Zachary Munro

Is the normalize-by-median.py script deterministic?

2

Trying to recreate some previous;y computed results and there are a few places where nondeterminism could be present and I was wondering if it could be present in this script.

Normalize-by-median.py script as a module

1

The `normalize-by-median.py` script (under /scripts) would be very useful as a module. I want to be able to do something like: ``` import khmer khmer.normalize_by_median(input=fastqgz_filepath, output=output_fastqgz) ``` Is something like...

Conda package support for Python 3.7+

4

Is there support for Python3.7+? I am trying to install ariba into my conda environment following the guide on [this page](https://anaconda.org/bioconda/ariba). I tried using the first command there which is...

Pyopenms not installable on new Macs with M1 chip

17

I have been trying for days to get pyopenms installed on my mac and I believe the issue is the M1 chip that my laptop has. When I try to...

This produces some useful statistics, and I am wondering I can use it to find the kmers the true kmers of a sequence.

Kraken2 Translate script and README formatting

2

Wrote this script the other day that I thought would be helpful for people. It generates a file similar to the output of kraken1's `kraken-translate` command using an classification output...

Cuda version

2

What Cuda version is needed to run Racon in GPU mode? I am running with Cuda v11.1.105 and it is not working. The readme says Cuda 9.0+. When I run...

Does not work with python3.7

1

These are the commands I ran: `python3.7 -m pip install pylint_runner` `pylint_runner -v` output: `zsh: command not found: pylint_runner` OS: Ubuntu 16.04

Python 3 pip installation failing

1

I have tried running installation with python3.6, 3.7, and 3.8 and I get a similar error message with each: ``` $ python3.6 -m pip install pymummer Collecting pymummer Cache entry...