commit: be33780bc70d6cc463c236d5e2ceb2273170c191 Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Tue Jun 26 08:51:34 2018 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Tue Jun 26 08:51:34 2018 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=be33780b
sci-biology/salmon: fix variablenames Thanks to @kiwifb for spotting two improperly used variablenames https://github.com/gentoo/sci/commit/a1d0487c37ba900c1f239f5d73f7d429f018359d#commitcomment-29493393 https://github.com/gentoo/sci/commit/a1d0487c37ba900c1f239f5d73f7d429f018359d#commitcomment-29493465 Package-Manager: Portage-2.3.40, Repoman-2.3.9 .../salmon/files/salmon-0.10.2_TestSalmonQuasi.cmake.patch | 11 +++++++++++ sci-biology/salmon/salmon-0.10.2.ebuild | 3 ++- sci-biology/salmon/salmon-9999.ebuild | 3 ++- 3 files changed, 15 insertions(+), 2 deletions(-) diff --git a/sci-biology/salmon/files/salmon-0.10.2_TestSalmonQuasi.cmake.patch b/sci-biology/salmon/files/salmon-0.10.2_TestSalmonQuasi.cmake.patch new file mode 100644 index 000000000..81edf96f5 --- /dev/null +++ b/sci-biology/salmon/files/salmon-0.10.2_TestSalmonQuasi.cmake.patch @@ -0,0 +1,11 @@ +--- salmon-0.10.2/cmake/TestSalmonQuasi.cmake 2018-06-26 10:39:51.061971241 +0200 ++++ salmon-0.10.2/cmake/TestSalmonQuasi.cmake 2018-06-26 10:40:22.372822258 +0200 +@@ -5,7 +5,7 @@ + ) + + if (SALMON_QUASI_INDEX_RESULT) +- message(FATAL_ERROR "Error running ${SALMON_QUASI_INDEX_COMMAND}") ++ message(FATAL_ERROR "Error running ${SALMON_QUASI_INDEX_CMD}") + endif() + + set(SALMON_QUANT_COMMAND ${CMAKE_BINARY_DIR}/salmon quant -i sample_salmon_quasi_index -l IU -1 reads_1.fastq -2 reads_2.fastq -o sample_salmon_quasi_quant) diff --git a/sci-biology/salmon/salmon-0.10.2.ebuild b/sci-biology/salmon/salmon-0.10.2.ebuild index 84d73ea9e..088fea331 100644 --- a/sci-biology/salmon/salmon-0.10.2.ebuild +++ b/sci-biology/salmon/salmon-0.10.2.ebuild @@ -24,7 +24,8 @@ PATCHES=( "${FILESDIR}"/${P}-no-boost-static.patch "${FILESDIR}"/salmon-0.10.2_remove_curl_call.patch "${FILESDIR}"/salmon-0.10.2_remove_curl_calls.patch "${FILESDIR}"/salmon-0.10.2_fix_lib_dir.patch - "${FILESDIR}"/salmon-0.10.2_fix_tests.patch ) + "${FILESDIR}"/salmon-0.10.2_fix_tests.patch + "${FILESDIR}"/salmon-0.10.2_TestSalmonQuasi.cmake.patch ) RDEPEND="${DEPEND}" # budled copies of: diff --git a/sci-biology/salmon/salmon-9999.ebuild b/sci-biology/salmon/salmon-9999.ebuild index 0b19da725..8862ff790 100644 --- a/sci-biology/salmon/salmon-9999.ebuild +++ b/sci-biology/salmon/salmon-9999.ebuild @@ -23,7 +23,8 @@ PATCHES=( "${FILESDIR}"/salmon-0.10.2-no-boost-static.patch "${FILESDIR}"/salmon-0.10.2_remove_curl_call.patch "${FILESDIR}"/salmon-0.10.2_remove_curl_calls.patch "${FILESDIR}"/salmon-0.10.2_fix_lib_dir.patch - "${FILESDIR}"/salmon-0.10.2_fix_tests.patch ) + "${FILESDIR}"/salmon-0.10.2_fix_tests.patch + "${FILESDIR}"/salmon-0.10.2_TestSalmonQuasi.cmake.patch ) # budled copies of: # sci-biology/bwa-0.7.12.5
