Skip to content
Open
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
56 changes: 56 additions & 0 deletions docs/_static/config/beginner.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,56 @@
hash_length: 7
container_framework: docker
unpack_singularity: false
container_registry:
base_url: docker.io
owner: reedcompbio

# Each algorithm has an 'include' parameter. By toggling 'include' to true/false the user can change
# which algorithms are run in a given experiment.
#
# algorithm-specific parameters are embedded in lists so that users can specify multiple. If multiple
# parameters are specified then the algorithm will be run as many times as needed to cover all parameter
# combinations. For instance if we have the following:
# - name: "myAlg"
# params:
# include: true
# a: [1,2]
# b: [0.5,0.75]
#
# then myAlg will be run on (a=1,b=0.5),(a=1,b=0.75),(a=2,b=0.5), and (a=2,b=0,75). Pretty neat, but be
# careful: too many parameters might make your runs take a long time.

algorithms:
- name: "pathlinker"
params:
include: true
run1:
k: 1
# run2: # uncomment for step 3.2
# k: [10, 100] # uncomment for step 3.2

# Here we specify which pathways to run and other file location information.
# Assume that if a dataset label does not change, the lists of associated input files do not change
datasets:
- # Labels can only contain letters, numbers, or underscores
label: egfr
node_files: ["tps-egfr-prizes.txt"] # the input nodes
edge_files: ["phosphosite-irefindex13.0-uniprot.txt"] # the interactome
# Placeholder
other_files: []
# Relative path from the spras directory where these files live
data_dir: "input"

reconstruction_settings:

# Set where everything is saved
locations:
reconstruction_dir: "output/basic"

analysis:
# Create one summary per pathway file and a single summary table for all pathways for each dataset
summary:
include: false # set to true for step 3.3
# Create Cytoscape session file with all pathway graphs for each dataset
cytoscape:
include: false # set to true for step 3.3
Empty file.
Binary file added docs/_static/images/100_pathway.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added docs/_static/images/10_pathway.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added docs/_static/images/1_pathway.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added docs/_static/images/cytoscape-open-cys-file.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added docs/_static/images/cytoscape-opened.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added docs/_static/images/cytoscape_upload_network.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added docs/_static/images/summary-stats.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
9 changes: 9 additions & 0 deletions docs/index.rst
Original file line number Diff line number Diff line change
Expand Up @@ -56,6 +56,15 @@ methods (PRMs) to omics data.
contributing/index
contributing/maintain

.. toctree::
:maxdepth: 1
:caption: Tutorials

tutorial/introduction
tutorial/beginner
tutorial/intermediate
tutorial/advanced

Indices and tables
==================

Expand Down
20 changes: 20 additions & 0 deletions docs/tutorial/advanced.rst
Original file line number Diff line number Diff line change
@@ -0,0 +1,20 @@
Advanced Capabilities and Features
======================================

More like these are all the things we can do with this, but will not be showing

- mention parameter tuning
- say that parameters are not preset and need to be tuned for each dataset

CHTC integration
Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

CHTC is local to our university. The way to say it may be Snakemake integration with cloud and high-throughput computing resources, which we've prototyped in our local cluster. If we start testing in OSG that would be different because many people are eligible for accounts.


Anything not included in the config file

1. Global Workflow Control

Sets options that apply to the entire workflow.

- Examples: the container framework (docker, singularity, dsub) and where to pull container images from

running spras with multiple parameter combinations with multiple algorithms on multiple Datasets
- for the tutorial we are only doing one dataset
Loading
Loading