From d2df0a29ceab157864c8a6d7d6a9a873a067a053 Mon Sep 17 00:00:00 2001 From: pabloaledo <112545720+pabloaledo@users.noreply.github.com> Date: Fri, 4 Aug 2023 02:57:17 +0200 Subject: salmon: update version (#39202) * salmon: update version --------- Signed-off-by: Pablo --- var/spack/repos/builtin/packages/salmon/fix_hts.patch | 11 +++++++++++ var/spack/repos/builtin/packages/salmon/package.py | 9 +++++++++ 2 files changed, 20 insertions(+) create mode 100644 var/spack/repos/builtin/packages/salmon/fix_hts.patch (limited to 'var') diff --git a/var/spack/repos/builtin/packages/salmon/fix_hts.patch b/var/spack/repos/builtin/packages/salmon/fix_hts.patch new file mode 100644 index 0000000000..c5eb36482f --- /dev/null +++ b/var/spack/repos/builtin/packages/salmon/fix_hts.patch @@ -0,0 +1,11 @@ +--- a/cmake/Modules/Findlibstadenio.cmake ++++ /dev/null +@@ -13,7 +13,7 @@ find_path(STADEN_INCLUDE_DIR io_lib + find_library(STADEN_LIBRARY NAMES staden-read libstaden-read + HINTS ${STADEN_ROOT} ENV STADEN_ROOT PATH_SUFFIXES lib lib64) + +-find_library(HTSCODEC_LIBRARY NAMES htscodecs libhtscodecs ++find_library(HTSCODEC_LIBRARY NAMES htscodecs libhtscodecs hts + HINTS ${STADEN_ROOT} ENV STADEN_ROOT PATH_SUFFIXES lib lib64) + + if(STADEN_INCLUDE_DIR) diff --git a/var/spack/repos/builtin/packages/salmon/package.py b/var/spack/repos/builtin/packages/salmon/package.py index 553a2d1767..2aa2239dd6 100644 --- a/var/spack/repos/builtin/packages/salmon/package.py +++ b/var/spack/repos/builtin/packages/salmon/package.py @@ -13,6 +13,7 @@ class Salmon(CMakePackage): url = "https://github.com/COMBINE-lab/salmon/archive/v0.8.2.tar.gz" maintainers("snehring") + version("1.10.2", sha256="976989182160fef3afb4429ee8b85d8dd39ed6ca212bb14d6a65cde0e985fb98") version("1.9.0", sha256="450d953a5c43fe63fd745733f478d3fbaf24d926cb52731fd38ee21c4990d613") version("1.4.0", sha256="6d3e25387450710f0aa779a1e9aaa9b4dec842324ff8551d66962d7c7606e71d") version("0.14.1", sha256="05289170e69b5f291a8403b40d6b9bff54cc38825e9f721c210192b51a19273e") @@ -55,10 +56,18 @@ class Salmon(CMakePackage): depends_on("libgff") depends_on("pkgconfig") depends_on("curl", when="@0.14.1:") + depends_on("htslib", when="@1.10.2") + + patch("fix_hts.patch", when="@1.10.2") conflicts("%gcc@:5.1", when="@0.14.1:") resources = [ + ( + "1.10.2", + "pufferfish", + "f225b74833f71dcf767a565345224357fb091f90ce79717abc836814d9ccd101", + ), ( "1.9.0", "pufferfish", -- cgit v1.2.3-70-g09d2