git: c9bd01bdf4c1 - main - biology/kallisto: Update to 0.48.0
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Date: Wed, 19 Jan 2022 14:00:10 UTC
The branch main has been updated by jwb:
URL: https://cgit.FreeBSD.org/ports/commit/?id=c9bd01bdf4c1dae17b53482e9dabe000d310cf50
commit c9bd01bdf4c1dae17b53482e9dabe000d310cf50
Author: Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2022-01-19 13:57:36 +0000
Commit: Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2022-01-19 13:57:36 +0000
biology/kallisto: Update to 0.48.0
Fixes segfault with --genomebam in 0.46.2
Unbundle htslib
A few new features and performance improvements
Changes: https://github.com/pachterlab/kallisto/tags
---
biology/kallisto/Makefile | 10 +++++---
biology/kallisto/distinfo | 6 ++---
biology/kallisto/files/kallisto-test.in | 29 +++++++++++++++++++--
biology/kallisto/files/patch-CMakeLists.txt | 30 ++++++++++++++++------
.../kallisto/files/patch-ext_htslib_configure.ac | 11 --------
biology/kallisto/files/patch-src_CMakeLists.txt | 26 +++++++++++++++++++
biology/kallisto/files/patch-src_kseq.h | 12 +++++++++
7 files changed, 97 insertions(+), 27 deletions(-)
diff --git a/biology/kallisto/Makefile b/biology/kallisto/Makefile
index 996d22ee8720..3d4aecd0b9d3 100644
--- a/biology/kallisto/Makefile
+++ b/biology/kallisto/Makefile
@@ -1,6 +1,6 @@
PORTNAME= kallisto
DISTVERSIONPREFIX= v
-DISTVERSION= 0.46.1
+DISTVERSION= 0.48.0
PORTEPOCH= 1
CATEGORIES= biology
@@ -12,7 +12,8 @@ LICENSE_FILE= ${WRKSRC}/license.txt
BUILD_DEPENDS= autoconf>=0:devel/autoconf
LIB_DEPENDS= libhdf5.so:science/hdf5 \
- libsz.so:science/szip
+ libsz.so:science/szip \
+ libhts.so:biology/htslib
USES= cmake:noninja compiler:c++11-lang gmake localbase:ldflags
USE_GITHUB= yes
@@ -29,10 +30,13 @@ EXAMPLES_PLIST_FILES= bin/kallisto-test
# downstream tools. Remove this after Sleuth et al catch up.
CMAKE_ARGS+= -DUSE_HDF5:BOOL=ON
MAKE_JOBS_UNSAFE= yes
-LDFLAGS+= -lz
+LDFLAGS+= -lhts -lz
OPTIONS_DEFINE= EXAMPLES
+post-extract:
+ ${RM} -rf ${WRKSRC}/ext/htslib
+
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 98722ba0c842..1f2de73cccd4 100644
--- a/biology/kallisto/distinfo
+++ b/biology/kallisto/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1595454023
-SHA256 (pachterlab-kallisto-v0.46.1_GH0.tar.gz) = 492ef081395e8858fcd9832aceb8b61c79358f00afb45e6709146c0fb51dd231
-SIZE (pachterlab-kallisto-v0.46.1_GH0.tar.gz) = 2254560
+TIMESTAMP = 1642516764
+SHA256 (pachterlab-kallisto-v0.48.0_GH0.tar.gz) = 1797ac4d1f0771e3f1f25dd7972bded735fcb43f853cf52184d3d9353a6269b0
+SIZE (pachterlab-kallisto-v0.48.0_GH0.tar.gz) = 2706838
diff --git a/biology/kallisto/files/kallisto-test.in b/biology/kallisto/files/kallisto-test.in
old mode 100644
new mode 100755
index f713e9dc44c2..952063e4e66b
--- a/biology/kallisto/files/kallisto-test.in
+++ b/biology/kallisto/files/kallisto-test.in
@@ -16,6 +16,20 @@ usage()
}
+##########################################################################
+# Function description:
+# Pause until user presses return
+##########################################################################
+
+pause()
+{
+ local junk
+
+ printf "Press return to continue..."
+ read junk
+}
+
+
##########################################################################
# Main
##########################################################################
@@ -32,9 +46,20 @@ fi
cp -iR %%EXAMPLESDIR%% "$dir"
cd "$dir"
-kallisto index -i transcripts.idx transcripts.fasta.gz
-kallisto quant -i transcripts.idx -o output -b 100 reads_1.fastq.gz reads_2.fastq.gz
+kallisto index --index=transcripts.idx transcripts.fasta.gz
+pause
+
+kallisto quant --index=transcripts.idx --genomebam --chromosomes=chrom.txt \
+ --gtf=transcripts.gtf.gz --output-dir=output \
+ --boostrap-samples=100 reads_1.fastq.gz reads_2.fastq.gz
+pause
+
ls -l output
+pause
+
+# Test genomebam
+samtools view output/pseudoalignments.bam | more
+
more output/abundance.tsv
cat << EOM
diff --git a/biology/kallisto/files/patch-CMakeLists.txt b/biology/kallisto/files/patch-CMakeLists.txt
index b122ef10d345..fb498f8a945b 100644
--- a/biology/kallisto/files/patch-CMakeLists.txt
+++ b/biology/kallisto/files/patch-CMakeLists.txt
@@ -1,11 +1,25 @@
---- CMakeLists.txt.orig 2020-07-22 22:36:50 UTC
+--- CMakeLists.txt.orig 2019-11-04 16:28:52 UTC
+++ CMakeLists.txt
-@@ -42,7 +42,7 @@ ExternalProject_Add(htslib
- BUILD_IN_SOURCE 1
- CONFIGURE_COMMAND autoheader && autoconf && ${PROJECT_SOURCE_DIR}/ext/htslib/configure
- --prefix=${PREFIX} --disable-bz2 --disable-lzma --disable-libcurl
+@@ -34,22 +34,6 @@ ELSE(LINK MATCHES shared)
+ message("shared build")
+ ENDIF(LINK MATCHES static)
+
+-
+-include(ExternalProject)
+-ExternalProject_Add(htslib
+- PREFIX ${PROJECT_SOURCE_DIR}/ext/htslib
+- SOURCE_DIR ${PROJECT_SOURCE_DIR}/ext/htslib
+- BUILD_IN_SOURCE 1
+- CONFIGURE_COMMAND autoheader && autoconf && ${PROJECT_SOURCE_DIR}/ext/htslib/configure
+- --prefix=${PREFIX} --disable-bz2 --disable-lzma --disable-libcurl
- BUILD_COMMAND make lib-static
-+ BUILD_COMMAND gmake lib-static
- INSTALL_COMMAND ""
- )
+- INSTALL_COMMAND ""
+-)
+-
+-include_directories(${htslib_PREFIX}/src/htslib)
+-
+-
+-
+ # add_compile_options(-Wdeprecated-register)
+ add_subdirectory(src)
diff --git a/biology/kallisto/files/patch-ext_htslib_configure.ac b/biology/kallisto/files/patch-ext_htslib_configure.ac
deleted file mode 100644
index 0482cc554c45..000000000000
--- a/biology/kallisto/files/patch-ext_htslib_configure.ac
+++ /dev/null
@@ -1,11 +0,0 @@
---- ext/htslib/configure.ac.orig 2019-11-04 16:28:52 UTC
-+++ ext/htslib/configure.ac
-@@ -23,7 +23,7 @@
- # DEALINGS IN THE SOFTWARE.
-
- dnl Process this file with autoconf to produce a configure script
--AC_INIT([HTSlib], m4_esyscmd_s([make print-version]),
-+AC_INIT([HTSlib], [1.4.1],
- [samtools-help@lists.sourceforge.net], [], [http://www.htslib.org/])
- AC_PREREQ(2.63) dnl This version introduced 4-argument AC_CHECK_HEADER
- AC_CONFIG_SRCDIR(hts.c)
diff --git a/biology/kallisto/files/patch-src_CMakeLists.txt b/biology/kallisto/files/patch-src_CMakeLists.txt
new file mode 100644
index 000000000000..fbeb9128522a
--- /dev/null
+++ b/biology/kallisto/files/patch-src_CMakeLists.txt
@@ -0,0 +1,26 @@
+--- src/CMakeLists.txt.orig 2021-11-24 14:45:50 UTC
++++ src/CMakeLists.txt
+@@ -3,15 +3,13 @@ file(GLOB headers *.h *.hpp)
+
+ list(REMOVE_ITEM sources main.cpp)
+
+-include_directories(../ext/htslib)
+-
+ add_library(kallisto_core ${sources} ${headers})
+ target_include_directories(kallisto_core PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
+
+ add_executable(kallisto main.cpp)
+
+ find_package( Threads REQUIRED )
+-target_link_libraries(kallisto kallisto_core pthread ${CMAKE_CURRENT_SOURCE_DIR}/../ext/htslib/libhts.a)
++target_link_libraries(kallisto kallisto_core pthread)
+
+ if(LINK MATCHES static)
+ set(BUILD_SHARED_LIBS OFF)
+@@ -56,4 +54,4 @@ else()
+ endif(LINK MATCHES static)
+
+
+-install(TARGETS kallisto DESTINATION "${CMAKE_INSTALL_BINDIR}")
+\ No newline at end of file
++install(TARGETS kallisto DESTINATION "${CMAKE_INSTALL_BINDIR}")
diff --git a/biology/kallisto/files/patch-src_kseq.h b/biology/kallisto/files/patch-src_kseq.h
new file mode 100644
index 000000000000..f7712a023fda
--- /dev/null
+++ b/biology/kallisto/files/patch-src_kseq.h
@@ -0,0 +1,12 @@
+--- src/kseq.h.orig 2019-11-04 16:28:52 UTC
++++ src/kseq.h
+@@ -32,6 +32,9 @@
+ #include <string.h>
+ #include <stdlib.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)