Commit a7e74199 authored by Michael R. Crusoe's avatar Michael R. Crusoe 🏳️‍🌈
Browse files

New upstream version 2.6.6+dfsg

parent e6bd23d0

Analysis/DifferentialExpression/PtR

+2 −1
Original line number Diff line number Diff line
@@ -567,6 +567,7 @@ main: { 
    #$Rscript .= "library(gplots)\n";

    $Rscript .= "library(Biobase)\n";

    $Rscript .= "library(qvalue)\n";

    $Rscript .= "library(fastcluster)\n";



    $Rscript .= "options(stringsAsFactors = FALSE)\n";
@@ -1674,7 +1675,7 @@ main: { 
    print $ofh $Rscript;

    close $ofh;

    

    &process_cmd("R --vanilla -q < $R_script_file");

    &process_cmd("R --no-save --no-restore --no-site-file --no-init-file -q < $R_script_file");



    exit(0);

Analysis/DifferentialExpression/cut_tree_into_clusters.pl

+2 −1
Original line number Diff line number Diff line
@@ -87,6 +87,7 @@ main: { 
    print $ofh "library(cluster)\n";

    #print $ofh "library(gplots)\n";

    print $ofh "library(Biobase)\n";

    print $ofh "library(fastcluster)\n";

    print $ofh "source(\"$FindBin::RealBin/R/heatmap.3.R\")\n";

    

    print $ofh "load(\"$R_data_file\")\n";
@@ -126,7 +127,7 @@ main: { 
    close $ofh;

    



    &process_cmd("R --vanilla -q < $R_script");

    &process_cmd("R --no-save --no-restore --no-site-file --no-init-file -q < $R_script");



    exit(0);

Analysis/DifferentialExpression/define_clusters_by_cutting_tree.pl

+2 −1
Original line number Diff line number Diff line
@@ -88,6 +88,7 @@ main: { 
    print $ofh "library(cluster)\n";

    #print $ofh "library(gplots)\n";

    print $ofh "library(Biobase)\n";

    print $ofh "library(fastcluster)\n";

    print $ofh "source(\"$FindBin::RealBin/R/heatmap.3.R\")\n";

    

    print $ofh "load(\"$R_data_file\")\n";
@@ -180,7 +181,7 @@ main: { 
    close $ofh;





    &process_cmd("R --vanilla -q < $R_script");

    &process_cmd("R --no-save --no-restore --no-site-file --no-init-file -q < $R_script");



    

    ###################################################

Analysis/DifferentialExpression/diff_expr_analysis_to_heatmap_html.pl

+1 −1
Original line number Diff line number Diff line
@@ -84,7 +84,7 @@ main: { 
        print $ofh "get_cluster_info(\"$R_data_file\")\n";

        close $ofh;

        

        &process_cmd("R --vanilla -q --slave < $R_script");

        &process_cmd("R --no-save --no-restore --no-site-file --no-init-file -q --slave < $R_script");



        

        open (my $fh, $matrix_data) or die "Error, cannot open file $matrix_data";

Analysis/DifferentialExpression/matrix_to_gene_plots.pl

+1 −1
Original line number Diff line number Diff line
@@ -108,7 +108,7 @@ main: { 
    close $ofh;

    



    &process_cmd("R --vanilla -q < $R_script");

    &process_cmd("R --no-save --no-restore --no-site-file --no-init-file -q < $R_script");

    



    exit(0);