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phylogenetic_tree_software_with_matlab_wrappers/all_tests/build_trees_for_ralphs_simple_data_set_on_all_tools.m

@@ -13,7 +13,7 @@
 %% running all tools on Ralph's simple data set
 %% load the data set
 
-input_file = '/home/surjray/Phylogeny_repo/phylogenetic_tree_software_with_matlab_wrappers/all_tests/Sample_test_data/ralphs_simple_data_set_all_mutations_except_mut_5';
+input_file = [pwd, '/../all_tests/Sample_test_data/ralphs_simple_data_set_all_mutations_except_mut_5'];
 
 %input_file = '/home/surjray/Phylogeny_repo/phylogenetic_tree_software_with_matlab_wrappers/all_tests/Sample_test_data/ralphs_second_simple_data_set_all_mutations';
 
@@ -24,7 +24,7 @@
 
 figure;
 %% run our code
-base_folder = '/home/surjray/Phylogeny_repo/phylogenetic_tree_software_with_matlab_wrappers/EXACT';
+base_folder = [pwd, '/../EXACT'];
 
 run([base_folder, '/distribution/cvx/cvx/cvx_setup']);
 
@@ -98,7 +98,7 @@
 set(gca,'visible','off')
 
 %% run PhyloWGS
-base_folder = '/home/surjray/Phylogeny_repo/phylogenetic_tree_software_with_matlab_wrappers/phylowgs';
+base_folder = [pwd, '/../phylowgs'];
 
 %Constants for PhyloWGS, should not be changed for sequencing data
 mu_r = 0.999;
@@ -166,7 +166,7 @@
 set(gca,'visible','off')
 %% run AncesTree
 
-base_folder = '/home/surjray/Phylogeny_repo/phylogenetic_tree_software_with_matlab_wrappers/AncesTree';
+base_folder = [pwd, '/../AncesTree'];
 
 alpha = 0.3; % if alpha is big, lots of things will be clustered together
 beta = 0.8; % to choose a larger beta we need more samples , i.e. larger T_samples
@@ -222,7 +222,7 @@
 set(gca,'visible','off')
 %% run Canopy
 
-base_folder =  '/home/surjray/backups_of_phylo_project/Dropbox_Phylogeny_project_11th_July_2019/phylogenetic_tree_software_with_matlab_wrappers/Canopy-master';
+base_folder = [pwd, '/../Canopy'];
 
 path_to_folder = [base_folder, '/demo_code/'];
 
@@ -278,7 +278,7 @@
 generate_simple_muller_plots(U2,M_target,cum_nodelbs,node_col);
 set(gca,'visible','off')
 %% run CITUP
-base_folder = '/home/surjray/Phylogeny_repo/phylogenetic_tree_software_with_matlab_wrappers/citup';
+base_folder = [pwd, '/../citup'];
 
 % parameters
 wrapper_working_directory = [base_folder,'/distribution/'];

phylogenetic_tree_software_with_matlab_wrappers/all_tests/comparing_all_tools_on_CLL_003_four_diff_error_types_schuh_2012_predicted_results.m

@@ -12,6 +12,8 @@
 % citup_error_rates = array object with four rows, each row containing the value of a particular error type, for CITUP, contrasting the inferred tree vs the ground truth from Schuh et. al.
 % canopy_error_rates = array object with four rows, each row containing the value of a particular error type, for Canopy, contrasting the inferred tree vs the ground truth from Schuh et. al.
 
+% adding path for the all_tests subfolders
+addpath(genpath(pwd));
 
 % INPUTS
 CLL3_T = [
@@ -54,7 +56,7 @@
 file_count_id = 23;
 
 %getting EXACT data for real file no. 23
-ourcode_output = load('/home/surjray/Phylogeny_repo/phylogenetic_tree_software_with_matlab_wrappers/all_tests/all_results/our_code_on_real_data_tree_sizes_6_9_top_20.mat','all_our_code_outputs');
+ourcode_output = load([pwd, '/../all_tests/all_results/our_code_on_real_data_tree_sizes_6_9_top_20.mat'],'all_our_code_outputs');
 ourcode_output_check = ourcode_output.all_our_code_outputs{file_count_id};
 
 U2 = inv(eye(size(ourcode_output_check{3})) - ourcode_output_check{3});
@@ -64,7 +66,7 @@
 [exact_error_rates] = compare_trees_using_U_matrices_and_clustering(U1, clust1, U2, clust2);
 
 %getting AncesTree data for real file no. 23
-ancestree_output = load('/home/surjray/Phylogeny_repo/phylogenetic_tree_software_with_matlab_wrappers/all_tests/all_results/ancestree_all_files_minus_a_few_ELKEBIR_real_data.mat','all_ancestree_output');
+ancestree_output = load([pwd, '/../all_tests/all_results/ancestree_all_files_minus_a_few_ELKEBIR_real_data.mat'],'all_ancestree_output');
 ancestree_output = ancestree_output.all_ancestree_output{file_count_id};
 
 U2 = ancestree_output{3}{1};
@@ -80,7 +82,7 @@
 [ancestree_error_rates] = compare_trees_using_U_matrices_and_clustering(U1, clust1, U2, clust2);
 
 %getting PhyloWGS data for real file no. 23
-phyloWGS_output = load('/home/surjray/Phylogeny_repo/phylogenetic_tree_software_with_matlab_wrappers/all_tests/all_results/phyloWGS_all_files_ELKEBIR_real_data.mat','all_phylosub_outputs');
+phyloWGS_output = load([pwd, '/../all_tests/all_results/phyloWGS_all_files_ELKEBIR_real_data.mat'],'all_phylosub_outputs');
 phyloWGS_output = phyloWGS_output.all_phylosub_outputs{file_count_id};
 
 U2 = phyloWGS_output{1}{1};
@@ -109,7 +111,7 @@
 [phylowgs_error_rates] = compare_trees_using_U_matrices_and_clustering(U1, clust1, U2, clust2);
 
 %getting CITUP data for real file no. 23
-citup_output = load('/home/surjray/Phylogeny_repo/phylogenetic_tree_software_with_matlab_wrappers/all_tests/all_results/citup_all_files_ELKEBIR_real_data.mat','all_citup_outputs');
+citup_output = load([pwd, '/../all_tests/all_results/citup_all_files_ELKEBIR_real_data.mat'],'all_citup_outputs');
 citup_output = citup_output.all_citup_outputs{file_count_id};
 
 U2 = citup_output{1}{1}{1};
@@ -136,7 +138,7 @@
 [citup_error_rates] = compare_trees_using_U_matrices_and_clustering(U1, clust1, U2, clust2);
 
 %getting CANOPY data for real file no. 23
-canopy_output = load('/home/surjray/Phylogeny_repo/phylogenetic_tree_software_with_matlab_wrappers/all_tests/all_results/all_canopy_outputs_on_real_Elkebir_data.mat','all_canopy_outputs');
+canopy_output = load([pwd, '/../all_tests/all_results/all_canopy_outputs_on_real_Elkebir_data.mat'],'all_canopy_outputs');
 canopy_output = canopy_output.all_canopy_outputs{file_count_id};
 
 [U2, clust2] = extract_U_mat_and_clust_from_canopy_output(canopy_output);

phylogenetic_tree_software_with_matlab_wrappers/all_tests/comparing_all_tools_on_M_matrices_shuh_2012_predicted_results.m

@@ -12,11 +12,11 @@
 
 %% Loading workspaces with results of EXACT, AncesTree, PhyloWGS, CITUP and Canopy respectively. 
 % The results were generated by running the tools on the real data provided in the paper: https://www.ncbi.nlm.nih.gov/pubmed/26072510
-load('/home/surjray/Phylogeny_repo/phylogenetic_tree_software_with_matlab_wrappers/all_tests/all_results/our_code_on_real_data_tree_sizes_6_9_top_20.mat','all_our_code_outputs');
-load('/home/surjray/Phylogeny_repo/phylogenetic_tree_software_with_matlab_wrappers/all_tests/all_results/ancestree_all_files_minus_a_few_ELKEBIR_real_data.mat','all_ancestree_output');
-load('/home/surjray/Phylogeny_repo/phylogenetic_tree_software_with_matlab_wrappers/all_tests/all_results/phyloWGS_all_files_ELKEBIR_real_data.mat','all_phylosub_outputs');
-load('/home/surjray/Phylogeny_repo/phylogenetic_tree_software_with_matlab_wrappers/all_tests/all_results/citup_all_files_ELKEBIR_real_data.mat','all_citup_outputs');
-load('/home/surjray/Phylogeny_repo/phylogenetic_tree_software_with_matlab_wrappers/all_tests/all_results/all_canopy_outputs_on_real_Elkebir_data.mat','all_canopy_outputs');
+load([pwd, '/../all_tests/all_results/our_code_on_real_data_tree_sizes_6_9_top_20.mat'],'all_our_code_outputs');
+load([pwd, '/../all_tests/all_results/ancestree_all_files_minus_a_few_ELKEBIR_real_data.mat'],'all_ancestree_output');
+load([pwd, '/../all_tests/all_results/phyloWGS_all_files_ELKEBIR_real_data.mat'],'all_phylosub_outputs');
+load([pwd, '/../all_tests/all_results/citup_all_files_ELKEBIR_real_data.mat'],'all_citup_outputs');
+load([pwd, '/../all_tests/all_results/all_canopy_outputs_on_real_Elkebir_data.mat'],'all_canopy_outputs');
 
 %% comparing all tools on Schuh et al predicted outputs
 % Here we are focusing on the real data files that were obtained from the

phylogenetic_tree_software_with_matlab_wrappers/all_tests/comparing_all_tools_on_shuh_2012_predicted_results.m

@@ -12,11 +12,11 @@
 
 %% Loading workspaces with results of EXACT, AncesTree, PhyloWGS, CITUP and Canopy respectively. 
 % The results were generated by running the tools on the real data provided in the paper: https://www.ncbi.nlm.nih.gov/pubmed/26072510
-load('/home/surjray/Phylogeny_repo/phylogenetic_tree_software_with_matlab_wrappers/all_tests/all_results/our_code_on_real_data_tree_sizes_6_9_top_20.mat','all_our_code_outputs');
-load('/home/surjray/Phylogeny_repo/phylogenetic_tree_software_with_matlab_wrappers/all_tests/all_results/ancestree_all_files_minus_a_few_ELKEBIR_real_data.mat','all_ancestree_output');
-load('/home/surjray/Phylogeny_repo/phylogenetic_tree_software_with_matlab_wrappers/all_tests/all_results/phyloWGS_all_files_ELKEBIR_real_data.mat','all_phylosub_outputs');
-load('/home/surjray/Phylogeny_repo/phylogenetic_tree_software_with_matlab_wrappers/all_tests/all_results/citup_all_files_ELKEBIR_real_data.mat','all_citup_outputs');
-load('/home/surjray/Phylogeny_repo/phylogenetic_tree_software_with_matlab_wrappers/all_tests/all_results/all_canopy_outputs_on_real_Elkebir_data.mat','all_canopy_outputs');
+load([pwd, '/../all_tests/all_results/our_code_on_real_data_tree_sizes_6_9_top_20.mat'],'all_our_code_outputs');
+load([pwd, '/../all_tests/all_results/ancestree_all_files_minus_a_few_ELKEBIR_real_data.mat'],'all_ancestree_output');
+load([pwd, '/../all_tests/all_results/phyloWGS_all_files_ELKEBIR_real_data.mat'],'all_phylosub_outputs');
+load([pwd, '/../all_tests/all_results/citup_all_files_ELKEBIR_real_data.mat'],'all_citup_outputs');
+load([pwd, '/../all_tests/all_results/all_canopy_outputs_on_real_Elkebir_data.mat'],'all_canopy_outputs');
 
 %% comparing all tools on Schuh et al predicted outputs
 % Here we are focusing on the real data files that were obtained from the

phylogenetic_tree_software_with_matlab_wrappers/all_tests/comparing_all_tools_on_usage_of_M_matrices_shuh_2012_predicted_results.m

@@ -11,11 +11,11 @@
 % GNU General Public License for more details.
 
 %% Loading workspaces with results of EXACT, AncesTree, PhyloWGS, CITUP and Canopy respectively. 
-load('/home/surjray/Phylogeny_repo/phylogenetic_tree_software_with_matlab_wrappers/all_tests/all_results/our_code_on_real_data_tree_sizes_6_9_top_20.mat','all_our_code_outputs');
-load('/home/surjray/Phylogeny_repo/phylogenetic_tree_software_with_matlab_wrappers/all_tests/all_results/ancestree_all_files_minus_a_few_ELKEBIR_real_data.mat','all_ancestree_output');
-load('/home/surjray/Phylogeny_repo/phylogenetic_tree_software_with_matlab_wrappers/all_tests/all_results/phyloWGS_all_files_ELKEBIR_real_data.mat','all_phylosub_outputs');
-load('/home/surjray/Phylogeny_repo/phylogenetic_tree_software_with_matlab_wrappers/all_tests/all_results/citup_all_files_ELKEBIR_real_data.mat','all_citup_outputs');
-load('/home/surjray/Phylogeny_repo/phylogenetic_tree_software_with_matlab_wrappers/all_tests/all_results/all_canopy_outputs_on_real_Elkebir_data.mat','all_canopy_outputs');
+load([pwd, '/../all_tests/all_results/our_code_on_real_data_tree_sizes_6_9_top_20.mat'],'all_our_code_outputs');
+load([pwd, '/../all_tests/all_results/ancestree_all_files_minus_a_few_ELKEBIR_real_data.mat'],'all_ancestree_output');
+load([pwd, '/../all_tests/all_results/phyloWGS_all_files_ELKEBIR_real_data.mat'],'all_phylosub_outputs');
+load([pwd, '/../all_tests/all_results/citup_all_files_ELKEBIR_real_data.mat'],'all_citup_outputs');
+load([pwd, '/../all_tests/all_results/all_canopy_outputs_on_real_Elkebir_data.mat'],'all_canopy_outputs');
 
 
 alg = 1;

phylogenetic_tree_software_with_matlab_wrappers/citup/run_me.m

@@ -1,8 +1,16 @@
 %% example of how to use CITUP
 
+% first install CVX, if it is not install yet
+% we recommend downloading, and installing, the latest CVX version from
+% www.cvxr.com/cvx
+run([pwd, '/../EXACT/distribution/cvx/cvx/cvx_setup']);
+
 % adding path for the CITUP folders
 addpath(genpath(pwd));
 
+% to find functions to produce plots and compute errors
+addpath([pwd, '/../all_tests/']);
+
 % input file
 pwd_CITUP = pwd;
 input_file = [pwd_CITUP, '/../all_tests/Sample_test_data/AncesTree_data/simulated/Cov_1000_Samples_6_Mut_100_Clone_10_PCR_Removed/sim_4.input'];