From 2e088155bb29d7aa327b84719f7cf7a99203316b Mon Sep 17 00:00:00 2001
From: Kevin Hsieh <kevin899@gmail.com>
Date: Wed, 28 Nov 2018 10:30:08 -0800
Subject: [PATCH] Re-enable metaphlan

---
 README.md  |  2 +-
 install.sh | 19 ++++++-------------
 rop.sh     |  8 ++++----
 3 files changed, 11 insertions(+), 18 deletions(-)

diff --git a/README.md b/README.md
index 1458b6c..54abf01 100644
--- a/README.md
+++ b/README.md
@@ -74,7 +74,7 @@ of the pipeline. The following options are available:
     - A comma-separated list of one or more of the following: lowq, rdna,
       reference, repeats, circrna, immune, microbiome (which may be subdivided
       into metaphlan, bacteria, viral, fungi, protozoa).
-    - circrna, metaphlan, and bacteria are not available in the current release.
+    - circrna and bacteria are not available in the current release.
     - `-s all` selects everything.
 - `-a|--fasta`: Input unmapped reads in .fasta format instead of .fastq format.
   Forcibly disables low-quality read filtering.
diff --git a/install.sh b/install.sh
index fa1d121..4144218 100755
--- a/install.sh
+++ b/install.sh
@@ -182,13 +182,13 @@ else
     cd ..
 
     # Download MetaPhlAn 2.
-    #echo '----- Downloading MetaPhlAn 2 --------------------------------------------------'
-    #hg clone https://bitbucket.org/biobakery/metaphlan2
-    #cd metaphlan2
+    echo '----- Downloading MetaPhlAn 2 --------------------------------------------------'
+    hg clone https://bitbucket.org/biobakery/metaphlan2
+    cd metaphlan2
     #ln -s ../../db_human/databases
-    #cd ..
+    cd ..
 
-    # Download MiniConda and add shebangs.
+    # Download MiniConda.
     echo '----- Setting up Python environment --------------------------------------------'
     if [ $NATIVE = false ]; then
         ./install-MiniConda.sh
@@ -196,13 +196,6 @@ else
         ln -s libncursesw.so.5 libtinfow.so.5
         cd ../..
         MiniConda="$PWD/MiniConda/bin/python"
-    #    sed -i "1c #!$MiniConda" metaphlan2/metaphlan2.py
-    #    sed -i "1c #!$MiniConda" metaphlan2/strainphlan.py
-    #    sed -i "1c #!$MiniConda" metaphlan2/utils/read_fastx.py
-    #else
-    #    sed -i '1c #!/usr/bin/env python2.7' metaphlan2/metaphlan2.py
-    #    sed -i '1c #!/usr/bin/env python2.7' metaphlan2/strainphlan.py
-    #    sed -i '1c #!/usr/bin/env python2.7' metaphlan2/utils/read_fastx.py
     fi
 fi
 
@@ -260,7 +253,7 @@ for database in $SELECT_DB; do
             download_list+=$'\nmetaphlan\nviral\nviral_vipr\nfungi\nprotozoa'
             ;;
         metaphlan)
-            #download_list+=$'\nmetaphlan'
+            download_list+=$'\nmetaphlan'
             ;;
         viral)
             download_list+=$'\nviral\nviral_vipr'
diff --git a/rop.sh b/rop.sh
index 3adbadd..432c82a 100755
--- a/rop.sh
+++ b/rop.sh
@@ -45,9 +45,9 @@ eval set -- "$PARSED"
 
 # Set default options.
 ORGANISM='human'
-STEPS='rdna reference repeats viral fungi protozoa'
+STEPS='rdna reference repeats immune metaphlan viral fungi protozoa'
     # Non-default: lowq
-    # Disabled: circrna immune metaphlan bacteria
+    # Disabled: circrna bacteria
 FASTA=false
 BAM=false
 GZIP=false
@@ -553,8 +553,8 @@ echo '7a. MetaPhlAn profiling (-s metaphlan)...'
 cd "${DIRS['07a_metaphlan']}"
 # No post file (don't reduce unmapped reads using MetaPhlAn results).
 
-if ! grep -qE 'metaphlan|microbiome' <<<"$STEPS" || ! reads_present "$current" \
-    || ! grep -q 'override' <<<"$STEPS"; then  # Disabled (broken).
+if ! grep -qE 'metaphlan|microbiome' <<<"$STEPS" || ! reads_present "$current";
+then
     echo '--> Skipped MetaPhlAn profiling.'
 else
     python "$DIR/tools/metaphlan2/metaphlan2.py" "$current" \