From dc016fadc5d013447da2a2f891d5eea5b54b8d82 Mon Sep 17 00:00:00 2001
From: Marcel Bargull <mbargull@users.noreply.github.com>
Date: Thu, 9 Aug 2018 06:09:52 +0200
Subject: [PATCH] lumpy: trying to fix skipped build (#10338)

* lumpy: use python version restriction instead of selector

* lumpy: pass on compiler/linker flags to make

* lumpy: add C(PLUS)?_INCLUDE_PATH exports again because the world ain't perfect

* lumpy-sv: also export LIBRARY_PATH...

* lumpy-sv: fix extractSplitReads_BwaMem path
---
 recipes/lumpy-sv/build.sh  | 21 +++++++++++++++------
 recipes/lumpy-sv/meta.yaml |  7 ++-----
 2 files changed, 17 insertions(+), 11 deletions(-)

diff --git a/recipes/lumpy-sv/build.sh b/recipes/lumpy-sv/build.sh
index 15cf21daf3daa..d22a5a419af31 100644
--- a/recipes/lumpy-sv/build.sh
+++ b/recipes/lumpy-sv/build.sh
@@ -1,10 +1,11 @@
 #!/bin/bash
 set -eu -o pipefail
 
-export CPPFLAGS="-I$PREFIX/include"
-export LDFLAGS="-L$PREFIX/lib"
-export C_INCLUDE_PATH=${PREFIX}/include
-export CPLUS_INCLUDE_PATH=${PREFIX}/include
+# The project's Makefiles don't use {CPP,C,CXX,LD}FLAGS everywhere.
+# We can try to patch all of those or export the following *_PATH variables.
+export C_INCLUDE_PATH="${PREFIX}/include"
+export CPLUS_INCLUDE_PATH="${PREFIX}/include"
+export LIBRARY_PATH="${PREFIX}/lib"
 
 outdir=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM
 mkdir -p $outdir
@@ -12,7 +13,15 @@ mkdir -p $outdir/scripts
 mkdir -p $outdir/scripts/bamkit
 mkdir -p $PREFIX/bin
 
-make
+make \
+    CC="${CC}" \
+    CXX="${CXX}" \
+    CPPFLAGS="${CPPFLAGS}" \
+    CFLAGS="${CFLAGS}" \
+    CXXFLAGS="${CXXFLAGS}" \
+    LDFLAGS="${LDFLAGS}" \
+    ZLIB_PATH="${PREFIX/lib}"
+
 cp bin/lumpy $PREFIX/bin
 cp bin/lumpy_filter $PREFIX/bin
 cp scripts/lumpyexpress $PREFIX/bin
@@ -29,6 +38,6 @@ cp scripts/bamkit/* $outdir/scripts/bamkit
 
 cp $RECIPE_DIR/lumpyexpress.config $outdir
 ln -s $outdir/lumpyexpress.config $PREFIX/bin
-ln -s $outdir/extractSplitReads_BwaMem /$PREFIX/bin
+ln -s $outdir/scripts/extractSplitReads_BwaMem $PREFIX/bin
 
 chmod +x $PREFIX/bin/extractSplitReads_BwaMem
diff --git a/recipes/lumpy-sv/meta.yaml b/recipes/lumpy-sv/meta.yaml
index 7b5b7af889046..559ecdd63b554 100644
--- a/recipes/lumpy-sv/meta.yaml
+++ b/recipes/lumpy-sv/meta.yaml
@@ -1,4 +1,3 @@
-
 package:
   name: lumpy-sv
   version: 0.2.14a
@@ -10,8 +9,7 @@ source:
   #sha256: 1a7a5d18875b297acaa68ee1e864ca048654ebc85348920b518dc689d2b7a3cf
 
 build:
-  number: 3
-  skip: True # [py3k]
+  number: 2
 
 requirements:
   build:
@@ -21,10 +19,9 @@ requirements:
   host:
     - zlib
     - curl
-
   run:
     - zlib
-    - python
+    - python 2.7.*
     - samtools
     - gawk
     - curl