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| author |   Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> | 2018-06-26 10:51:34 +0200 |
|---|---|---|
| committer | Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> | 2018-06-26 10:51:34 +0200 |
| commit | be33780bc70d6cc463c236d5e2ceb2273170c191 (patch) | |
| tree | f00b885d650811ea973c0df7a67a8bd3d54e67c1 | |
| parent | sci-biology/salmon: fix tests (diff) | |
| download | sci-be33780bc70d6cc463c236d5e2ceb2273170c191.tar.gz sci-be33780bc70d6cc463c236d5e2ceb2273170c191.tar.bz2 sci-be33780bc70d6cc463c236d5e2ceb2273170c191.zip | |
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
| -rw-r--r-- | sci-biology/salmon/files/salmon-0.10.2_TestSalmonQuasi.cmake.patch | 11 | ||||
| -rw-r--r-- | sci-biology/salmon/salmon-0.10.2.ebuild | 3 | ||||
| -rw-r--r-- | 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 |