`sobjects` commands

This is the main snakeobjects’ command line tools. The general usage has the sobjects <command> [<option 1> <option 2> ...]. The available commands are described below:

version

$ sobjects help version
Snakeobjects 3.1.4

prints the version

help

$ sobjects help help
Snakeobjects 3.1.4

sobjects help [command]

Shows description of the command line interface. 
Without an argument, prints help for all the commands. If one argument 
is given, it should be one of the available commands and help for the given 
command is shown.

describe

$ sobjects help describe
Snakeobjects 3.1.4

Prints basic information about the project and the pipeline
that are used.

buildObjectGraph

$ sobjects help buildObjectGraph
Snakeobjects 3.1.4

sobjects buildObjectGraph [<arguments to build_object_graph.py>]

Uses the build_object_graph.py in the pipeline directory to create a new object 
graph and stores it on the file OG.json in the project directory.

createSnakefile

$ sobjects help createSnakefile
Snakeobjects 3.1.4

sobjects createSnakefile

First, the command finds the list of implemented object types by obtaining the names 
(without the .snakefile suffix) of *.snakefile files in the pipeline directory. The 
createSnakefile command then checks if the object graph of the current project uses 
object types that have no corresponding <object type>.snakefile. In such cases, it 
creates dummy *.snakefiles for the new object types and extends the list of object 
types. (The check for new object types in the current project is an esoteric feature 
helpful for pipeline developers during the development or extension of pipelines.) 
The command then creates a Snakefile in the pipeline directory based on the complete 
list of the object types. 

createSymbolicLinks

$ sobjects help createSymbolicLinks
Snakeobjects 3.1.4

sobjects createSymbolicLinks

Uses the objectGraph OG.json to create object directories for objects that have symbolic 
links in object's parameters.

prepare

$ sobjects help prepare
Snakeobjects 3.1.4

sobjects prepare [<arguments to build_object_graph.py>]

    This is a short-cut command equivallent to:
        sobjects buildObjectGraph [<arguments to build_object_graph.py>] 
        sobjects createSnakefile
        sobjects createSymlinks

prepareTest

$ sobjects help prepareTest
Snakeobjects 3.1.4

sobjects prepareTest [<arguments to build_object_graph.py>]

Uses the build_object_graph.py in the pipeline directory to create a new object 
graph and prints statistics of the current and the new object graph. The project 
is not modified at all.

run

$ sobjects help run
Snakeobjects 3.1.4

sobjects run [<arguments to snakemake>]

Creates targets for objects in the object graph by running snakemake. The 
<arguments to snakemake> determine which targets will be created and what resources 
will be used.

cleanProject

$ sobjects help cleanProject
Snakeobjects 3.1.4

sobjects cleanProject [ -f]

Will ask user to remove OG.json, .snakemake, and all objects directories. With -f option all is removed silently.

submit

$ sobjects help submit
Snakeobjects 3.1.4

sobjects submit [<arguments to snakemake>]

Creates targets for objects in the object graph by running snakemake with
profile specified in default_snakemake_args directive of so_project.yaml. The
<arguments to snakemake> determine which targets will be created and what
resources will be used.

printEnv

$ sobjects help printEnv
Snakeobjects 3.1.4

sobjects printEnv

Prints out on the standart output the shell commands defining shell environment variables, such as PATH, PYTHONPATH, etc.

graph

$ sobjects help graph
Snakeobjects 3.1.4

sobject graph [-w width] [-p penwidth] [-a arrowsize] [-l legend] [-o out] [-i id] [-s shape]

optional arguments:
  -h, --help            show this help message and exit
  -w width, --width width
                        width of node, default is 0.75
  -p penwidth, --penwidth penwidth
                        thickness of edges, default is 1.0
  -a arrowsize, --arrowsize arrowsize
                        multiplicative scale factor for arrowheads, default is 1.0
  -l legend, --legend legend
                        Name of the output legend file, default is no legend
  -o out, --out out     name of the output file, default is stdout
  -t text, --text text  place text in nodes: [|oId|oType:oId|params], default no text
  -s shape, --shape shape
                        shape of the node, default is circle, for all shape names see https://www.graphviz.org/doc/info/shapes.html

sobjects commands

`sobjects` commands