bioconda · dpryan79 · Jul 30, 2018 · Jul 29, 2018 · Jul 30, 2018 · Jul 30, 2018
diff --git a/build-fail-blacklist b/build-fail-blacklist
@@ -1593,25 +1593,6 @@ recipes/pout2mzid
 # checksum always fails
 recipes/ms
 
-# gsl missing
-recipes/mlrho
-
-# squid.h is missing
-recipes/compalignp
-
-# zlib?
-recipes/filtlong
-recipes/fermi2
-recipes/fermi-lite
-recipes/fermi
-recipes/prophasm
-recipes/preseq
-
-#/opt/conda/conda-bld/famseq_1531342570854/work/conda_build.sh: line 140: cd: src: No such file or directory
-recipes/famseq
-
-
-
 # GL missing, needs the extended base image
 recipes/emperor
 

diff --git a/recipes/compalignp/build.sh b/recipes/compalignp/build.sh
@@ -15,5 +15,7 @@ make install
 
 popd
 
+export C_INCLUDE_PATH="squid-1.9g"
+export LIBRARY_PATH="squid-1.9g"
 make
-cp compalignp $PREFIX/bin
+mv compalignp $PREFIX/bin/
diff --git a/recipes/famseq/build.sh b/recipes/famseq/build.sh
@@ -1,8 +1,6 @@
 #!/bin/sh
 
-mkdir bin
-cd src
+cd FamSeq/src
 make
-cd ..
-
-cp ${SRC_DIR}/src/FamSeq $PREFIX/bin/FamSeq 
+mkdir -p ${PREFIX}/bin
+mv FamSeq $PREFIX/bin/FamSeq 
diff --git a/recipes/famseq/meta.yaml b/recipes/famseq/meta.yaml
@@ -14,7 +14,7 @@ build:
 
 requirements:
   build:
-    - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
   run:
 
 test:
@@ -24,5 +24,4 @@ test:
 about:
   home: http://bioinformatics.mdanderson.org/main/FamSeq
   license: GPL-3
-  license_file: LICENSE
   summary: 'Peng G, Fan Y, Palculict TB, Shen P, Ruteshouser EC, Chi A, Davis RW, Huff V, Scharfe C, Wang W. Rare variant detection using family-based sequencing analysis. Proceedings of the National Academy of Sciences. 2013 Mar 5;110(10):3985-90'
diff --git a/recipes/fermi-lite/build.sh b/recipes/fermi-lite/build.sh
@@ -1,5 +1,7 @@
 #!/bin/bash
 
+export C_INCLUDE_PATH=${PREFIX}/include
+export LIBRARY_PATH=${PREFIX}/lib
 make
 cp fml-asm ${PREFIX}/bin
 cp *.h ${PREFIX}/include
diff --git a/recipes/fermi/build.sh b/recipes/fermi/build.sh
@@ -2,9 +2,12 @@
 export CFLAGS="-I$PREFIX/include"
 export LDFLAGS="-L$PREFIX/lib"
 export CPATH=${PREFIX}/include
+export C_INCLUDE_PATH=${PREFIX}/include
+export LIBRARY_PATH=${PREFIX}/lib
 
 mkdir -p $PREFIX/bin
+sed -i.bak "s/inline void ld_set/static inline void ld_set/g" bcr.c
 
-make 
+make CC=$CC
 mv fermi  $PREFIX/bin
 mv run-fermi.pl $PREFIX/bin
diff --git a/recipes/fermi2/build.sh b/recipes/fermi2/build.sh
@@ -2,6 +2,8 @@
 
 mkdir -p $PREFIX/bin
 
+export C_INCLUDE_PATH=${PREFIX}/include
+export LIBRARY_PATH=${PREFIX}/lib
 make
 mv fermi2  $PREFIX/bin
 mv fermi2.pl  $PREFIX/bin

diff --git a/recipes/filtlong/build.sh b/recipes/filtlong/build.sh
@@ -2,5 +2,9 @@
 
 mkdir -p "$PREFIX/bin"
 
+export CPP_INCLUDE_PATH=${PREFIX}/include
+export CPLUS_INCLUDE_PATH=${PREFIX}/include
+export CXX_INCLUDE_PATH=${PREFIX}/include
+export LIBRARY_PATH=${PREFIX}/lib
 make -j
 cp bin/filtlong $PREFIX/bin
diff --git a/recipes/filtlong/meta.yaml b/recipes/filtlong/meta.yaml
@@ -15,7 +15,7 @@ build:
 
 requirements:
   build:
-    - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
   host:
     - zlib
   run:

diff --git a/recipes/mlrho/build.sh b/recipes/mlrho/build.sh
@@ -1,4 +1,6 @@
 #!/bin/bash
+export C_INCLUDE_PATH=${PREFIX}/include
+export LIBRARY_PATH=${PREFIX}/lib
 make
 cp mlRho $PREFIX/bin
-chmod +x $PREFIX/bin/mlRho
+chmod +x $PREFIX/bin/mlRho
diff --git a/recipes/mlrho/meta.yaml b/recipes/mlrho/meta.yaml
@@ -17,8 +17,10 @@ requirements:
     - {{ compiler('c') }}
   host:
     - gsl
+    - openblas
   run:
     - gsl
+    - openblas
 
 test:
   commands:

diff --git a/recipes/preseq/build.sh b/recipes/preseq/build.sh
@@ -1,5 +1,11 @@
 #!/bin/bash
 
 export C_INCLUDE_PATH=${PREFIX}/include
+export CPP_INCLUDE_PATH=${PREFIX}/include
+export CXX_INCLUDE_PATH=${PREFIX}/include
+export CPLUS_INCLUDE_PATH=${PREFIX}/include
 export LIBRARY_PATH=${PREFIX}/lib
+if [ "$(uname)" == "Darwin" ]; then
+    CXXFLAGS="-stdlib=libstdc++"
+fi
 make install ROOT="."
diff --git a/recipes/preseq/meta.yaml b/recipes/preseq/meta.yaml
@@ -9,10 +9,12 @@ source:
 
 build:
   number: 2
+  skip: True  # [osx]
 
 requirements:
   build:
     - {{ compiler('cxx') }}
+    - {{ compiler('c') }}
   host:
     - zlib
     - gsl

diff --git a/recipes/prophasm/build.sh b/recipes/prophasm/build.sh
@@ -1,6 +1,8 @@
 #!/bin/bash
 
-export C_INCLUDE_PATH=${PREFIX}/include
+export CPP_INCLUDE_PATH=${PREFIX}/include
+export CPLUS_INCLUDE_PATH=${PREFIX}/include
+export CXX_INCLUDE_PATH=${PREFIX}/include
 export LIBRARY_PATH=${PREFIX}/lib
 
 make
-Original file line number
+Diff line change
@@ Expand Up / @@ -15,7 +15,7 @@ build: @@
     requirements:
       build:
-        - {{ compiler('c') }}
+        - {{ compiler('cxx') }}
       host:
         - zlib
       run:
@@ Expand Down @@