | 359232b58f6a |
| children |
| rev | line source |
|---|---|
| 0 | 1 Hi, I’m GECCO! |
| 2 ============== | |
| 3 | |
| 1 | 4 .. image:: https://raw.githubusercontent.com/zellerlab/GECCO/v0.6.2/static/gecco-square.png |
| 5 :target: https://github.com/zellerlab/GECCO/ | |
| 6 | |
| 7 | |
| 0 | 8 🦎 ️Overview |
| 9 --------------- | |
| 10 | |
| 11 GECCO (Gene Cluster prediction with Conditional Random Fields) is a fast | |
| 12 and scalable method for identifying putative novel Biosynthetic Gene | |
| 13 Clusters (BGCs) in genomic and metagenomic data using Conditional Random | |
| 14 Fields (CRFs). | |
| 15 | |
| 16 |GitLabCI| |License| |Coverage| |Docs| |Source| |Mirror| |Changelog| | |
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17 |Issues| |Preprint| |PyPI| |Bioconda| |Galaxy| |Versions| |Wheel| |
| 0 | 18 |
| 19 🔧 Installing GECCO | |
| 20 ------------------- | |
| 21 | |
| 22 GECCO is implemented in `Python <https://www.python.org/>`__, and | |
| 23 supports `all versions <https://endoflife.date/python>`__ from Python | |
| 24 3.6. It requires additional libraries that can be installed directly | |
| 25 from `PyPI <https://pypi.org>`__, the Python Package Index. | |
| 26 | |
| 1 | 27 Use `pip <https://pip.pypa.io/en/stable/>`__ to install GECCO on |
| 28 your machine:: | |
| 0 | 29 |
| 30 $ pip install gecco-tool | |
| 31 | |
| 32 If you’d rather use `Conda <https://conda.io>`__, a package is available | |
| 1 | 33 in the `bioconda <https://bioconda.github.io/>`__ channel. You can |
| 34 install with:: | |
| 0 | 35 |
| 36 $ conda install -c bioconda gecco | |
| 37 | |
| 38 This will install GECCO, its dependencies, and the data needed to run | |
| 39 predictions. This requires around 100MB of data to be downloaded, so it | |
| 40 could take some time depending on your Internet connection. Once done, | |
| 41 you will have a ``gecco`` command available in your $PATH. | |
| 42 | |
| 1 | 43 *Note that GECCO uses* `HMMER3 <http://hmmer.org/>`__, *which can |
| 0 | 44 only run on PowerPC and recent x86-64 machines running a POSIX operating |
| 45 system. Therefore, Linux and OSX are supported platforms, but GECCO will | |
| 46 not be able to run on Windows.* | |
| 47 | |
| 48 🧬 Running GECCO | |
| 49 ----------------- | |
| 50 | |
| 51 Once ``gecco`` is installed, you can run it from the terminal by giving | |
| 52 it a FASTA or GenBank file with the genomic sequence you want to | |
| 1 | 53 analyze, as well as an output directory:: |
| 0 | 54 |
| 55 $ gecco run --genome some_genome.fna -o some_output_dir | |
| 56 | |
| 57 Additional parameters of interest are: | |
| 58 | |
| 59 - ``--jobs``, which controls the number of threads that will be spawned | |
| 60 by GECCO whenever a step can be parallelized. The default, *0*, will | |
| 61 autodetect the number of CPUs on the machine using | |
| 1 | 62 `os.cpu_count <https://docs.python.org/3/library/os.html#os.cpu_count>`__. |
| 0 | 63 - ``--cds``, controlling the minimum number of consecutive genes a BGC |
| 64 region must have to be detected by GECCO (default is 3). | |
| 65 - ``--threshold``, controlling the minimum probability for a gene to be | |
| 66 considered part of a BGC region. Using a lower number will increase | |
| 67 the number (and possibly length) of predictions, but reduce accuracy. | |
| 68 | |
| 69 🔖 Reference | |
| 70 ------------- | |
| 71 | |
| 72 GECCO can be cited using the following preprint: | |
| 73 | |
| 74 **Accurate de novo identification of biosynthetic gene clusters with | |
| 75 GECCO**. Laura M Carroll, Martin Larralde, Jonas Simon Fleck, Ruby | |
| 76 Ponnudurai, Alessio Milanese, Elisa Cappio Barazzone, Georg Zeller. | |
| 77 bioRxiv 2021.05.03.442509; | |
| 78 `doi:10.1101/2021.05.03.442509 <https://doi.org/10.1101/2021.05.03.442509>`__ | |
| 79 | |
| 80 💭 Feedback | |
| 81 ------------ | |
| 82 | |
| 83 ⚠️ Issue Tracker | |
| 84 ~~~~~~~~~~~~~~~~ | |
| 85 | |
| 86 Found a bug ? Have an enhancement request ? Head over to the `GitHub | |
| 87 issue tracker <https://github.com/zellerlab/GECCO/issues>`__ if you need | |
| 88 to report or ask something. If you are filing in on a bug, please | |
| 89 include as much information as you can about the issue, and try to | |
| 90 recreate the same bug in a simple, easily reproducible situation. | |
| 91 | |
| 92 🏗️ Contributing | |
| 93 ~~~~~~~~~~~~~~~~ | |
| 94 | |
| 95 Contributions are more than welcome! See | |
| 2 | 96 `CONTRIBUTING.md <https://github.com/zellerlab/GECCO/blob/master/CONTRIBUTING.md>`__ |
| 0 | 97 for more details. |
| 98 | |
| 99 ⚖️ License | |
| 100 ---------- | |
| 101 | |
| 102 This software is provided under the `GNU General Public License v3.0 or | |
| 103 later <https://choosealicense.com/licenses/gpl-3.0/>`__. GECCO is | |
| 104 developped by the `Zeller | |
| 105 Team <https://www.embl.de/research/units/scb/zeller/index.html>`__ at | |
| 106 the `European Molecular Biology Laboratory <https://www.embl.de/>`__ in | |
| 107 Heidelberg. | |
| 108 | |
| 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 | |
| 110 :target: https://git.embl.de/grp-zeller/GECCO/-/pipelines/ | |
| 111 .. |License| image:: https://img.shields.io/badge/license-GPLv3-blue.svg?style=flat-square&maxAge=2678400 | |
| 112 :target: https://choosealicense.com/licenses/gpl-3.0/ | |
| 113 .. |Coverage| image:: https://img.shields.io/codecov/c/gh/zellerlab/GECCO?style=flat-square&maxAge=600 | |
| 114 :target: https://codecov.io/gh/zellerlab/GECCO/ | |
| 115 .. |Docs| image:: https://img.shields.io/badge/docs-gecco.embl.de-green.svg?maxAge=2678400&style=flat-square | |
| 116 :target: https://gecco.embl.de | |
| 117 .. |Source| image:: https://img.shields.io/badge/source-GitHub-303030.svg?maxAge=2678400&style=flat-square | |
| 118 :target: https://github.com/zellerlab/GECCO/ | |
| 119 .. |Mirror| image:: https://img.shields.io/badge/mirror-EMBL-009f4d?style=flat-square&maxAge=2678400 | |
| 120 :target: https://git.embl.de/grp-zeller/GECCO/ | |
| 121 .. |Changelog| image:: https://img.shields.io/badge/keep%20a-changelog-8A0707.svg?maxAge=2678400&style=flat-square | |
| 122 :target: https://github.com/zellerlab/GECCO/blob/master/CHANGELOG.md | |
| 123 .. |Issues| image:: https://img.shields.io/github/issues/zellerlab/GECCO.svg?style=flat-square&maxAge=600 | |
| 124 :target: https://github.com/zellerlab/GECCO/issues | |
| 125 .. |Preprint| image:: https://img.shields.io/badge/preprint-bioRxiv-darkblue?style=flat-square&maxAge=2678400 | |
| 126 :target: https://www.biorxiv.org/content/10.1101/2021.05.03.442509v1 | |
| 127 .. |PyPI| image:: https://img.shields.io/pypi/v/gecco-tool.svg?style=flat-square&maxAge=3600 | |
| 128 :target: https://pypi.python.org/pypi/gecco-tool | |
| 129 .. |Bioconda| image:: https://img.shields.io/conda/vn/bioconda/gecco?style=flat-square&maxAge=3600 | |
| 130 :target: https://anaconda.org/bioconda/gecco | |
| 131 .. |Versions| image:: https://img.shields.io/pypi/pyversions/gecco-tool.svg?style=flat-square&maxAge=3600 | |
| 132 :target: https://pypi.org/project/gecco-tool/#files | |
| 133 .. |Wheel| image:: https://img.shields.io/pypi/wheel/gecco-tool?style=flat-square&maxAge=3600 | |
| 134 :target: https://pypi.org/project/gecco-tool/#files | |
|
3
359232b58f6a
"Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
2
diff
changeset
|
135 .. |Galaxy| image:: https://img.shields.io/badge/Galaxy-GECCO-darkblue?style=flat-square&maxAge=3600 |
|
359232b58f6a
"Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
2
diff
changeset
|
136 :target: https://toolshed.g2.bx.psu.edu/repository?repository_id=c29bc911b3fc5f8c |