From 79777573a56c7df55f5e64bfa414ab75b7ac52a2 Mon Sep 17 00:00:00 2001
From: Marcel Bargull <marcel.bargull@udo.edu>
Date: Sat, 9 Jun 2018 08:37:04 +0200
Subject: [PATCH] r-ngsplot: patch all scripts, avoid activation script

---
 recipes/r-ngsplot/build.sh              | 26 ++++++++++---------------
 recipes/r-ngsplot/scripts/deactivate.sh |  4 ----
 2 files changed, 10 insertions(+), 20 deletions(-)
 delete mode 100644 recipes/r-ngsplot/scripts/deactivate.sh

diff --git a/recipes/r-ngsplot/build.sh b/recipes/r-ngsplot/build.sh
index 61b519ff5c7c5..3ec522d58bca1 100644
--- a/recipes/r-ngsplot/build.sh
+++ b/recipes/r-ngsplot/build.sh
@@ -3,23 +3,17 @@ outdir=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM
 mkdir -p $outdir
 mkdir -p $PREFIX/bin
 cp -R {bin,database,example,galaxy,lib,LICENSE} ${outdir}/
-#Set up links for 
+# Set up links for 
 for f in ${outdir}/bin/*; do
     ln -s ${f} ${PREFIX}/bin
 done
 
-#Activate/Deactivate dir
-ACTIVATE_DIR=$PREFIX/etc/conda/activate.d
-DEACTIVATE_DIR=$PREFIX/etc/conda/deactivate.d
-mkdir -p $ACTIVATE_DIR
-mkdir -p $DEACTIVATE_DIR
-cp $RECIPE_DIR/scripts/deactivate.sh $DEACTIVATE_DIR/${PKG_NAME}-deactivate.sh
-#Create activate.sh script
-echo > "${ACTIVATE_DIR}/${PKG_NAME}-activate.sh" <<EOF
-#!/bin/bash
-export NGSPLOT="${outdir}"
-export _CONDA_SET_NGSPLOT_ENV=1
-EOF
-
-#Patch ngs.plot.R to use proper path
-sed -i "s#^progpath.*#progpath=$outdir#g" ${outdir}/bin/ngs.plot.r
\ No newline at end of file
+# Patch scripts to use proper path and not depend on NGSPLOT env variable
+for f in "${outdir}"/bin/*.py ; do
+    sed -Ei.bak "s|os\.environ\[\"NGSPLOT\"\]|\"${outdir}\"|g" "${f}"
+    rm "${f}.bak"
+done
+for f in "${outdir}"/bin/{,backup}/*.r ; do
+    sed -Ei.bak "s|Sys\.getenv\('NGSPLOT'\)|\"${outdir}\"|g" "${f}"
+    rm "${f}.bak"
+done
diff --git a/recipes/r-ngsplot/scripts/deactivate.sh b/recipes/r-ngsplot/scripts/deactivate.sh
deleted file mode 100644
index 9dd8e8e66515e..0000000000000
--- a/recipes/r-ngsplot/scripts/deactivate.sh
+++ /dev/null
@@ -1,4 +0,0 @@
-if [[ -n "$_CONDA_SET_NGSPLOT_ENV" ]]; then
-	unset NGSPLOT
-	unset _CONDA_SET_NGSPLOT_ENV
-fi
\ No newline at end of file