Additional Examples

Snakeobjects Paper Example

This section explains how to load and execute small project described Supplementary of snakeobjects paper. We assume that you will work or a Linux or Mac. In addition, we assume that you have a conda or miniconda installed (Conda Installation, to speed up the environment createtion install Mamba ). Everything else needed is inclucded in the snakeobjectsPaperExample.tgz. When you download and extract (tar xzf snakeobjectsPaperExample.tgz) file, you will get a directory called snakeobjectsPaperExample. We assume here that this directory is placed in /tmp, but you can place it elsewhere. Next execute following commands:

(base) .............$ cd /tmp/snakeobjectsPaperExample/pipeline

(base) /tmp/snakeobjectsPaperExample/pipeline$ mamba env create

(base) /tmp/snakeobjectsPaperExample/pipeline$ conda activate snakeobjectsPaperExample

(snakeobjectsPaperExample) /tmp/snakeobjectsPaperExample/pipeline$ cd ../project

(snakeobjectsPaperExample) /tmp/snakeobjectsPaperExample/project$ sobjects prepare

(snakeobjectsPaperExample) /tmp/snakeobjectsPaperExample/project$ sobjects run -j -q

In the subdirectory denovos/all you will find allDenovoCalls.txt file. Opening it in excel with a little formatting can get:

Snakemake Tutorial Example

This section explains how to load and execute the small project reimplementing in snakeobject Snakemake Tutorial example. We assume that you will work or a Linux or Mac. In addition, we assume that you have conda or miniconda installed (Conda Installation). Everything else needed is inclucded in the SnakemakeTutorialExample.tgz. When you download and extract (tar xzf SnakemakeTutorialExample.tgz) file, you will get a directory called snakeomakeTutorialExample. We assume here that this directory is placed in /tmp, but you can place it elsewhere. You can then follow the same steps as described in the Paper Supplementary example above.

Tests Demo Examples

There are nine mini projects in the directory snakeobjects/tests/demos. Each mini project describes some features of snakeobjects.