[ci skip] Merge PR 20099

Merge PR #20099, commits were: 
 * Patch percolator Globals.cpp to avoid null termination problem with the conda build/run process, see conda/conda-build#1674
 * Merge branch 'master' into perco_testmsgf
 * Add tandem2pin, msgf2pin tests to recipe, both failing

recipes/percolator/build.sh

@@ -2,16 +2,19 @@
 
 mkdir percobuild && cd percobuild
 cmake -DTARGET_ARCH=x86_64 -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=$PREFIX -DXML_SUPPORT=ON -DCMAKE_PREFIX_PATH="$PREFIX;$PREFIX/lib" -DCMAKE_CXX_FLAGS="-std=c++14" $SRC_DIR
-
 make && make install
 cd ..
 
+# First make sure we dont get problems with truncated PREFIX due to null terminators:
+# see percolator/percolator#251 and conda/conda-build#1674
+sed -i '54s/WRITABLE_DIR/std::string(WRITABLE_DIR).c_str()/' $SRC_DIR/src/Globals.cpp
 mkdir converterbuild && cd converterbuild 
-cmake -DTARGET_ARCH=x86_64 -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=$PREFIX -DBOOST_ROOT=$PREFIX -DBOOST_LIBRARYDIR=$PREFIX/lib -DSERIALIZE="Boost" -DCMAKE_CXX_FLAGS="-std=c++14" -DCMAKE_PREFIX_PATH=$PREFIX $SRC_DIR/src/converters
+cmake -DTARGET_ARCH=x86_64 -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX="$PREFIX" -DBOOST_ROOT=$PREFIX -DBOOST_LIBRARYDIR=$PREFIX/lib -DSERIALIZE="Boost" -DCMAKE_CXX_FLAGS="-std=c++11" -DCMAKE_PREFIX_PATH="$PREFIX" $SRC_DIR/src/converters
 make install
 cd ..
 
 mkdir $PREFIX/testdata
 cp $SRC_DIR/src/converters/data/converters/sqt2pin/target.sqt $PREFIX/testdata/target.sqt
+cp $SRC_DIR/src/converters/data/converters/msgf2pin/target.mzid $PREFIX/testdata/target.mzid
+cp $SRC_DIR/src/converters/data/converters/tandem2pin/target.t.xml $PREFIX/testdata/target.t.xml
 cp $SRC_DIR/data/percolator/tab/percolatorTab $PREFIX/testdata/percolatorTab
-

recipes/percolator/meta.yaml

@@ -10,7 +10,7 @@ source:
   sha256: ee094039b60aa2e2e15ec8228da087328ca523fa73b89cd69721621eb219cf4d
 
 build:
-  number: 0
+  number: 1
   skip: True # [osx]
 
 requirements:
@@ -31,7 +31,9 @@ requirements:
 
 test:
   commands:
-    - sqt2pin -o test.txt $PREFIX/testdata/target.sqt $PREFIX/testdata/target.sqt
+    - sqt2pin -o testsqt.txt $PREFIX/testdata/target.sqt $PREFIX/testdata/target.sqt
+    - tandem2pin -o testtandem.txt $PREFIX/testdata/target.t.xml $PREFIX/testdata/target.t.xml
+    - msgf2pin -o testmzid.txt $PREFIX/testdata/target.mzid $PREFIX/testdata/target.mzid
     - percolator -X test.xml $PREFIX/testdata/percolatorTab
 
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