git: 64ae45e8c91f - main - biology/kallisto: Update to 0.52.0,1
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Date: Wed, 04 Mar 2026 23:31:44 UTC
The branch main has been updated by jwb:
URL: https://cgit.FreeBSD.org/ports/commit/?id=64ae45e8c91f8484d2740b98a432a53d338a6111
commit 64ae45e8c91f8484d2740b98a432a53d338a6111
Author: Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2026-03-04 23:28:49 +0000
Commit: Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2026-03-04 23:28:49 +0000
biology/kallisto: Update to 0.52.0,1
Release 0.52.0 brings back --genomebam and --pseudobam options
Changes: https://github.com/pachterlab/kallisto/releases
Reported by: portscout
---
biology/kallisto/Makefile | 10 +++++--
biology/kallisto/distinfo | 6 ++--
biology/kallisto/files/kallisto-test.in | 0
biology/kallisto/files/patch-CMakeLists.txt | 35 ++++++++++++----------
.../kallisto/files/patch-ext_bifrost_src_BooPHF.h | 33 ++++++++++++++++++++
.../kallisto/files/patch-ext_bifrost_src_kseq.h | 15 ++++++++++
biology/kallisto/files/patch-src_main.cpp | 16 +++++-----
7 files changed, 85 insertions(+), 30 deletions(-)
diff --git a/biology/kallisto/Makefile b/biology/kallisto/Makefile
index ee2b20397ca6..16751e9f67b4 100644
--- a/biology/kallisto/Makefile
+++ b/biology/kallisto/Makefile
@@ -1,7 +1,6 @@
PORTNAME= kallisto
DISTVERSIONPREFIX= v
-DISTVERSION= 0.51.1
-PORTREVISION= 1
+DISTVERSION= 0.52.0
PORTEPOCH= 1
CATEGORIES= biology
@@ -37,12 +36,17 @@ EXAMPLES_PLIST_FILES= bin/kallisto-test
CMAKE_ARGS+= -DUSE_HDF5:BOOL=ON -DUSE_BAM:BOOL=ON
# WIP: Remove before committing
CMAKE_ARGS+= -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON
+CMAKE_ARGS+= -DLOCALBASE:STRING=${LOCALBASE}
MAKE_JOBS_UNSAFE= yes
CXXFLAGS+= -Wno-unqualified-std-cast-call
-LDFLAGS+= -lhts -lz
+LDFLAGS+= -lhdf5 -lhts -lz
OPTIONS_DEFINE= EXAMPLES
+pre-configure:
+ ${REINPLACE_CMD} -e "s|-Wno-return-type|& -I${LOCALBASE}/include|g" \
+ ${WRKSRC}/CMakeLists.txt
+
post-install-EXAMPLES-on:
${INSTALL_SCRIPT} ${WRKDIR}/kallisto-test ${STAGEDIR}${PREFIX}/bin
cd ${WRKSRC}/test && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR}
diff --git a/biology/kallisto/distinfo b/biology/kallisto/distinfo
index a207db3e922d..c13840c32511 100644
--- a/biology/kallisto/distinfo
+++ b/biology/kallisto/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1748283025
-SHA256 (pachterlab-kallisto-v0.51.1_GH0.tar.gz) = a8bcc23bca6ac758f15e30bb77e9e169e628beff2da3be2e34a53e1d42253516
-SIZE (pachterlab-kallisto-v0.51.1_GH0.tar.gz) = 5954250
+TIMESTAMP = 1772127559
+SHA256 (pachterlab-kallisto-v0.52.0_GH0.tar.gz) = 68184e41706d77e409f05a598a87dacdf3cf227f18c028175e2bce8b284bdea4
+SIZE (pachterlab-kallisto-v0.52.0_GH0.tar.gz) = 5961651
diff --git a/biology/kallisto/files/kallisto-test.in b/biology/kallisto/files/kallisto-test.in
old mode 100755
new mode 100644
diff --git a/biology/kallisto/files/patch-CMakeLists.txt b/biology/kallisto/files/patch-CMakeLists.txt
index 7d56e7d9b1a1..71b8ffeb1233 100644
--- a/biology/kallisto/files/patch-CMakeLists.txt
+++ b/biology/kallisto/files/patch-CMakeLists.txt
@@ -1,30 +1,26 @@
---- CMakeLists.txt.orig 2024-07-20 19:07:27 UTC
+--- CMakeLists.txt.orig 2026-01-20 17:34:25 UTC
+++ CMakeLists.txt
-@@ -50,10 +50,11 @@ else()
- # remove this block once CMake >=3.1 has fixated in the ecosystem
- add_compile_options(-std=c++11)
- else()
-+ # Use c++11 to silence warnings
+@@ -60,7 +60,7 @@ else()
include(CheckCXXCompilerFlag)
check_cxx_compiler_flag(-std=c++17 COMPILER_SUPPORTS_CXX17)
if(COMPILER_SUPPORTS_CXX17)
-- set(CMAKE_CXX_STANDARD 17)
-+ set(CMAKE_CXX_STANDARD 11)
+- set(CMAKE_CXX_STANDARD 17)
++ set(CMAKE_CXX_STANDARD 11)
else()
- set(CMAKE_CXX_STANDARD 11)
+ set(CMAKE_CXX_STANDARD 11)
endif()
-@@ -61,9 +62,7 @@ endif()
+@@ -69,9 +69,7 @@ endif()
set(CMAKE_CXX_EXTENSIONS OFF)
endif()
-#add_compile_options(-Wall -Wno-unused-function)
--add_compile_options(-Wno-subobject-linkage) # Suppress bifrost warning
+-add_compile_options(-Wno-deprecated-declarations -Wno-subobject-linkage) # Suppress bifrost warning
-set(PROJECT_BIFROST_CMAKE_CXX_FLAGS "-Wno-subobject-linkage -Wno-return-type") # Suppress bifrost warning
+set(PROJECT_BIFROST_CMAKE_CXX_FLAGS "-Wno-return-type") # Suppress bifrost warning
if(LINK MATCHES static)
message("static build")
-@@ -73,24 +72,13 @@ include(ExternalProject)
+@@ -81,24 +79,13 @@ include(ExternalProject)
include(ExternalProject)
@@ -33,9 +29,9 @@
- PREFIX ${PROJECT_SOURCE_DIR}/ext/htslib
- SOURCE_DIR ${PROJECT_SOURCE_DIR}/ext/htslib
- BUILD_IN_SOURCE 1
-- CONFIGURE_COMMAND autoreconf -i && autoheader && autoconf && ${PROJECT_SOURCE_DIR}/ext/htslib/configure
-- --prefix=${PREFIX} --disable-bz2 --disable-lzma --disable-libcurl
-- BUILD_COMMAND make lib-static
+- CONFIGURE_COMMAND "" #autoreconf -i && autoheader && autoconf && ${PROJECT_SOURCE_DIR}/ext/htslib/configure
+- #--prefix=${PREFIX} --disable-bz2 --disable-lzma --disable-libcurl
+- BUILD_COMMAND "" #make lib-static
- INSTALL_COMMAND ""
-)
-endif(USE_BAM)
@@ -50,7 +46,7 @@
INSTALL_COMMAND ""
)
-@@ -101,7 +89,7 @@ if (ZLIBNG)
+@@ -109,13 +96,13 @@ if (ZLIBNG)
SOURCE_DIR ${PROJECT_SOURCE_DIR}/ext/zlib-ng
BUILD_IN_SOURCE 1
CONFIGURE_COMMAND mkdir -p zlib-ng && cd zlib-ng && cmake .. -DZLIB_COMPAT=ON -DZLIB_ENABLE_TESTS=OFF -DCMAKE_INSTALL_PREFIX=${PREFIX}
@@ -59,3 +55,10 @@
INSTALL_COMMAND ""
)
endif(ZLIBNG)
+
+ if (USE_BAM)
+- include_directories(${htslib_PREFIX}/src/htslib)
++ include_directories(${LOCALBASE}/htslib)
+ endif(USE_BAM)
+
+ include_directories(${EXT_PROJECTS_DIR}/bifrost/build/src)
diff --git a/biology/kallisto/files/patch-ext_bifrost_src_BooPHF.h b/biology/kallisto/files/patch-ext_bifrost_src_BooPHF.h
new file mode 100644
index 000000000000..680e38d9fe8a
--- /dev/null
+++ b/biology/kallisto/files/patch-ext_bifrost_src_BooPHF.h
@@ -0,0 +1,33 @@
+--- ext/bifrost/src/BooPHF.h.orig 2026-02-26 17:50:47 UTC
++++ ext/bifrost/src/BooPHF.h
+@@ -8,6 +8,7 @@
+ #include <stdlib.h>
+ #include <iostream>
+ #include <math.h>
++#include <inttypes.h>
+
+ #include <array>
+ #include <unordered_map>
+@@ -533,11 +534,11 @@ we need this 2-functors scheme because HashFunctors wo
+ //for debug purposes
+ void print() const
+ {
+- printf("bit array of size %llu: \n",_size);
++ printf("bit array of size %" PRIu64 ": \n",_size);
+ for(uint64_t ii = 0; ii< _size; ii++)
+ {
+ if(ii%10==0)
+- printf(" (%llu) ",ii);
++ printf(" (%" PRIu64 ") ",ii);
+ int val = (_bitArray[ii >> 6] >> (ii & 63 ) ) & 1;
+ printf("%i",val);
+ }
+@@ -546,7 +547,7 @@ we need this 2-functors scheme because HashFunctors wo
+ printf("rank array : size %lu \n",_ranks.size());
+ for (uint64_t ii = 0; ii< _ranks.size(); ii++)
+ {
+- printf("%llu : %llu, ",ii,_ranks[ii]);
++ printf("%" PRIu64 " : %" PRIu64 ", ",ii,_ranks[ii]);
+ }
+ printf("\n");
+ }
diff --git a/biology/kallisto/files/patch-ext_bifrost_src_kseq.h b/biology/kallisto/files/patch-ext_bifrost_src_kseq.h
new file mode 100644
index 000000000000..70ac3c179968
--- /dev/null
+++ b/biology/kallisto/files/patch-ext_bifrost_src_kseq.h
@@ -0,0 +1,15 @@
+--- ext/bifrost/src/kseq.h.orig 2026-01-20 17:34:25 UTC
++++ ext/bifrost/src/kseq.h
+@@ -32,6 +32,12 @@
+ #include <string.h>
+ #include <stdlib.h>
+
++// Prevent redefinition of kstring_t below
++#include <htslib/kstring.h>
++
++// Prevent redefinition of kstring_t below
++#include <htslib/kstring.h>
++
+ #define KS_SEP_SPACE 0 // isspace(): \t, \n, \v, \f, \r
+ #define KS_SEP_TAB 1 // isspace() && !' '
+ #define KS_SEP_LINE 2 // line separator: "\n" (Unix) or "\r\n" (Windows)
diff --git a/biology/kallisto/files/patch-src_main.cpp b/biology/kallisto/files/patch-src_main.cpp
index 2eadc428781c..b0e9ad94526a 100644
--- a/biology/kallisto/files/patch-src_main.cpp
+++ b/biology/kallisto/files/patch-src_main.cpp
@@ -1,10 +1,10 @@
---- src/main.cpp.orig 2023-11-02 11:38:09 UTC
+--- src/main.cpp.orig 2026-01-20 17:34:25 UTC
+++ src/main.cpp
-@@ -11,6 +11,7 @@
- #include <limits>
+@@ -1,6 +1,7 @@
+ #include <getopt.h>
+ #include <sys/stat.h>
+ #include <time.h>
++#include <unistd.h>
- #include <cstdio>
-+#include <unistd.h> // rmdir()
-
- #include "common.h"
- #include "ProcessReads.h"
+ #include <CompactedDBG.hpp>
+ #include <algorithm>