stacks: fix for @ in exe_path (#11580)

* stacks: fix for @ in exe_path * stacks: fixed path
bioconda · Oct 26, 2018 · 68165e2 · 68165e2
1 parent 3d03503
commit 68165e2
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Showing 2 changed files with 12 additions and 3 deletions.
diff --git a/recipes/stacks/2.2/build.sh b/recipes/stacks/2.2/build.sh
@@ -11,8 +11,17 @@ fi
 
 export CXXFLAGS="${CXXFLAGS} -std=c++11"
 
-./configure --prefix=$PREFIX --enable-bam
+./configure --prefix="$PREFIX" --enable-bam
 make
 make install
 # copy missing scripts
-cp -p scripts/{convert_stacks.pl,extract_interpop_chars.pl} $PREFIX/bin/
+cp -p scripts/{convert_stacks.pl,extract_interpop_chars.pl} "$PREFIX/bin/"
+
+# after installation the exe_dir is set to the absolute binary path 
+# this is not necessary and leads to an error if there are characters 
+# like @ included (Galaxy)
+for i in ref_map.pl denovo_map.pl
+do
+	sed -i -e 's/\(my $exe_path\s\+= \).*/\1"";/' "$PREFIX/bin/$i"
+done
+
diff --git a/recipes/stacks/2.2/meta.yaml b/recipes/stacks/2.2/meta.yaml
@@ -6,7 +6,7 @@ package:
   version: {{ version }}
 
 build:
-  number: 0
+  number: 1
 
 source:
   sha256: {{ hash }}