From nobody Wed Jan 19 14:00:10 2022 X-Original-To: dev-commits-ports-all@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 80FE0196217F; Wed, 19 Jan 2022 14:00:10 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4Jf6j62W5Mz3DXp; Wed, 19 Jan 2022 14:00:10 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1642600810; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=a65MsijfWlBaO1AEed0C4xc7piaI9eOj8SjPYhpXCGQ=; b=Cnm0O5UB6lDo7/Vg4VThdmTTEvD0zFVcMEKjAZcHY0qURx0DlGY0evzIhasrvNgoxot2pX cVL8P5Nyvu/zMyCXcT+4C1yARnnMMfD5U1lMrwHdYsVwC5ebwtBt/N3SW5Cpj1Z7SbQDHI FMrJsm9v7JLWp+zzwyJwz0rs+McbEBev7+Q4E9NlOHxLO61X0fM5rnWlZU9dESWcfvRVKd 2mpAnPyyR7OKjlkdVCz86SpziRPCB+dI7kadmhe9B6Uf258CfOakA5JhmwRiYnu94ufqYn 9QfANWU+ZYYpg80LJc1jUs3mKrZeY2UuMZR+gphf3rvrzwz4N9R7J0haD+2DMA== Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 2C93D15DDE; Wed, 19 Jan 2022 14:00:10 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.16.1/8.16.1) with ESMTP id 20JE0Atd074587; Wed, 19 Jan 2022 14:00:10 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 20JE0A1B074583; Wed, 19 Jan 2022 14:00:10 GMT (envelope-from git) Date: Wed, 19 Jan 2022 14:00:10 GMT Message-Id: <202201191400.20JE0A1B074583@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: "Jason W. Bacon" Subject: git: c9bd01bdf4c1 - main - biology/kallisto: Update to 0.48.0 List-Id: Commit messages for all branches of the ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-all List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-all@freebsd.org X-BeenThere: dev-commits-ports-all@freebsd.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: jwb X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: c9bd01bdf4c1dae17b53482e9dabe000d310cf50 Auto-Submitted: auto-generated ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1642600810; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=a65MsijfWlBaO1AEed0C4xc7piaI9eOj8SjPYhpXCGQ=; b=M4ifhi7XsByd9H74k/1UBxDcgp+iN1B7YAysruf+RMvjN7scDY/Q60KrrLhRxl2yhm+/e7 GNnSzhk4nfDNDRRFZhWreYFHH2P4JTSud+Au9954AD2+y9pOcVWWjoDWc624wGW5HfBb+O A9DXJ2WK+aR0bfuw/GZmPkaFtELujGRzx8Cs97ljFL3/jHRhYlwiUWnIzOV9wgejebWUNk ubbSMs3ixxbbw1y2QJIJrIKcTRu9W++YH0bab/oIUkZnqCLhl277FqVhC0QzoeEGnxkZlh JeT8toJKJyFLortiTwUmab7pvJ7q6Frww/1Kf7aXYWQoAjwiGtoP2geqNTKVCg== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1642600810; a=rsa-sha256; cv=none; b=tePFYG4XvMP6kkzmO16zy9JMOX8uXozAgiE9ff/S8ieIZ5XYhzAVnzreW+DdVnVhm9wyq/ JFg0eri3+140MgeZL4/gNg1Gyvx4ZPHJ4cnVe7zq+dXs9Ki4GhRULBRlqpPMRL390pTh44 7XER1ShW0ExuJ5d3thzFMd4DM0pr2aqQX8EbpW3uGu7L2Aty8AJD/einiQFTV4Kgxd+K+u nWA2wRUD6ycKOcWHDyHU761vQIki92BnCdmKlLKPWi75UgH212YrHABij4EN0plV1sNGfb tXBeqjmaqSBM/7/994YYSN4orlcj8uGcKKk1HNEkp8tDQcvS4HLz9YhCJNpZAQ== ARC-Authentication-Results: i=1; mx1.freebsd.org; none X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=c9bd01bdf4c1dae17b53482e9dabe000d310cf50 commit c9bd01bdf4c1dae17b53482e9dabe000d310cf50 Author: Jason W. Bacon AuthorDate: 2022-01-19 13:57:36 +0000 Commit: Jason W. Bacon 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 + #include + ++// Prevent redefinition of kstring_t below ++#include ++ + #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)