Merge pull request #125 from AlexandrovLab/u67

U67

Author: mdbarnesUCSD

MANIFEST.in

@@ -1,4 +1,5 @@
 include README.md
+include SigProfilerAssignment/controllers/*
 include SigProfilerAssignment/data/*
 include SigProfilerAssignment/data/Reference_Signatures/GRCh37/*
 include SigProfilerAssignment/data/Reference_Signatures/GRCh38/*

README.md

@@ -68,6 +68,7 @@ Analyze.cosmic_fit(samples, output, input_type="matrix", context_type="96",
 | make_plots | Boolean | Toggle on and off for making and saving plots. The default value is True. |
 | sample_reconstruction_plots | String | Select the output format for sample reconstruction plots. Valid inputs are {'pdf', 'png', 'both', None}. The default value is None. |
 | verbose | Boolean | Prints detailed statements. The default value is False. |
+| volume | String | Path to SigProfilerAssignment volumes. Used for Docker/Singularity. Environmental variable "SIGPROFILERASSIGNMENT_VOLUME" takes precedence. Default value is None. |
 
 
 

SigProfilerAssignment/Analyzer.py

@@ -23,6 +23,7 @@ def decompose_fit(
     context_type="96",
     export_probabilities=True,
     export_probabilities_per_mutation=False,
+    volume=None,
 ):
     decomp.spa_analyze(
         samples=samples,
@@ -49,6 +50,7 @@ def decompose_fit(
         context_type=context_type,
         export_probabilities=export_probabilities,
         export_probabilities_per_mutation=export_probabilities_per_mutation,
+        volume=volume,
     )
 
 
@@ -73,6 +75,7 @@ def denovo_fit(
     context_type="96",
     export_probabilities=True,
     export_probabilities_per_mutation=False,
+    volume=None,
 ):
     decomp.spa_analyze(
         samples=samples,
@@ -98,6 +101,7 @@ def denovo_fit(
         context_type=context_type,
         export_probabilities=export_probabilities,
         export_probabilities_per_mutation=export_probabilities_per_mutation,
+        volume=volume,
     )
 
 
@@ -123,6 +127,7 @@ def cosmic_fit(
     export_probabilities=True,
     export_probabilities_per_mutation=False,
     sample_reconstruction_plots=False,
+    volume=None,
 ):
     decomp.spa_analyze(
         samples=samples,
@@ -149,4 +154,5 @@ def cosmic_fit(
         export_probabilities=export_probabilities,
         export_probabilities_per_mutation=export_probabilities_per_mutation,
         sample_reconstruction_plots=sample_reconstruction_plots,
+        volume=volume,
     )