# HG changeset patch
# User pjbriggs
# Date 1576071905 0
# Node ID 4bfa62618f7c106e056c632d5609e86603b0139d
# Parent  213b5cdecb70c42237f88a0f5eb80f09eba13b2a
planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 3dcfecb6c83d655529be44366d9e55913df9dffd

diff -r 213b5cdecb70 -r 4bfa62618f7c amplicon_analysis_pipeline.xml
--- a/amplicon_analysis_pipeline.xml	Mon Dec 09 13:00:31 2019 +0000
+++ b/amplicon_analysis_pipeline.xml	Wed Dec 11 13:45:05 2019 +0000
@@ -85,7 +85,7 @@
   cp fastqc_quality_boxplots.html "${fastqc_quality_boxplots_html}" &&
 
   ## OTU table heatmap
-  cp RESULTS/${pipeline_name}_${reference_database_name}/Heatmap.pdf "${heatmap_otu_table_pdf}"" &&
+  cp RESULTS/${pipeline_name}_${reference_database_name}/Heatmap.pdf "${heatmap_otu_table_pdf}" &&
 
   ## HTML outputs
 
diff -r 213b5cdecb70 -r 4bfa62618f7c install_amplicon_analysis-1.3.5.sh
--- a/install_amplicon_analysis-1.3.5.sh	Mon Dec 09 13:00:31 2019 +0000
+++ b/install_amplicon_analysis-1.3.5.sh	Wed Dec 11 13:45:05 2019 +0000
@@ -88,6 +88,9 @@
     wget -q https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
     bash ./Miniconda2-latest-Linux-x86_64.sh -b -p ${CONDA_DIR}
     echo Installed conda in ${CONDA_DIR}
+    echo -n "Adding conda bin to PATH..."
+    export PATH=${CONDA_BIN}:$PATH
+    echo "ok"
     # Reset the conda version to a known working version
     # (to avoid problems observed with e.g. conda 4.7.10)
     echo ""
@@ -100,9 +103,6 @@
     echo -n "Rewriting conda shebangs..."
     rewrite_conda_shebangs
     echo "ok"
-    echo -n "Adding conda bin to PATH..."
-    export PATH=${CONDA_BIN}:$PATH
-    echo "ok"
     cd $cwd
     rm -rf $wd/*
     rmdir $wd