methylpy | seq Data Processing & Differential Methylation Analysis | Genomics library

The easiest way of installing methylpy will be through PyPI by running pip install methylpy. The command pip install --upgrade methylpy updates methylpy to latest version. Methylpy can also be installed through anaconda or [miniconda] (https://docs.conda.io/en/latest/miniconda.html). Alternatively, methylpy can be installed through github: enter the directory where you would like to install methylpy and run. If you would like to install methylpy in path of your choice, run python setup.py install --prefix=/USER/PATH/. Then, try methylpy and if no error pops out, the setup is likely successful. See Test methylpy for more rigorious test. Last, processing large dataset will require large spare space for temporary files. Usually, the default directory for temporary files will not meet the need. You may want to set the TMPDIR environmental variable to the (absolute) path of a directory on hard drive with sufficient space (e.g. /YOUR/TMP/DIR/). This can be done by adding the below command to ~/.bashrc file: export TMPDIR=/YOUR/TMP/DIR/ and run source ~/.bashrc. python is required for running methylpy. Both python2 (>=2.7.9) and python3 (>=3.6.2) will work. methylpy also depends on two python modules, numpy and scipy. The easiest way to get these dependencies is to install anaconda. In addition, some features of methylpy depend on several publicly available tools (not all of them are required if you only use a subset of methylpy functions). Lastly, if paths to cutadapt, bowtie/bowtie2, samtools and wigToBigWig are included in PATH variable, methylpy can run these tools directly. Otherwise, the paths have to be passed to methylpy as augments. Path to Picard needs to be passed to methylpy as a parameter to run PCR duplicate removal. DMR finding requires an executable methylpy/methylpy/run_rms_tests.out, which was compiled from C++ code methylpy/methylpy/rms.cpp. In most cases, the precompiled file can be used directly. To test this, simply run execute methylpy/methylpy/run_rms_tests.out. If help page shows, recompiling is not required. If error turns up, the executable needs to be regenerated by compiling rms.cpp and this step requires GSL installed correctly. In most linux operating system, the below commands will do the job. In Ubuntu (>=16.04), please try the below commands first.
cutadapt (>=1.9) for raw read trimming
bowtie and/or bowtie2 for alignment
samtools (>=1.3) for alignment result manipulation. Samtools can also be installed using conda conda install -c bioconda samtools
Picard (>=2.10.8) for PCR duplicate removal
java for running Picard (its path needs to be included in PATH environment variable) .
wigToBigWig for converting methylpy output to bigwig format