diff --git a/workflow/qhtcp-workflow b/workflow/qhtcp-workflow index dc21c9e2..c702e946 100755 --- a/workflow/qhtcp-workflow +++ b/workflow/qhtcp-workflow @@ -530,7 +530,7 @@ install_dependencies() { depends_rpm=(graphviz pandoc pdftk-java gd-devel perl-CPAN shdoc nano rsync coreutils libcurl-devel openssl-devel) depends_deb=(graphviz pandoc pdftk-java libgd-dev perl shdoc nano rsync coreutils libcurl-dev openssl-dev) depends_brew=(graphiz pandoc gd pdftk-java shdoc nano perl rsync coreutils) - depends_perl=(File::Map Sub::Uplevel ExtUtils::Config ExtUtils::PkgConfig Module::Build::Tiny GD GO::TermFinder) + depends_perl=(File::Map Sub::Uplevel ExtUtils::Config ExtUtils::PkgConfig Module::Build::Tiny IPC::Run GD GO::TermFinder) depends_r=(BiocManager ontologyIndex ggrepel tidyverse sos openxlsx ggplot2 plyr extrafont gridExtra gplots stringr plotly ggthemes pandoc rmarkdown plotly htmlwidgets) @@ -568,7 +568,7 @@ install_dependencies() { # Install perl CPAN modules echo "Installing perl CPAN modules" echo "It is recommended to use the local::lib perl library if prompted" - debug "cpan -I ${depends_perl[*]}" + debug "cpan -I -i ${depends_perl[*]}" cpan -I -i "${depends_perl[@]}" # Install R packages