diff --git a/tools/fragpipe/fragpipe.xml b/tools/fragpipe/fragpipe.xml
index 0ba0abbc4..cb053f90f 100644
--- a/tools/fragpipe/fragpipe.xml
+++ b/tools/fragpipe/fragpipe.xml
@@ -42,8 +42,8 @@
                 --workflow fp.workflow --manifest fp.manifest
                 --workdir outputs
                 --config-msfragger \${CONDA_PREFIX}/share/msfragger-*/MSFragger-*/MSFragger-*.jar
-                --config-philosopher `which philosopher`
-                --config-python `which python`
+                --config-philosopher \$(which philosopher)
+                --config-python \$(which python)
                 --config-ionquant \${CONDA_PREFIX}/share/ionquant-*/IonQuant.jar &&
 
             @PREPARE_OUTPUTS@
diff --git a/tools/fragpipe/macros.xml b/tools/fragpipe/macros.xml
index d546e174b..e5f64c690 100644
--- a/tools/fragpipe/macros.xml
+++ b/tools/fragpipe/macros.xml
@@ -47,7 +47,7 @@
       Annotation files are copied into the scan directory for TMT workflows.
     -->
     <token name="@LINK_SAMPLES@"><![CDATA[
-        CWD=`pwd | sed 's/\//\\\\\//g'` &&
+        CWD=\$(pwd | sed 's/\//\\\//g') &&
 
         mkdir -p scans &&
         #if $wf.workflow_name == "TMT10" or $wf.workflow_name == "TMT11"
@@ -110,12 +110,12 @@
         ## For example, the entries sample1/psm.tsv and sample2/psm.tsv would be combined to concat_psm.tsv, a single psm.tsv header as its first line.
         for f in psm.tsv ion.tsv peptide.tsv protein.tsv; do
             n=0;
-            for i in `find * -name \${f}`; do
+            for i in \$(find * -name \${f}); do
                 d=\${i%/*};
                 if [[ \$n == 0 ]]; then
                     awk 'NR==1{printf("Experiment\t%s\n",\$0);}' \$i > concat_\${f};
                 fi;
-                awk 'NR>1{printf("'"\${d}"'\t%s\n",\$0);}' \$i >> concat_\${f}; t=`echo \${i} | tr '/' '.'`;
+                awk 'NR>1{printf("'"\${d}"'\t%s\n",\$0);}' \$i >> concat_\${f}; t=\$(echo \${i} | tr '/' '.');
                 mv \${i} \${t}; n=\$((n+1));
             done;
         done