From e94ff3af6b15b9561d7a94cba63ce065b5dcb9a8 Mon Sep 17 00:00:00 2001 From: "V. Karch" Date: Fri, 4 Sep 2026 11:34:25 -0400 Subject: [PATCH 1/3] [kallisto] patch sz_link issue --- repos/spack_repo/builtin/packages/kallisto/package.py | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/repos/spack_repo/builtin/packages/kallisto/package.py b/repos/spack_repo/builtin/packages/kallisto/package.py index f671ea91d97..c717ea3ecca 100644 --- a/repos/spack_repo/builtin/packages/kallisto/package.py +++ b/repos/spack_repo/builtin/packages/kallisto/package.py @@ -45,7 +45,14 @@ class Kallisto(CMakePackage): patch("link_zlib.patch", when="@:0.43") patch("limits.patch", when="@:0.46") patch("htslib_configure.patch", when="@0.44.0:0.48.0^autoconf@2.70:") - + + # https://github.com/pachterlab/kallisto/pull/506 + patch( + "https://github.com/pachterlab/kallisto/commit/a5caefb.patch", + sha256="a7002ce51d4dfeab8bce3e1d696ad034328b38e6d794de0c1400d07fb77e018a", + when="@0.50.1:" + ) + @run_before("cmake") def autoreconf(self): # Versions of autoconf greater than 2.69 need config.guess and From 60555e6fcf37a6ea850b788d13d4490086286c53 Mon Sep 17 00:00:00 2001 From: V-Karch <179492080+V-Karch@users.noreply.github.com> Date: Fri, 4 Sep 2026 15:37:04 +0000 Subject: [PATCH 2/3] [@spackbot] updating style on behalf of V-Karch --- .../spack_repo/builtin/packages/kallisto/package.py | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/repos/spack_repo/builtin/packages/kallisto/package.py b/repos/spack_repo/builtin/packages/kallisto/package.py index c717ea3ecca..6624d962ca9 100644 --- a/repos/spack_repo/builtin/packages/kallisto/package.py +++ b/repos/spack_repo/builtin/packages/kallisto/package.py @@ -45,14 +45,14 @@ class Kallisto(CMakePackage): patch("link_zlib.patch", when="@:0.43") patch("limits.patch", when="@:0.46") patch("htslib_configure.patch", when="@0.44.0:0.48.0^autoconf@2.70:") - + # https://github.com/pachterlab/kallisto/pull/506 - patch( - "https://github.com/pachterlab/kallisto/commit/a5caefb.patch", - sha256="a7002ce51d4dfeab8bce3e1d696ad034328b38e6d794de0c1400d07fb77e018a", - when="@0.50.1:" + patch( + "https://github.com/pachterlab/kallisto/commit/a5caefb.patch", + sha256="a7002ce51d4dfeab8bce3e1d696ad034328b38e6d794de0c1400d07fb77e018a", + when="@0.50.1:", ) - + @run_before("cmake") def autoreconf(self): # Versions of autoconf greater than 2.69 need config.guess and From 46bd318b3593ab2dec9ba194a3dabf4a5f25e8d2 Mon Sep 17 00:00:00 2001 From: "V. Karch" Date: Fri, 4 Sep 2026 11:41:31 -0400 Subject: [PATCH 3/3] Update patch URL for Kallisto package --- repos/spack_repo/builtin/packages/kallisto/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/repos/spack_repo/builtin/packages/kallisto/package.py b/repos/spack_repo/builtin/packages/kallisto/package.py index 6624d962ca9..8ac58643530 100644 --- a/repos/spack_repo/builtin/packages/kallisto/package.py +++ b/repos/spack_repo/builtin/packages/kallisto/package.py @@ -48,7 +48,7 @@ class Kallisto(CMakePackage): # https://github.com/pachterlab/kallisto/pull/506 patch( - "https://github.com/pachterlab/kallisto/commit/a5caefb.patch", + "https://github.com/pachterlab/kallisto/commit/a5caefb.patch?full_index=1", sha256="a7002ce51d4dfeab8bce3e1d696ad034328b38e6d794de0c1400d07fb77e018a", when="@0.50.1:", )