removed installation of all perl dependencies

INSTALL.sh

@@ -37,7 +37,6 @@ fi
 export R_LIBS="$ROOTDIR/ext/lib/R:$R_LIBS:$R_LIBS_USER"
 
 # Minimum Required versions of dependencies
-# cpanm_VER=1.7039
 miniconda_VER=4.3.21
 samtools_VER=1.3.1
 bamtools_VER=2.4.0
@@ -53,10 +52,6 @@ subread_VER=1.5.0
 # perl5_VER=5.16.3
 python2_VER=2.7.12
 
-#minimum required version of Perl modules
-# perl_String_Approx_VER=3.27
-# perl_Parllel_ForkManager_VER=1.17
-
 #minimum required version of R modules
 R_edgeR_VER=3.14.0
 R_DESeq2_VER=1.12.4
@@ -207,22 +202,6 @@ echo "
 "
 }
 
-# install_perl_Parallel_ForkManager()
-# {
-# echo "--------------------------------------------------------------------------
-#   Installing Perl Module Parallel-ForkManager v$perl_Parllel_ForkManager_VER
-# --------------------------------------------------------------------------------
-# "
-
-# cpanm Parallel::ForkManager@$perl_Parllel_ForkManager_VER -l $ROOTDIR/ext
-# # conda install --yes -c bioconda perl-parallel-forkmanager=$perl_Parllel_ForkManager_VER
-# echo "
-# --------------------------------------------------------------------------------
-#       Parallel-ForkManager-$perl_Parllel_ForkManager_VER Installed
-# --------------------------------------------------------------------------------
-# "
-# }
-
 install_samtools()
 {
 echo "--------------------------------------------------------------------------
@@ -252,21 +231,6 @@ echo "
 "
 }
 
-# install_cpanm()
-# {
-# echo "--------------------------------------------------------------------------
-#                            Installing cpanm
-# --------------------------------------------------------------------------------
-# "
-# conda install --yes -c bioconda perl-app-cpanminus=$cpanm_VER -p $ROOTDIR/thirdParty/miniconda
-# ln -sf $ROOTDIR/thirdParty/miniconda/bin/cpanm $ROOTDIR/bin/cpanm
-# echo "
-# --------------------------------------------------------------------------------
-#                            cpanm installed
-# --------------------------------------------------------------------------------
-# "
-# }
-
 install_R()
 {
 echo "--------------------------------------------------------------------------
@@ -342,31 +306,6 @@ echo "
 "
 }
 
-
-# install_perl_string_approx()
-# {
-# echo "------------------------------------------------------------------------------
-#                  Installing Perl Module String-Approx-3.27
-# ------------------------------------------------------------------------------
-# "
-# cd $ROOTDIR/thirdParty
-# tar xvzf String-Approx-3.27.tar.gz
-# cd String-Approx-3.27
-# perl Makefile.PL 
-# make
-# mkdir -p $ROOTDIR/ext/lib/perl5/auto
-# mkdir -p $ROOTDIR/ext/lib/perl5/auto/String
-# mkdir -p $ROOTDIR/ext/lib/perl5/auto/String/Approx
-# cp -fR blib/lib/* $ROOTDIR/ext/lib/perl5
-# cp -fR blib/arch/auto/String/Approx/Approx.* $ROOTDIR/ext/lib/perl5/auto/String/Approx/
-# cd $ROOTDIR/thirdParty
-# echo "
-# ------------------------------------------------------------------------------
-#                         String-Approx-3.27 Installed
-# ------------------------------------------------------------------------------
-# "
-# }
-
 install_gffread()
 {
 echo "--------------------------------------------------------------------------
@@ -440,10 +379,6 @@ echo "
 "
 }
 
-
-
-
-
 checkSystemInstallation()
 {
     IFS=:
@@ -703,10 +638,6 @@ else
     install_R_DESeq2
 fi
 
-
-
-
-
 ################################################################################
 if ( checkSystemInstallation featureCounts )
 then
@@ -771,22 +702,6 @@ fi
 #   install_jbrowse
 # fi
 
-################################################################################
-# if ( checkSystemInstallation cpanm )
-# then
-#   cpanm_installed_VER=`cpanm -V 2>&1| head -n 1 | grep 'version' | perl -nle 'print $& if m{version \d+\.\d+}'`;
-#   if  ( echo $cpanm_installed_VER $cpanm_VER | awk '{if($2>=$3) exit 0; else exit 1}' )
-#   then 
-#     echo " - found cpanm $cpanm_installed_VER"
-#   else
-#   echo "Required version of cpanm was not found"
-#   install_cpanm
-#   fi
-# else 
-#   echo "cpanm was not found"
-#   install_cpanm
-# fi
-
 ################################################################################
 if ( checkSystemInstallation gffread )
 then
@@ -804,42 +719,6 @@ else
  echo "FaQCs is not found"
  install_FaQCs
 fi
-################################################################################
-#                        Perl Modules
-################################################################################
-
-# if ( checkPerlModule Parallel::ForkManager )
-# then
-#   perl_Parallel_ForkManager_installed_VER=`perl -MParallel::ForkManager -e 'print $Parallel::ForkManager::VERSION ."\n";'`
-#   if ( echo $perl_Parallel_ForkManager_installed_VER $perl_Parallel_ForkManager_VER | awk '{if($1>=$2) exit 0; else exit 1}')
-#   then
-#     echo " - found Perl module Parallel::ForkManager $perl_Parallel_ForkManager_installed_VER"
-#   else
-#     echo "Required version of Parallel::ForkManager $perl_Parallel_ForkManager_VER was not found"
-#     install_perl_Parallel_ForkManager
-#   fi
-# else
-#   echo "Perl Parallel::ForkManager is not found"
-#   install_perl_Parallel_ForkManager
-# fi
-
-################################################################################
-
-# if ( checkPerlModule String::Approx )
-# then
-
-#   perl_String_Approx_installed_VER=`perl -MString::Approx -e 'print $String::Approx::VERSION ."\n";'`
-#   if ( echo $perl_String_Approx_installed_VER $perl_String_Approx_VER | awk '{if($1>=$2) exit 0; else exit 1}' )
-#   then
-#     echo " - found Perl module String::Approx $perl_String_Approx_installed_VER"
-#   else
-#     echo "Required version of String::Approx $perl_String_Approx_VER was not found"
-#     install_perl_string_approx
-#   fi
-# else
-#   echo "Perl String::Approx was not found"
-#   install_perl_string_approx
-# fi
 
 ################################################################################
 #                        Python Modules