Update medaka to 2.0.0 (#48523)

* Update medaka to 1.12.0 * clean up recipe * medaka: Update libcurl to 8.x and openssl to 3.x Drop linux-aarch64 Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * Revert back to openssl 1.1.1 * Update medaka to 1.12.1 * Update medaka to 2.0.0 * replace tensorflow with pytorch * fix license_file name and add aarch64 build * do not build aarch64 for now * clean up recipe * add identifiers * fix typo * fix tests * do not build on aarch64 --------- Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> Co-authored-by: mencian <[email protected]> Co-authored-by: Alicia A. Evans <[email protected]> Co-authored-by: Martin Tzvetanov Grigorov <[email protected]> Co-authored-by: Martin Grigorov <[email protected]> Co-authored-by: Joshua Zhuang <[email protected]>
bioconda · Sep 17, 2024 · 78abb40 · 78abb40
1 parent ded2e01
commit 78abb40
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diff --git a/recipes/medaka/LICENSE.md b/recipes/medaka/LICENSE.md
diff --git a/recipes/medaka/build.sh b/recipes/medaka/build.sh
@@ -1,10 +1,10 @@
-#!/bin/bash
+#!/bin/bash -euo
 
 export INCLUDE_PATH="${PREFIX}/include"
 export LIBRARY_PATH="${PREFIX}/lib"
 export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
 
-export CFLAGS="-I${PREFIX}/include ${LDFLAGS}"
+export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}"
 
 # disable Makefile driven build of htslib.a
 sed -i.bak "s/'build_ext': HTSBuild//" setup.py
@@ -13,4 +13,6 @@ sed -i.bak "s/'build_ext': HTSBuild//" setup.py
 sed -i.bak 's/extra_objects.*//' build.py
 sed -i.bak 's/^libraries=\[/libraries=\["hts",/' build.py
 
-$PYTHON -m pip install . --no-deps --ignore-installed -vvv
+rm -rf *.bak
+
+${PYTHON} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv