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locks; strict;
comment	@# @;


1.6
date	2024.09.20.00.03.15;	author bacon;	state Exp;
branches;
next	1.5;
commitid	vGzFMkGm3GMJAtqF;

1.5
date	2024.07.27.12.22.54;	author bacon;	state Exp;
branches;
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commitid	OLdxWtcRDO02stjF;

1.4
date	2023.11.04.14.35.07;	author bacon;	state Exp;
branches;
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1.3
date	2022.02.27.01.57.27;	author bacon;	state Exp;
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1.2
date	2020.07.30.07.59.19;	author wiz;	state dead;
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1.1
date	2018.12.21.19.00.56;	author bacon;	state Exp;
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desc
@@


1.6
log
@biology/kallisto: Update to 0.51.1

Enhancements to ir-kallisto and pseudoalignments

Changes: https://github.com/pachterlab/kallisto/releases
Reported by: portscout
@
text
@$NetBSD$

# Use external htslib

--- src/CMakeLists.txt.orig	2024-07-23 11:52:01.089699466 +0000
+++ src/CMakeLists.txt
@@@@ -3,10 +3,6 @@@@ file(GLOB headers *.h *.hpp)
 
 list(REMOVE_ITEM sources main.cpp)
 
-if (USE_BAM)
-include_directories(../ext/htslib)
-endif(USE_BAM)
-
 if(NOT MAX_KMER_SIZE)
 set(MAX_KMER_SIZE "32")
 endif()
@@@@ -21,7 +17,7 @@@@ add_executable(kallisto main.cpp)
 find_package( Threads REQUIRED )
 ExternalProject_Get_Property(bifrost install_dir)
 if (USE_BAM)
-target_link_libraries(kallisto kallisto_core pthread ${CMAKE_CURRENT_SOURCE_DIR}/../ext/htslib/libhts.a ${install_dir}/build/src/libbifrost.a  -DMAX_KMER_SIZE=${MAX_KMER_SIZE})
+target_link_libraries(kallisto kallisto_core pthread hts ${install_dir}/build/src/libbifrost.a  -DMAX_KMER_SIZE=${MAX_KMER_SIZE})
 else()
 target_link_libraries(kallisto kallisto_core pthread ${install_dir}/build/src/libbifrost.a -DMAX_KMER_SIZE=${MAX_KMER_SIZE})
 endif(USE_BAM)
@


1.5
log
@biology/kallisto: Update to 0.51.0,1

Add support for long reads to kallisto bus and kallisto quant-tcc

Changes: https://github.com/pachterlab/kallisto/releases
Reported by: portscout
@
text
@@


1.4
log
@biology/kallisto: Update to 0.50.1

Update kallisto index version to 13
A few other new features
Changes: https://github.com/pachterlab/kallisto/releases
@
text
@d3 1
a3 1
# Unbundle htslib
d5 1
a5 1
--- src/CMakeLists.txt.orig	2023-07-06 14:07:38 UTC
d15 4
a18 4
 add_compile_options(-Wno-subobject-linkage) # Suppress bifrost warning
 
 add_library(kallisto_core ${sources} ${headers})
@@@@ -17,7 +13,7 @@@@ add_executable(kallisto main.cpp)
d22 2
a23 2
-target_link_libraries(kallisto kallisto_core pthread ${CMAKE_CURRENT_SOURCE_DIR}/../ext/htslib/libhts.a ${install_dir}/build/src/libbifrost.a)
+target_link_libraries(kallisto kallisto_core pthread hts ${install_dir}/build/src/libbifrost.a)
d25 1
a25 1
 target_link_libraries(kallisto kallisto_core pthread ${install_dir}/build/src/libbifrost.a)
@


1.3
log
@biology/kallisto: Update to 0.48.0

Long awaited bug fix release
Also unbundled htslib
Changes: https://github.com/pachterlab/kallisto/tags
@
text
@d5 1
a5 1
--- src/CMakeLists.txt.orig	2022-02-26 16:35:26.912550601 +0000
d7 1
a7 1
@@@@ -3,15 +3,13 @@@@ file(GLOB headers *.h *.hpp)
d11 1
d13 1
d15 2
d18 1
a18 4
 target_include_directories(kallisto_core PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
 
 add_executable(kallisto main.cpp)
 
d20 7
a26 12
-target_link_libraries(kallisto kallisto_core pthread ${CMAKE_CURRENT_SOURCE_DIR}/../ext/htslib/libhts.a)
+target_link_libraries(kallisto kallisto_core pthread hts)
 
 if(LINK MATCHES static)
     set(BUILD_SHARED_LIBS OFF)
@@@@ -62,4 +60,4 @@@@ else()
 endif(LINK MATCHES static)
 
 
-install(TARGETS kallisto DESTINATION "${CMAKE_INSTALL_BINDIR}")
\ No newline at end of file
+install(TARGETS kallisto DESTINATION "${CMAKE_INSTALL_BINDIR}")
@


1.2
log
@kallisto: remove patches that were removed from distinfo during update
@
text
@d1 1
a1 1
$NetBSD: patch-src_CMakeLists.txt,v 1.1 2018/12/21 19:00:56 bacon Exp $
d5 1
a5 1
--- src/CMakeLists.txt.orig	2018-10-17 23:58:22 UTC
d24 1
a24 1
@@@@ -56,4 +54,4 @@@@ else()
@


1.1
log
@biology/kallisto: import kallisto-0.45.0

Kallisto is a program for quantifying abundances of transcripts from RNA-Seq
data, or more generally of target sequences using high-throughput sequencing
reads. It is based on the novel idea of pseudoalignment for rapidly determining
the compatibility of reads with targets, without the need for alignment.
@
text
@d1 1
a1 1
$NetBSD$
@