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John Lees' blog

Pathogens, informatics and modelling at EMBL-EBI

Creating a conda package with compilation and dependencies

I’ve just finished, what was for me, a difficult compiler/packaging attempt – creating a working bioconda package for seer. You can look at the pull request to see how many times I failed: https://github.com/bioconda/bioconda-recipes/pull/11263 (I would note I have made this package for legacy users. I would direct anyone interested in the software itself to the reimplementation pyseer) The reason this was difficult was due to my own inclusion of a number of packages, all of which also need compilation, further adding to the complexity.

conda build: libarchive: cannot open shared object file: No such file or directory

I was getting the following error, attempting to run conda-build on a package, using a conda env: Traceback (most recent call last): File "/nfs/users/nfs_j/jl11/pathogen_nfs/large_installations/miniconda3/envs/conda_py36/bin/conda-build", line 7, in <module> from conda_build.cli.main_build import main File "/nfs/users/nfs_j/jl11/pathogen_nfs/large_installations/miniconda3/envs/conda_py36/lib/python3.6/site-packages/conda_build/cli/main_build.py", line 18, in <module> import conda_build.api as api File "/nfs/users/nfs_j/jl11/pathogen_nfs/large_installations/miniconda3/envs/conda_py36/lib/python3.6/site-packages/conda_build/api.py", line 22, in <module> from conda_build.config import Config, get_or_merge_config, DEFAULT_PREFIX_LENGTH as _prefix_length File "/nfs/users/nfs_j/jl11/pathogen_nfs/large_installations/miniconda3/envs/conda_py36/lib/python3.6/site-packages/conda_build/config.py", line 17, in <module> from .variants import get_default_variant File "/nfs/users/nfs_j/jl11/pathogen_nfs/large_installations/miniconda3/envs/conda_py36/lib/python3.6/site-packages/conda_build/variants.py", line 15, in <module> from conda_build.

Linear scaling of covariances

In our software PopPUNK we draw a plot of a Gaussian mixture model that uses both the implementation and the excellent example in the scikit-learn documentation: Gaussian mixture model with mixture components plotted as ellipses My input is 2D distance, which I first use StandardScaler to normalise each axes between 0 and 1, which helps standardise methods across various parts of the code. This is fine if you then create these plots in the scaled space, and as it is a simple linear scaling it is generally trivial to convert back into the original co-ordinates:

Expression modules in S. pneumoniae

I recently read a pre-print from the Veening lab where they had reconstructed various (22 total) physiological conditions in vitro and then measured expression levels with RNA-seq. I thought it was a great bit of research, and would encourage you to read it here if you’re interested: https://doi.org/10.1101/283739 They’ve also done a really good job with data availability, having released a browser for their data (PneumoExpress), and they have put their raw data on zenodo.

Installing phyx without sudo

I saw this phylogenetics package today, phyx: https://github.com/FePhyFoFum/phyx To install without admin rights/sudo I needed to do the following (my software is installed in my home ~/software, rather than e.g. /usr, /usr/local): Compile armadillo as follows cmake -DINSTALL_PREFIX=$(HOME)/software make make install Compile nlopt as follows ./configure --with-cxx --without-octave --without-matlab --prefix=$(HOME)/software make make install Compile phyx as follows (slightly hacky, maybe there’s a ‘proper’ way) ./configure --prefix=$(HOME)/software change line 11 of the Makefile (CPP_LIBS) to add the library path:

setup.py not found using pip install

Trying to install PyVCF under a python (3) virtual environment gave me the following error: (venv)johnlees@hpc:~$ pip install pyvcf Downloading/unpacking pyvcf Downloading PyVCF-0.6.8.linux-x86_64.tar.gz (1.1MB): 1.1MB downloaded Saved /tmp/downloadcache/PyVCF-0.6.8.linux-x86_64.tar.gz Running setup.py egg_info for package pyvcf Traceback (most recent call last): File "", line 16, in FileNotFoundError: \[Errno 2\] No such file or directory: '~/venv/build/pyvcf/setup.py' Complete output from command python setup.py egg_info: Traceback (most recent call last): File "", line 16, in FileNotFoundError: \[Errno 2\] No such file or directory: '~/venv/build/pyvcf/setup.