From 6d1a403bf745719a59f9eaa5fedc0bf4de130347 Mon Sep 17 00:00:00 2001
From: Vyacheslav Brover <vyacheslav.brover@nih.gov>
Date: Fri, 14 Feb 2025 10:05:41 -0500
Subject: [PATCH] phylogeny/inc/genome/Fungi/

---
 phylogeny/inc/genome/Fungi/genogroup2db.sh           |  8 ++++----
 phylogeny/inc/genome/Fungi/object2closest.sh         | 12 ++++++------
 phylogeny/inc/genome/Fungi/objects_in_tree.sh        |  8 ++++----
 phylogeny/inc/genome/Fungi/outlier2db.sh             |  6 +++---
 phylogeny/inc/genome/Fungi/pair2report.sh            |  2 +-
 phylogeny/inc/genome/Fungi/pairs2dissim.sh           |  2 +-
 phylogeny/inc/genome/bacteria_type/object2closest.sh |  4 ++--
 7 files changed, 21 insertions(+), 21 deletions(-)

diff --git a/phylogeny/inc/genome/Fungi/genogroup2db.sh b/phylogeny/inc/genome/Fungi/genogroup2db.sh
index 05ca255f..5bdd1730 100755
--- a/phylogeny/inc/genome/Fungi/genogroup2db.sh
+++ b/phylogeny/inc/genome/Fungi/genogroup2db.sh
@@ -8,10 +8,10 @@ fi
 IN=$1
 
 
-INC=`dirname $0`
-SERVER=`cat $INC/server`
-DATABASE=`cat $INC/database`
-BULK_REMOTE=`cat $INC/bulk_remote`
+INC=$( dirname $0 )
+SERVER=$( cat $INC/server )
+DATABASE=$( cat $INC/database )
+BULK_REMOTE=$( cat $INC/bulk_remote )
 
 CPP_DIR/bulk.sh $SERVER $INC/bulk $BULK_REMOTE $IN $DATABASE..ListC
 
diff --git a/phylogeny/inc/genome/Fungi/object2closest.sh b/phylogeny/inc/genome/Fungi/object2closest.sh
index f969aa8a..30c5ee14 100755
--- a/phylogeny/inc/genome/Fungi/object2closest.sh
+++ b/phylogeny/inc/genome/Fungi/object2closest.sh
@@ -14,16 +14,16 @@ SUBSET=$3
 OUT=$4
 
 
-INC=`dirname $0`
-SERVER=`cat $INC/server`
-DATABASE=`cat $INC/database`
-BULK_REMOTE=`cat $INC/bulk_remote`
-TAX=`cat $INC/../tax_id`
+INC=$( dirname $0 )
+SERVER=$( cat $INC/server )
+DATABASE=$( cat $INC/database )
+BULK_REMOTE=$( cat $INC/bulk_remote )
+TAX=$( cat $INC/../tax_id )
 
 if [ -z $DIR ]; then
   DIR=$INC/../genome
   if [ -e $INC/large ]; then
-    H=`CPP_DIR/file2hash $GENOME`
+    H=$( CPP_DIR/file2hash $GENOME )
     DIR=$DIR/$H/$GENOME
   fi
 fi
diff --git a/phylogeny/inc/genome/Fungi/objects_in_tree.sh b/phylogeny/inc/genome/Fungi/objects_in_tree.sh
index bd05daa3..59b83c5f 100755
--- a/phylogeny/inc/genome/Fungi/objects_in_tree.sh
+++ b/phylogeny/inc/genome/Fungi/objects_in_tree.sh
@@ -10,10 +10,10 @@ OBJ_LIST=$1
 IN_TREE=$2
 
 
-INC=`dirname $0`
-SERVER=`cat $INC/server`
-DATABASE=`cat $INC/database`
-BULK_REMOTE=`cat $INC/bulk_remote`
+INC=$( dirname $0 )
+SERVER=$( cat $INC/server )
+DATABASE=$( cat $INC/database )
+BULK_REMOTE=$( cat $INC/bulk_remote )
 
 CPP_DIR/bulk.sh $SERVER $INC/bulk $BULK_REMOTE $OBJ_LIST $DATABASE..List
 
diff --git a/phylogeny/inc/genome/Fungi/outlier2db.sh b/phylogeny/inc/genome/Fungi/outlier2db.sh
index 90fd69de..a142fd47 100755
--- a/phylogeny/inc/genome/Fungi/outlier2db.sh
+++ b/phylogeny/inc/genome/Fungi/outlier2db.sh
@@ -8,9 +8,9 @@ if [ $# -ne 2 ]; then
 fi
 
 
-INC=`dirname $0`
-SERVER=`cat $INC/server`
-DATABASE=`cat $INC/database`
+INC=$( dirname $0 )
+SERVER=$( cat $INC/server )
+DATABASE=$( cat $INC/database )
 
 sqsh-ms -S $SERVER  -D $DATABASE  << EOT
   update Genome
diff --git a/phylogeny/inc/genome/Fungi/pair2report.sh b/phylogeny/inc/genome/Fungi/pair2report.sh
index c80da070..ae21e5d6 100755
--- a/phylogeny/inc/genome/Fungi/pair2report.sh
+++ b/phylogeny/inc/genome/Fungi/pair2report.sh
@@ -24,7 +24,7 @@ if [ $NEW == 0 ]; then
   H1=$( CPP_DIR/file2hash $OBJ1 )
   PATH1=$GENOME/$H1/$OBJ1/$OBJ1
 else
-  PATH1=$OBJ1/`basename $OBJ1`
+  PATH1=$OBJ1/$( basename $OBJ1 )
 fi
 
 H2=$( CPP_DIR/file2hash $OBJ2 )
diff --git a/phylogeny/inc/genome/Fungi/pairs2dissim.sh b/phylogeny/inc/genome/Fungi/pairs2dissim.sh
index fad0d346..c4a6e1e9 100755
--- a/phylogeny/inc/genome/Fungi/pairs2dissim.sh
+++ b/phylogeny/inc/genome/Fungi/pairs2dissim.sh
@@ -4,7 +4,7 @@ if [ $# -ne 4 ]; then
   echo "Compute dissimilarities for pairs of objects"
   echo "#1: input dissimilarity requests (pairs of objects)"
   echo "#2: new object path or ''. Object name is basename"
-  echo "#3: output dissimilarities added to the pairs of objects"
+  echo "#3: output dissimilarities added to the pairs of objects (absolute pathname)"
   echo "#4: error log"
   exit 1
 fi
diff --git a/phylogeny/inc/genome/bacteria_type/object2closest.sh b/phylogeny/inc/genome/bacteria_type/object2closest.sh
index 438f7571..2fdf1d3b 100755
--- a/phylogeny/inc/genome/bacteria_type/object2closest.sh
+++ b/phylogeny/inc/genome/bacteria_type/object2closest.sh
@@ -14,12 +14,12 @@ SUBSET=$3
 OUT=$4
 
 
-INC=`dirname $0`
+INC=$( dirname $0 )
 
 if [ -z $DIR ]; then
   DIR=$INC/../genome
   if [ -e $INC/large ]; then
-    H=`CPP_DIR/file2hash $GENOME`
+    H=$( CPP_DIR/file2hash $GENOME )
     DIR=$DIR/$H/$GENOME
   fi
 fi