Test running SINGE inside Octave Docker container

.travis.yml

@@ -2,3 +2,12 @@ sudo: required
 
 services:
   - docker
+
+env:
+  - OCTAVE_VERSION=5.1.0
+
+before_install:
+  - docker pull mtmiller/octave:${OCTAVE_VERSION}
+
+script:
+  - docker run -v $(pwd):/SCINGE -w /SCINGE --entrypoint "/bin/bash" mtmiller/octave:${OCTAVE_VERSION} -c "./install_glmnet_docker.sh; octave -v; octave SCINGE_Example.m"

SCINGE_Example.m

@@ -33,4 +33,4 @@
 gene_list = tf;
 
 %% Run SCINGE
-[ranked_edges, gene_influence] = SCINGE(gene_list,Data,outdir,num_replicates,param_list);
+[ranked_edges, gene_influence] = SCINGE(gene_list,Data,outdir,num_replicates,param_list);

code/GLG_Instance.m

@@ -6,43 +6,7 @@ function GLG_Instance(Data,varargin)
 %
 tic
 %%% InputParser
-p = inputParser;
-def_lambda = 0.01;
-def_dT = 1;
-def_rep = 0;
-def_width = 2;
-def_probzero = 0;
-def_family = 'gaussian';
-def_L = 15;
-def_ID = 0;
-def_outdir = 'Output';
-def_prob_remove_samples = 0.2;
-def_date = date;
-%
-expected_family = {'gaussian','poisson'};
-validScalar = @(x) isnumeric(x) && isscalar(x) && (x >= 0);
-validFile = @(x) isfilecomp(x);
-validString = @(x) ischar(x) && isempty(regexp(x,'[\/?*''."<>|]','once'));
-validInteger = @(x) (x - floor(x)==0) && (x >= 0);
-validLags = @(x) (x - floor(x)==0) && (p.Results.dT*x)<100;
-validProb = @(x) isnumeric(x) && isscalar(x) && (x >= 0) &&(x<1);
-validDate = @(x) any(ismember({datestr(datenum(x) ,['mm/dd/yyyy']) datestr(datenum(x))},x));
-addRequired(p,'Data',validFile);
-addParameter(p,'family',def_family,@(x) any(validatestring(x,expected_family)));
-addParameter(p,'outdir',def_outdir,validString);
-addParameter(p,'lambda',def_lambda,validScalar);
-addParameter(p,'dT',def_dT,validScalar);
-addParameter(p,'num_lags',def_L,validLags);
-addParameter(p,'kernel_width',def_width,validScalar);
-addParameter(p,'prob_zero_removal',def_probzero,validProb);
-addParameter(p,'prob_remove_samples',def_prob_remove_samples,validProb);
-addParameter(p,'replicate',def_rep,validInteger);
-addParameter(p,'ID',def_ID,validInteger);
-addParameter(p,'date',def_date,validDate);
-parse(p,Data,varargin{:});
-params = p.Results;
-params.p1 = p.Results.dT*p.Results.num_lags;
-params.DateNumber = datenum(params.date);
+params = parseParams(Data,varargin{:})
 mkdir(params.outdir)
 %%% End InputParser
 tic;
@@ -89,20 +53,4 @@ function GLG_Instance(Data,varargin)
 if isdeployed
     quit;
 end
-end
-
-function y = isfilecomp(x)
-if verLessThan('matlab','9.3')
-    if (exist([x '.mat'], 'file') == 2)||(exist(x, 'file') == 2)
-        y = 1;
-    else
-        y = 0;
-    end
-else
-    if (isfile([x '.mat'])||isfile(x))
-        y = 1;
-    else
-        y = 0;
-    end
-end
 end

code/parseParams.m

@@ -0,0 +1,47 @@
+function params = parseParams(Data,varargin)
+p = inputParser;
+def_lambda = 0.01;
+def_dT = 1;
+def_rep = 0;
+def_width = 2;
+def_probzero = 0;
+def_family = 'gaussian';
+def_L = 15;
+def_ID = 0;
+def_outdir = 'Output';
+def_prob_remove_samples = 0.2;
+def_date = date;
+%
+expected_family = {'gaussian','poisson'};
+validScalar = @(x) isnumeric(x) && isscalar(x) && (x >= 0);
+validFile = @(x) isfilecomp(x);
+validString = @(x) ischar(x) && isempty(regexp(x,'[\/?*''."<>|]','once'));
+validInteger = @(x) (x - floor(x)==0) && (x >= 0);
+validLags = @(x) (x - floor(x)==0) && (p.Results.dT*x)<100;
+validProb = @(x) isnumeric(x) && isscalar(x) && (x >= 0) &&(x<1);
+validDate = @(x) any(ismember({datestr(datenum(x) ,['mm/dd/yyyy']) datestr(datenum(x))},x));
+addRequired(p,'Data',validFile);
+addParameter(p,'family',def_family,@(x) any(validatestring(x,expected_family)));
+addParameter(p,'outdir',def_outdir,validString);
+addParameter(p,'lambda',def_lambda,validScalar);
+addParameter(p,'dT',def_dT,validScalar);
+addParameter(p,'num_lags',def_L,validLags);
+addParameter(p,'kernel_width',def_width,validScalar);
+addParameter(p,'prob_zero_removal',def_probzero,validProb);
+addParameter(p,'prob_remove_samples',def_prob_remove_samples,validProb);
+addParameter(p,'replicate',def_rep,validInteger);
+addParameter(p,'ID',def_ID,validInteger);
+addParameter(p,'date',def_date,validDate);
+parse(p,Data,varargin{:});
+params = p.Results;
+params.p1 = p.Results.dT*p.Results.num_lags;
+params.DateNumber = datenum(params.date);
+end
+
+function y = isfilecomp(x)
+    if (exist([x '.mat'], 'file') == 2)||(exist(x, 'file') == 2)
+        y = 1;
+    else
+        y = 0;
+    end
+end

install_glmnet_docker.sh

@@ -0,0 +1,15 @@
+#!/bin/bash
+# Install Glmnet by downloading from
+# http://web.stanford.edu/~hastie/glmnet_matlab/index.html
+# and compiling for Octave
+curl -O http://web.stanford.edu/~hastie/glmnet_matlab/glmnet_matlab.zip
+unzip glmnet_matlab.zip
+
+cd glmnet_matlab
+curl -O https://raw.githubusercontent.com/SheffieldML/GPmat/master/kern/mex/fintrf.h
+mkoctfile --verbose --mex glmnetMex.F GLMnet.f
+
+cd ..
+
+# To help debugging
+gfortran --version