Update Cloudspades

recipes/cloudspades/build.sh

@@ -2,10 +2,10 @@
 
 set -e -o pipefail -x
 
-export LIBRARY_PATH="${PREFIX}/lib"
-export INCLUDE_PATH="${PREFIX}/include"
-export CFLAGS="${CFLAGS} -O3 -fcommon"
-export CXXFLAGS="${CFLAGS} -O3 -fcommon -I${PREFIX}/include -D_LIBCPP_DISABLE_AVAILABILITY -fsigned-char"
+#export LIBRARY_PATH="${PREFIX}/lib"
+#export INCLUDE_PATH="${PREFIX}/include"
+#export CFLAGS="${CFLAGS} -O3 -fcommon"
+#export CXXFLAGS="${CFLAGS} -O3 -fcommon -I${PREFIX}/include -D_LIBCPP_DISABLE_AVAILABILITY"
 
 case $(uname) in
 	Linux)
@@ -16,5 +16,8 @@ case $(uname) in
 		;;
 esac
 
+mkdir -p ${PREFIX}/bin ${PREFIX}/share
 cd assembler
-PREFIX="${PREFIX}" bash spades_compile.sh "${THREADS}" -DSPADES_ENABLE_PROJECTS="all"
+./spades_compile.sh "${THREADS}"
+mv -r bin/* ${PREFIX}/bin
+mv -r share/spades ${PREFIX}/share

recipes/cloudspades/meta.yaml

@@ -39,6 +39,7 @@ test:
     - spades-kmercount -h 2>&1 | grep spades-kmercount
     - spades-gmapper 2>&1 | grep spades-gmapper
     - spades-gbuilder 2>&1 | grep spades-gbuilder
+    - spades.py --isolate --gemcode1-1 assembler/test_dataset_cloudspades/10x_format/test_1.fastq.gz --gemcode1-2 assembler/test_dataset_cloudspades/10x_format/test_2.fastq.gz  -o cloudspades_test
 
 about:
   home: "https://github.com/ablab/spades"