These are some of the things that I can never remember how to do in snakemake but they make life just that little bit easier.Continue reading
First, make sure everything is upto date in GitHub.
We are going to call this release version 4.0 and we will have release candidates, starting at rc1
First, create a release on GitHub. Strictly speaking you don’t need to do that but it is a great thing to do.
The PyPi instructions cover this, but I have abstracted out the parts we need to focus on (since we have a setup.py already!)
As a regular user we build everything. This make a new release that we will upload
python3 setup.py sdist
This will create the tarball and the wheel file in the
dist directory. Then we need to upload those to PyPi.
We are going to use the PyPi test interface to make sure that everything is OK. Do not skip this step!
If you need an API key, navigate to the PyPi login page . However, if you have done this before, you probably don’t need to save it again 😉
python3 -m twine upload --repository testpypi dist/PhiSpy-4.0.0rc1.tar.gz
Note that you can not upload the wheel. Binary wheels from linux are not supported.
Now we are going to test it out. Lets make a virtual environment and install it there
virtualenv test_phispy cd test_phispy source bin/activate which pip
This should tell you that the current pip is from your virtual environment. If it is not, solve that problem!
For PhiSpy, we have a couple of dependencies that you should install with regular
pip before you can install your new release candidate:
pip3 install scikit-learn biopython
This will install other things like
numpy that you need.
Now you can install your new release.
pip install -i https://test.pypi.org/simple/ PhiSpy==4.0.0rc1
If you are not sure exactly the URL, logging into the PyPi test login page will show your available repositories, including the newly uploaded repository. If you click on the version you want, you can get the link to download and install that.
Once you are happy and have run some tests, login to the real PyPi page (good to do anyway, even if you have an API key)
Now you can upload the final version to PyPi for everyone to access
python3 -m twine upload dist/PhiSpy-4.0.0.tar.gz
Its worth logging into the real PyPi page to make sure that you can download it!
Making a CONDA release
It turns out that for most code all you have to do is wait! The conda bots will take care of incrementing to the next version and running the continuous integration tests for you.
However, if you need to update the code manually, you probably need to change the version in
meta.yaml and then you should update the SHA hash:
wget -O- https://github.com/linsalrob/PhiSpy/archive/v4.1.16.tar.gz | shasum -a 256
and then paste the output of that into the SHA field. In this case, the shasum should be
One of the most essential tools in bioinformatics is counting k-mers. These are short, identical strings, of length k. Here, we will look at counting all the k-mers in string.
We are pleased to announce the second installment of the SoCal Bioinformatics Hackathon.
From 9-11 January, 2019, the NCBI will help run a bioinformatics hackathon in Southern California hosted by the Computational Sciences Research Center at San Diego State University! We are going to put a few hundred thousand metagenomic datasets on cloud infrastructure and identify known, taxonomically definable and novel viruses! We’re specifically looking for folks who have experience in Computational Virus Hunting or Adjacent Fields! If this describes you, please apply! This event is for researchers, including students and postdocs, who are already engaged in the use of bioinformatics data or in the development of pipelines for virological analyses from high-throughput experiments. The event is open to anyone selected for the hackathon and willing to travel to SDSU (see below).
If you are using utf-8 documents in Python, you may occasionally run into this error:
UnicodeDecodeError: 'ascii' codec can't decode byte 0xc2 in position 124106: ordinal not in range(128)
The fix is trivial!
How can we generate a list of all the lengths of all the proteins [in a specific group] in genbank? Its easy with ftp!
CentOS is great because it is secure, but not great because it doesn’t have the latest software. Here is how to install C++11 on CentOS6 or CentOS7, and temporarily activate it in a shell. This does not change the default compiler and should cause less problems with your system (but that is not a money back guarantee … you are own your own if it does!)
When writing scientific names: italicize family, genus, species, and variety or subspecies. Begin family and genus with a capital letter. Kingdom, phylum, class, order, and suborder begin with a capital letter but are not italicized.
Here is the complete taxonomy: