| Previous changeset 0:1625927fc16f (2021-11-21) Next changeset 2:e618ab1c78d9 (2021-11-21) |
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Commit message:
"Release v0.8.4" |
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modified:
README.rst |
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| diff -r 1625927fc16f -r 0699939e6dd6 README.rst --- a/README.rst Sun Nov 21 16:53:12 2021 +0000 +++ b/README.rst Sun Nov 21 17:00:40 2021 +0000 |
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| @@ -1,6 +1,10 @@ Hi, I’m GECCO! ============== +.. image:: https://raw.githubusercontent.com/zellerlab/GECCO/v0.6.2/static/gecco-square.png + :target: https://github.com/zellerlab/GECCO/ + + 🦎 ️Overview --------------- @@ -20,18 +24,14 @@ 3.6. It requires additional libraries that can be installed directly from `PyPI <https://pypi.org>`__, the Python Package Index. -Use ```pip`` <https://pip.pypa.io/en/stable/>`__ to install GECCO on -your machine: - -.. code:: console +Use `pip <https://pip.pypa.io/en/stable/>`__ to install GECCO on +your machine:: $ pip install gecco-tool If you’d rather use `Conda <https://conda.io>`__, a package is available -in the ```bioconda`` <https://bioconda.github.io/>`__ channel. You can -install with: - -.. code:: console +in the `bioconda <https://bioconda.github.io/>`__ channel. You can +install with:: $ conda install -c bioconda gecco @@ -40,7 +40,7 @@ could take some time depending on your Internet connection. Once done, you will have a ``gecco`` command available in your $PATH. -*Note that GECCO uses*\ `HMMER3 <http://hmmer.org/>`__\ *, which can +*Note that GECCO uses* `HMMER3 <http://hmmer.org/>`__, *which can only run on PowerPC and recent x86-64 machines running a POSIX operating system. Therefore, Linux and OSX are supported platforms, but GECCO will not be able to run on Windows.* @@ -50,9 +50,7 @@ Once ``gecco`` is installed, you can run it from the terminal by giving it a FASTA or GenBank file with the genomic sequence you want to -analyze, as well as an output directory: - -.. code:: console +analyze, as well as an output directory:: $ gecco run --genome some_genome.fna -o some_output_dir @@ -61,7 +59,7 @@ - ``--jobs``, which controls the number of threads that will be spawned by GECCO whenever a step can be parallelized. The default, *0*, will autodetect the number of CPUs on the machine using - ```os.cpu_count`` <https://docs.python.org/3/library/os.html#os.cpu_count>`__. + `os.cpu_count <https://docs.python.org/3/library/os.html#os.cpu_count>`__. - ``--cds``, controlling the minimum number of consecutive genes a BGC region must have to be detected by GECCO (default is 3). - ``--threshold``, controlling the minimum probability for a gene to be @@ -95,7 +93,7 @@ ~~~~~~~~~~~~~~~~ Contributions are more than welcome! See -```CONTRIBUTING.md`` <https://github.com/althonos/pyhmmer/blob/master/CONTRIBUTING.md>`__ +`CONTRIBUTING.md <https://github.com/althonos/pyhmmer/blob/master/CONTRIBUTING.md>`__ for more details. ⚖️ License |