svn commit: r544077 - in head/biology/kallisto: . files
Jason W. Bacon
jwb at FreeBSD.org
Mon Aug 3 15:45:23 UTC 2020
Author: jwb
Date: Mon Aug 3 15:45:21 2020
New Revision: 544077
URL: https://svnweb.freebsd.org/changeset/ports/544077
Log:
biology/kallisto: Revert to 0.46.1
0.46.2 has long-standing regressions that are not being addressed, including
a seg fault when using --genomebam.
Also revert to bundled htslib in preparation for biology/htslib upgrade
to 1.10. Kallisto source contains modified bits of htslib 1.4.1 that are
incompatible with htslib > 1.9.
Added:
head/biology/kallisto/files/patch-ext_htslib_configure.ac (contents, props changed)
Deleted:
head/biology/kallisto/files/patch-src_CMakeLists.txt
Modified:
head/biology/kallisto/Makefile
head/biology/kallisto/distinfo
head/biology/kallisto/files/patch-CMakeLists.txt
Modified: head/biology/kallisto/Makefile
==============================================================================
--- head/biology/kallisto/Makefile Mon Aug 3 15:30:38 2020 (r544076)
+++ head/biology/kallisto/Makefile Mon Aug 3 15:45:21 2020 (r544077)
@@ -2,8 +2,8 @@
PORTNAME= kallisto
DISTVERSIONPREFIX= v
-DISTVERSION= 0.46.2
-PORTREVISION= 1
+DISTVERSION= 0.46.1
+PORTEPOCH= 1
CATEGORIES= biology
MAINTAINER= jwb at FreeBSD.org
@@ -12,11 +12,11 @@ COMMENT= Quantify abundances of transcripts from RNA-S
LICENSE= BSD2CLAUSE
LICENSE_FILE= ${WRKSRC}/license.txt
+BUILD_DEPENDS= autoconf>=0:devel/autoconf
LIB_DEPENDS= libhdf5.so:science/hdf5 \
- libsz.so:science/szip \
- libhts.so:biology/htslib
+ libsz.so:science/szip
-USES= cmake:noninja compiler:c++11-lang localbase:ldflags
+USES= cmake:noninja compiler:c++11-lang gmake localbase:ldflags
USE_GITHUB= yes
GH_ACCOUNT= pachterlab
@@ -26,10 +26,11 @@ PORTEXAMPLES= *
PLIST_FILES= bin/kallisto
EXAMPLES_PLIST_FILES= bin/kallisto-test
-# hdf5 is being phased out and is no longer build in by default, but is still
-# required for Sleuth and other downstream tools. Remove this after Sleuth
-# et all catch up.
-CMAKE_ARGS+= -DUSE_HDF5:BOOL=ON
+# hdf5 is being phased out and is no longer built in by default, but is still
+# required for Sleuth (requires kallisto bootstrap estimates) and other
+# downstream tools. Remove this after Sleuth et all catch up.
+CMAKE_ARGS+= -DUSE_HDF5:BOOL=ON
+MAKE_JOBS_UNSAFE= yes
OPTIONS_DEFINE= EXAMPLES
Modified: head/biology/kallisto/distinfo
==============================================================================
--- head/biology/kallisto/distinfo Mon Aug 3 15:30:38 2020 (r544076)
+++ head/biology/kallisto/distinfo Mon Aug 3 15:45:21 2020 (r544077)
@@ -1,3 +1,3 @@
-TIMESTAMP = 1581611719
-SHA256 (pachterlab-kallisto-v0.46.2_GH0.tar.gz) = 10bab0c2929d8c345750e02735b305bbbfa89e8a48f42c4b9af44f3d44ff4c82
-SIZE (pachterlab-kallisto-v0.46.2_GH0.tar.gz) = 2693857
+TIMESTAMP = 1595454023
+SHA256 (pachterlab-kallisto-v0.46.1_GH0.tar.gz) = 492ef081395e8858fcd9832aceb8b61c79358f00afb45e6709146c0fb51dd231
+SIZE (pachterlab-kallisto-v0.46.1_GH0.tar.gz) = 2254560
Modified: head/biology/kallisto/files/patch-CMakeLists.txt
==============================================================================
--- head/biology/kallisto/files/patch-CMakeLists.txt Mon Aug 3 15:30:38 2020 (r544076)
+++ head/biology/kallisto/files/patch-CMakeLists.txt Mon Aug 3 15:45:21 2020 (r544077)
@@ -1,25 +1,11 @@
---- CMakeLists.txt.orig 2018-12-20 14:20:05 UTC
+--- CMakeLists.txt.orig 2020-07-22 22:36:50 UTC
+++ CMakeLists.txt
-@@ -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
+@@ -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
- BUILD_COMMAND make lib-static
-- INSTALL_COMMAND ""
--)
--
--include_directories(${htslib_PREFIX}/src/htslib)
--
--
--
- # add_compile_options(-Wdeprecated-register)
++ BUILD_COMMAND gmake lib-static
+ INSTALL_COMMAND ""
+ )
- add_subdirectory(src)
Added: head/biology/kallisto/files/patch-ext_htslib_configure.ac
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/kallisto/files/patch-ext_htslib_configure.ac Mon Aug 3 15:45:21 2020 (r544077)
@@ -0,0 +1,11 @@
+--- 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 at 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)
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