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| author | Glenn Johnson <glenn-johnson@uiowa.edu> | 2023-01-16 20:29:52 -0600 |
|---|---|---|
| committer | GitHub <noreply@github.com> | 2023-01-17 03:29:52 +0100 |
| commit | b7e416046f95b21f64f1ac0af7e8ce7a04ad4eec (patch) | |
| tree | 5ef454323584dcb26d11150d463d6ee323af4f92 /var | |
| parent | b2cc36109f8a0db954349427a3a79c191010797a (diff) | |
| download | spack-b7e416046f95b21f64f1ac0af7e8ce7a04ad4eec.tar.gz spack-b7e416046f95b21f64f1ac0af7e8ce7a04ad4eec.tar.bz2 spack-b7e416046f95b21f64f1ac0af7e8ce7a04ad4eec.tar.xz spack-b7e416046f95b21f64f1ac0af7e8ce7a04ad4eec.zip | |
sra-tools: add version 3.0.3 and fix build (#34965)
Diffstat (limited to 'var')
| -rw-r--r-- | var/spack/repos/builtin/packages/sra-tools/ngs-java.patch | 16 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/sra-tools/package.py | 5 |
2 files changed, 21 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/sra-tools/ngs-java.patch b/var/spack/repos/builtin/packages/sra-tools/ngs-java.patch new file mode 100644 index 0000000000..4791239bb0 --- /dev/null +++ b/var/spack/repos/builtin/packages/sra-tools/ngs-java.patch @@ -0,0 +1,16 @@ +--- a/ngs/ngs-java/CMakeLists.txt 2023-01-12 17:48:48.901017181 -0600 ++++ b/ngs/ngs-java/CMakeLists.txt 2023-01-12 18:46:26.833359507 -0600 +@@ -140,11 +140,8 @@ + set(SRC_FILES "${SRC_FILES} ${f}") + endforeach() + +- if( ${OS} STREQUAL "windows" ) +- set( NGS_JAVADOC_DIR ${TARGDIR} ) +- else() +- set( NGS_JAVADOC_DIR ${TARGDIR}/obj ) +- endif() ++ set( NGS_JAVADOC_DIR ${TARGDIR} ) ++ + if ( Java_JAR_EXECUTABLE AND NOT (${OS} STREQUAL "windows") ) + add_custom_target( + ngs-doc-jar ALL COMMAND diff --git a/var/spack/repos/builtin/packages/sra-tools/package.py b/var/spack/repos/builtin/packages/sra-tools/package.py index 2606013c20..d1a526b3e0 100644 --- a/var/spack/repos/builtin/packages/sra-tools/package.py +++ b/var/spack/repos/builtin/packages/sra-tools/package.py @@ -13,6 +13,7 @@ class SraTools(CMakePackage): homepage = "https://github.com/ncbi/sra-tools" git = "https://github.com/ncbi/sra-tools.git" + version("3.0.3", tags="3.0.3") version("3.0.0", tags="3.0.0") depends_on("openjdk") @@ -20,6 +21,10 @@ class SraTools(CMakePackage): depends_on("libxml2") depends_on("ncbi-vdb") + # The CMakeLists.txt file set the path to ${TARGDIR}/obj but the code + # actually uses ${TARGDIR}. + patch("ngs-java.patch") + def cmake_args(self): args = [ self.define("VDB_INCDIR", format(self.spec["ncbi-vdb"].prefix) + "/include"), |