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biology/kallisto: Update to 0.52.0,1

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Release 0.52.0 brings back --genomebam and --pseudobam options
Changes: https://github.com/pachterlab/kallisto/releases

Reported by:    portscout
This commit is contained in:
Jason W. Bacon
2026-03-04 17:28:49 -06:00
parent 8a854ca8fb
commit 64ae45e8c9
7 changed files with 85 additions and 30 deletions
Download Patch File Download Diff File Expand all files Collapse all files
biology/kallisto/Makefile
+7 -3
View File
@@ -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}
biology/kallisto/distinfo
+3 -3
View File
@@ -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
biology/kallisto/files/kallisto-test.in
Executable → Regular
View File
biology/kallisto/files/patch-CMakeLists.txt
+19 -16
View File
@@ -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)
biology/kallisto/files/patch-ext_bifrost_src_BooPHF.h
+33
View File
@@ -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");
}
biology/kallisto/files/patch-ext_bifrost_src_kseq.h
+15
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@@ -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)
biology/kallisto/files/patch-src_main.cpp
+8 -8
View File
@@ -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>