commit: 471ea137746e8ed32db3609114b071fb51cf4458 Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> AuthorDate: Tue Oct 11 19:20:02 2022 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> CommitDate: Tue Oct 11 19:20:02 2022 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=471ea137
sci-biology/*: remove revdeps of io_lib Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org> profiles/package.mask | 8 - sci-biology/caftools/caftools-2.0.2.ebuild | 45 ----- sci-biology/caftools/files/Makefile.in-2.0.2.patch | 43 ----- sci-biology/caftools/files/Makefile.in.patch | 49 ----- sci-biology/caftools/metadata.xml | 17 -- sci-biology/roche454ace2caf/metadata.xml | 12 -- .../roche454ace2caf-20100812.ebuild | 28 --- .../files/salmon-0.10.2-no-boost-static.patch | 18 -- .../salmon-0.10.2_TestSalmonQuasi.cmake.patch | 11 -- .../salmon/files/salmon-0.10.2_fix_lib_dir.patch | 22 --- .../salmon/files/salmon-0.10.2_fix_tests.patch | 10 -- .../files/salmon-0.10.2_remove_curl_call.patch | 12 -- .../files/salmon-0.10.2_remove_curl_calls.patch | 200 --------------------- .../salmon/files/salmon-1.6.0-find-boost.patch | 116 ------------ sci-biology/salmon/metadata.xml | 15 -- sci-biology/salmon/salmon-0.10.2.ebuild | 73 -------- sci-biology/salmon/salmon-1.6.0.ebuild | 70 -------- .../staden/files/staden-2.0.0_beta11-ldflags.patch | 30 ---- sci-biology/staden/metadata.xml | 15 -- sci-biology/staden/staden-2.0.0_beta11.ebuild | 76 -------- sci-biology/staden_doc/metadata.xml | 15 -- .../staden_doc/staden_doc-2.0.0_beta11.ebuild | 42 ----- 22 files changed, 927 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index a21bb9773..d39812beb 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -29,11 +29,3 @@ ## app-misc/some-package #--- END OF EXAMPLES --- - -# Andrew Ammerlaan <andrewammerl...@gentoo.org> (2022-08-22) -# Depends on removed sci-libs/io_lib. removal in 30 days -sci-biology/caftools -sci-biology/salmon -sci-biology/staden -sci-biology/staden_doc -sci-biology/roche454ace2caf diff --git a/sci-biology/caftools/caftools-2.0.2.ebuild b/sci-biology/caftools/caftools-2.0.2.ebuild deleted file mode 100644 index 7d58f3375..000000000 --- a/sci-biology/caftools/caftools-2.0.2.ebuild +++ /dev/null @@ -1,45 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="Manipulate CAF files and convert to GAP4 format (not GAP5), ACE, PHRAP" -HOMEPAGE="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC310697/"; -SRC_URI=" - ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/${P}.tar.gz - ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/${PN}-2.0.tar.gz"; - -LICENSE="GRL" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -DEPEND=" - sci-libs/io_lib - dev-lang/perl" -RDEPEND="${DEPEND}" - -PATCHES=( - "${FILESDIR}"/Makefile.in-"${PV}".patch -) - -src_prepare(){ - default - mv "${WORKDIR}"/caftools-2.0/man/*.{1,5} "${S}"/man/ || die -} - -src_configure(){ - default - sed \ - -e 's:prefix = /usr:prefix = $(DESTDIR)/usr:' \ - -i Makefile src/Makefile || die -} - -# TODO: the 2.0.2 archive lacks manpages compared to 2.0, FIXME -# The man/Makefile.in is screwed in 2.0.2 so we cannot use it to install the manpage files, -# not even copying over whole caftools-2.0/man/ to caftools-2.0.2/man does not help. -src_install(){ - default - doman man/*.[1-5] || die - elog "Some usage info is at http://sarton.imb-jena.de/software/consed2gap/"; - elog "for some reason caf_find_misassemblies is gone from 2.0.2 version" -} diff --git a/sci-biology/caftools/files/Makefile.in-2.0.2.patch b/sci-biology/caftools/files/Makefile.in-2.0.2.patch deleted file mode 100644 index 1e5160487..000000000 --- a/sci-biology/caftools/files/Makefile.in-2.0.2.patch +++ /dev/null @@ -1,43 +0,0 @@ ---- src/Makefile.in.ori 2010-12-05 22:59:40.000000000 +0100 -+++ src/Makefile.in 2010-12-05 23:01:19.000000000 +0100 -@@ -32,8 +32,6 @@ - includedir = @includedir@ - oldincludedir = /usr/include - --DESTDIR = -- - pkgdatadir = $(datadir)/@PACKAGE@ - pkglibdir = $(libdir)/@PACKAGE@ - pkgincludedir = $(includedir)/@PACKAGE@ -@@ -323,18 +321,18 @@ - - install-binPROGRAMS: $(bin_PROGRAMS) - @$(NORMAL_INSTALL) -- $(mkinstalldirs) $(DESTDIR)$(bindir) -+ $(mkinstalldirs) $(bindir) - @list='$(bin_PROGRAMS)'; for p in $$list; do \ - if test -f $$p; then \ -- echo " $(INSTALL_PROGRAM) $$p $(DESTDIR)$(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`"; \ -- $(INSTALL_PROGRAM) $$p $(DESTDIR)$(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`; \ -+ echo " $(INSTALL_PROGRAM) $$p $(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`"; \ -+ $(INSTALL_PROGRAM) $$p $(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`; \ - else :; fi; \ - done - - uninstall-binPROGRAMS: - @$(NORMAL_UNINSTALL) - list='$(bin_PROGRAMS)'; for p in $$list; do \ -- rm -f $(DESTDIR)$(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`; \ -+ rm -f $(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`; \ - done - - .c.o: -@@ -579,7 +577,7 @@ - $(MAKE) $(AM_MAKEFLAGS) AM_INSTALL_PROGRAM_FLAGS=-s install - installdirs: installdirs-recursive - installdirs-am: -- $(mkinstalldirs) $(DESTDIR)$(bindir) -+ $(mkinstalldirs) $(bindir) - - - mostlyclean-generic: diff --git a/sci-biology/caftools/files/Makefile.in.patch b/sci-biology/caftools/files/Makefile.in.patch deleted file mode 100644 index 4ddd9f628..000000000 --- a/sci-biology/caftools/files/Makefile.in.patch +++ /dev/null @@ -1,49 +0,0 @@ ---- src/Makefile.in.ori 2010-12-05 22:08:50.000000000 +0100 -+++ src/Makefile.in 2010-12-05 22:10:07.000000000 +0100 -@@ -18,7 +18,7 @@ - srcdir = @srcdir@ - top_srcdir = @top_srcdir@ - VPATH = @srcdir@ --prefix = @prefix@ -+prefix = $(DESTDIR)/@prefix@ - exec_prefix = @exec_prefix@ - - bindir = @bindir@ -@@ -394,14 +394,14 @@ - binPROGRAMS_INSTALL = $(INSTALL_PROGRAM) - install-binPROGRAMS: $(bin_PROGRAMS) - @$(NORMAL_INSTALL) -- $(mkinstalldirs) $(DESTDIR)$(bindir) -+ $(mkinstalldirs) $(bindir) - @list='$(bin_PROGRAMS)'; for p in $$list; do \ - p1=`echo $$p|sed 's/$(EXEEXT)$$//'`; \ - if test -f $$p \ - ; then \ - f=`echo "$$p1" | sed 's,^.*/,,;$(transform);s/$$/$(EXEEXT)/'`; \ -- echo " $(INSTALL_PROGRAM_ENV) $(binPROGRAMS_INSTALL) $$p $(DESTDIR)$(bindir)/$$f"; \ -- $(INSTALL_PROGRAM_ENV) $(binPROGRAMS_INSTALL) $$p $(DESTDIR)$(bindir)/$$f; \ -+ echo " $(INSTALL_PROGRAM_ENV) $(binPROGRAMS_INSTALL) $$p $(bindir)/$$f"; \ -+ $(INSTALL_PROGRAM_ENV) $(binPROGRAMS_INSTALL) $$p $(bindir)/$$f; \ - else :; fi; \ - done - -@@ -409,8 +409,8 @@ - @$(NORMAL_UNINSTALL) - @list='$(bin_PROGRAMS)'; for p in $$list; do \ - f=`echo "$$p" | sed 's,^.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/'`; \ -- echo " rm -f $(DESTDIR)$(bindir)/$$f"; \ -- rm -f $(DESTDIR)$(bindir)/$$f; \ -+ echo " rm -f $(bindir)/$$f"; \ -+ rm -f $(bindir)/$$f; \ - done - - clean-binPROGRAMS: -@@ -663,7 +663,7 @@ - all-am: Makefile $(PROGRAMS) config.h - installdirs: installdirs-recursive - installdirs-am: -- $(mkinstalldirs) $(DESTDIR)$(bindir) -+ $(mkinstalldirs) $(bindir) - - install: install-recursive - install-exec: install-exec-recursive diff --git a/sci-biology/caftools/metadata.xml b/sci-biology/caftools/metadata.xml deleted file mode 100644 index 224641279..000000000 --- a/sci-biology/caftools/metadata.xml +++ /dev/null @@ -1,17 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="person"> - <email>mmokr...@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biol...@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <longdescription> -CAF is a text format for describing sequence assemblies. It is acedb-compliant -and is an extension of the ace-file format used earlier, but with support for -base quality measures and a more extensive description of the Sequence data. -</longdescription> -</pkgmetadata> diff --git a/sci-biology/roche454ace2caf/metadata.xml b/sci-biology/roche454ace2caf/metadata.xml deleted file mode 100644 index 138cb7705..000000000 --- a/sci-biology/roche454ace2caf/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="person"> - <email>mmokr...@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biol...@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/roche454ace2caf/roche454ace2caf-20100812.ebuild b/sci-biology/roche454ace2caf/roche454ace2caf-20100812.ebuild deleted file mode 100644 index a3c4eee39..000000000 --- a/sci-biology/roche454ace2caf/roche454ace2caf-20100812.ebuild +++ /dev/null @@ -1,28 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="ace to gap4 converter" -HOMEPAGE="https://genome.imb-jena.de/software/roche454ace2caf/"; -SRC_URI="https://genome.imb-jena.de/software/roche454ace2caf/download/src/roche454ace2gap-2010-12-08.tgz"; - -LICENSE="FLI-Jena" -SLOT="0" -KEYWORDS="~amd64" - -DEPEND="" -RDEPEND="${DEPEND} - sci-biology/align_to_scf - sci-biology/sff_dump - sci-biology/caftools - sci-biology/staden - dev-lang/perl - app-shells/ksh" - -S="${WORKDIR}/roche2gap" - -src_install(){ - dobin bin/*.pl bin/roche454ace2gap - einstalldocs -} diff --git a/sci-biology/salmon/files/salmon-0.10.2-no-boost-static.patch b/sci-biology/salmon/files/salmon-0.10.2-no-boost-static.patch deleted file mode 100644 index ac561d793..000000000 --- a/sci-biology/salmon/files/salmon-0.10.2-no-boost-static.patch +++ /dev/null @@ -1,18 +0,0 @@ ---- salmon-0.10.2/CMakeLists.txt 2018-06-25 10:51:47.179712781 +0200 -+++ salmon-0.10.2/CMakeLists.txt 2018-06-25 10:52:47.951289159 +0200 -@@ -213,15 +213,6 @@ - set (CMAKE_LIBRARY_PATH ${CUSTOM_BOOST_PATH}/lib ${CMAKE_LIBRARY_PATH}) - endif ( DEFINED CUSTOM_BOOST_PATH ) - --## --# We want static, multithreaded boost libraries --## --if(CONDA_BUILD) -- set (Boost_USE_STATIC_LIBS OFF) --else () -- set (Boost_USE_STATIC_LIBS ON) --endif(CONDA_BUILD) -- - set (Boost_USE_MULTITHREADED ON) - #set (Boost_USE_STATIC_RUNTIME OFF) - diff --git a/sci-biology/salmon/files/salmon-0.10.2_TestSalmonQuasi.cmake.patch b/sci-biology/salmon/files/salmon-0.10.2_TestSalmonQuasi.cmake.patch deleted file mode 100644 index 81edf96f5..000000000 --- a/sci-biology/salmon/files/salmon-0.10.2_TestSalmonQuasi.cmake.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- salmon-0.10.2/cmake/TestSalmonQuasi.cmake 2018-06-26 10:39:51.061971241 +0200 -+++ salmon-0.10.2/cmake/TestSalmonQuasi.cmake 2018-06-26 10:40:22.372822258 +0200 -@@ -5,7 +5,7 @@ - ) - - if (SALMON_QUASI_INDEX_RESULT) -- message(FATAL_ERROR "Error running ${SALMON_QUASI_INDEX_COMMAND}") -+ message(FATAL_ERROR "Error running ${SALMON_QUASI_INDEX_CMD}") - endif() - - set(SALMON_QUANT_COMMAND ${CMAKE_BINARY_DIR}/salmon quant -i sample_salmon_quasi_index -l IU -1 reads_1.fastq -2 reads_2.fastq -o sample_salmon_quasi_quant) diff --git a/sci-biology/salmon/files/salmon-0.10.2_fix_lib_dir.patch b/sci-biology/salmon/files/salmon-0.10.2_fix_lib_dir.patch deleted file mode 100644 index eb606c00c..000000000 --- a/sci-biology/salmon/files/salmon-0.10.2_fix_lib_dir.patch +++ /dev/null @@ -1,22 +0,0 @@ ---- salmon-0.10.2/src/CMakeLists.txt 2018-06-25 13:35:45.723519730 +0200 -+++ salmon-0.10.2/src/CMakeLists.txt 2018-06-25 13:44:01.326139539 +0200 -@@ -296,6 +296,8 @@ - ) - ENDIF(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT) - -+include(GNUInstallDirs) -+ - set(INSTALL_LIB_DIR lib ) - set(INSTALL_BIN_DIR bin ) - set(INSTALL_INCLUDE_DIR include ) -@@ -311,8 +313,8 @@ - - install(TARGETS salmon salmon_core - RUNTIME DESTINATION bin -- LIBRARY DESTINATION lib -- ARCHIVE DESTINATION lib -+ LIBRARY DESTINATION "${CMAKE_INSTALL_FULL_LIBDIR}" -+ ARCHIVE DESTINATION "${CMAKE_INSTALL_FULL_LIBDIR}" - ) - - add_custom_command(TARGET unitTests POST_BUILD diff --git a/sci-biology/salmon/files/salmon-0.10.2_fix_tests.patch b/sci-biology/salmon/files/salmon-0.10.2_fix_tests.patch deleted file mode 100644 index 0a95757a8..000000000 --- a/sci-biology/salmon/files/salmon-0.10.2_fix_tests.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- salmon-0.10.2/src/CMakeLists.txt.ori 2018-06-26 10:34:29.293225671 +0200 -+++ salmon-0.10.2/src/CMakeLists.txt 2018-06-26 10:35:24.674730920 +0200 -@@ -335,6 +335,6 @@ - ) - - include(InstallRequiredSystemLibraries) --add_test( NAME unit_tests COMMAND ${CMAKE_COMMAND} -DTOPLEVEL_DIR=${CMAKE_INSTALL_PREFIX} -P ${GAT_SOURCE_DIR}/cmake/UnitTests.cmake ) -+add_test( NAME unit_tests COMMAND ${CMAKE_COMMAND} -DTOPLEVEL_DIR=${GAT_SOURCE_DIR} -P ${GAT_SOURCE_DIR}/cmake/UnitTests.cmake ) - add_test( NAME salmon_read_test_fmd COMMAND ${CMAKE_COMMAND} -DTOPLEVEL_DIR=${GAT_SOURCE_DIR} -P ${GAT_SOURCE_DIR}/cmake/TestSalmonFMD.cmake ) - add_test( NAME salmon_read_test_quasi COMMAND ${CMAKE_COMMAND} -DTOPLEVEL_DIR=${GAT_SOURCE_DIR} -P ${GAT_SOURCE_DIR}/cmake/TestSalmonQuasi.cmake ) diff --git a/sci-biology/salmon/files/salmon-0.10.2_remove_curl_call.patch b/sci-biology/salmon/files/salmon-0.10.2_remove_curl_call.patch deleted file mode 100644 index 8eddc6e3a..000000000 --- a/sci-biology/salmon/files/salmon-0.10.2_remove_curl_call.patch +++ /dev/null @@ -1,12 +0,0 @@ ---- salmon-9999/scripts/fetchRapMap.sh 2018-06-25 11:11:07.019798309 +0200 -+++ salmon-9999/scripts/fetchRapMap.sh 2018-06-25 11:12:25.131824486 +0200 -@@ -29,7 +29,8 @@ - EXPECTED_SHA256=c4ca27de299bee395b404d117d9d98ad9f0d6ee256ea1deb2890ea402893e688 - - mkdir -p ${EXTERNAL_DIR} --curl -k -L https://github.com/COMBINE-lab/RapMap/archive/${SVER}.zip -o ${EXTERNAL_DIR}/rapmap.zip -+# curl -k -L https://github.com/COMBINE-lab/RapMap/archive/${SVER}.zip -o ${EXTERNAL_DIR}/rapmap.zip -+cp ../../distdir/salmon-0.10.2_RapMap.zip ${EXTERNAL_DIR}/rapmap.zip - - hashcheck="" - if exists sha256sum; then diff --git a/sci-biology/salmon/files/salmon-0.10.2_remove_curl_calls.patch b/sci-biology/salmon/files/salmon-0.10.2_remove_curl_calls.patch deleted file mode 100644 index 438763960..000000000 --- a/sci-biology/salmon/files/salmon-0.10.2_remove_curl_calls.patch +++ /dev/null @@ -1,200 +0,0 @@ ---- salmon-0.10.2/CMakeLists.txt 2018-06-25 13:12:49.275828719 +0200 -+++ salmon-0.10.2/CMakeLists.txt 2018-06-25 13:12:38.945565690 +0200 -@@ -235,31 +235,7 @@ - - find_package (LibLZMA) - if (NOT LIBLZMA_FOUND) -- message ("Will attempt to fetch and build liblzma") -- message ("=======================================") --ExternalProject_Add(liblzma -- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external -- ## -- DOWNLOAD_COMMAND curl -k -L http://tukaani.org/xz/xz-5.2.2.tar.gz -o xz-5.2.2.tar.gz && -- ${SHASUM} 73df4d5d34f0468bd57d09f2d8af363e95ed6cc3a4a86129d2f2c366259902a2 xz-5.2.2.tar.gz && -- tar -xzvf xz-5.2.2.tar.gz -- #URL http://tukaani.org/xz/xz-5.2.2.tar.gz -- #URL_HASH SHA1=14663612422ab61386673be78fbb2556f50a1f08 -- ## -- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/xz-5.2.2 -- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install -- BUILD_IN_SOURCE TRUE -- CONFIGURE_COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/external/xz-5.2.2/configure --prefix=<INSTALL_DIR> CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CFLAGS=${EXTRA_CMAKE_INCLUDE_FLAGS} CPPFLAGS=${EXTRA_CMAKE_INCLUDE_FLAGS} LDFLAGS=${EXTRA_CMAKE_LIBRARY_FLAGS} -- BUILD_COMMAND make ${QUIET_MAKE} -- INSTALL_COMMAND make ${QUIET_MAKE} install --) -- --# Tell cmake that the external project generated a library so we can --# add dependencies here instead of later --set (LIBLZMA_LIBRARIES ${GAT_SOURCE_DIR}/external/install/lib/liblzma.a) --set (LIBSTADEN_LDFLAGS "-L${GAT_SOURCE_DIR}/external/install/lib") --set (LIBSTADEN_CFLAGS "-I${GAT_SOURCE_DIR}/external/install/include") --set (FETCHED_LIBLZMA TRUE) -+ message (FATAL_ERROR "liblzma must be installed before configuration & building can proceed") - else() - message("Found liblzma library: ${LIBLZMA_LIBRARIES}") - message("===========================================") -@@ -267,28 +243,7 @@ - - find_package (BZip2) - if (NOT BZIP2_FOUND) -- message ("Will attempt to fetch and build libbz2") -- message ("=======================================") --ExternalProject_Add(libbz2 -- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external -- DOWNLOAD_COMMAND curl -k -L http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz -o bzip2-1.0.6.tar.gz && -- ${SHASUM} a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd bzip2-1.0.6.tar.gz && -- tar -xzvf bzip2-1.0.6.tar.gz -- #URL http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz -- #URL_HASH SHA1=3f89f861209ce81a6bab1fd1998c0ef311712002 -- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/bzip2-1.0.6 -- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install -- BUILD_IN_SOURCE TRUE -- CONFIGURE_COMMAND "" -- BUILD_COMMAND make ${QUIET_MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} -- INSTALL_COMMAND make ${QUIET_MAKE} install PREFIX=<INSTALL_DIR> --) --# Tell cmake that the external project generated a library so we can --# add dependencies here instead of later --set (BZIP2_LIBRARIES ${GAT_SOURCE_DIR}/external/install/lib/libbz2.a) --set (LIBSTADEN_LDFLAGS "-L${GAT_SOURCE_DIR}/external/install/lib -I${GAT_SOURCE_DIR}/external/install/include") --set (LIBSTADEN_CFLAGS "-I${GAT_SOURCE_DIR}/external/install/include") --set (FETCHED_LIBBZ2 TRUE) -+ message (FATAL_ERROR "libbz2 must be installed before configuration & building can proceed") - else() - message("Found libbz2 library: ${BZIP2_LIBRARIES}") - message("===========================================") -@@ -333,61 +288,15 @@ - # Either inform the user of how to obtain Boost, or, if they passed in the FETCH_BOOST - # option, go and grab it for them. - ## --if ((NOT Boost_FOUND) AND (NOT FETCH_BOOST)) -+if (NOT Boost_FOUND) - message(FATAL_ERROR - "Salmon cannot be compiled without Boost.\n" - "It is recommended to visit http://www.boost.org/ and install Boost according to those instructions.\n" - "This build system can also download and install a local version of boost for you (this takes a lot of time).\n" - "To fetch and build boost locally, call cmake with -DFETCH_BOOST=TRUE" - ) --elseif(FETCH_BOOST) -- ## Let the rest of the build process know we're going to be fetching boost -- set (BOOST_LIB_SUBSET --with-iostreams --with-atomic --with-chrono --with-container --with-date_time --with-exception -- --with-filesystem --with-graph --with-graph_parallel --with-math -- --with-program_options --with-system --with-thread -- --with-timer) -- set (BOOST_WILL_RECONFIGURE TRUE) -- set (FETCH_BOOST FALSE) -- message("Build system will fetch and build Boost") -- message("==================================================================") -- ExternalProject_Add(libboost -- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external -- DOWNLOAD_COMMAND curl -k -L http://downloads.sourceforge.net/project/boost/boost/1.66.0/boost_1_66_0.tar.gz -o boost_1_66_0.tar.gz && -- ${SHASUM} bd0df411efd9a585e5a2212275f8762079fed8842264954675a4fddc46cfcf60 boost_1_66_0.tar.gz && -- tar xzf boost_1_66_0.tar.gz -- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/boost_1_66_0 -- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install -- #PATCH_COMMAND patch -p2 < ${CMAKE_CURRENT_SOURCE_DIR}/external/boost156.patch -- CONFIGURE_COMMAND CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} ${CMAKE_CURRENT_SOURCE_DIR}/external/boost_1_66_0/bootstrap.sh ${BOOST_CONFIGURE_TOOLSET} ${BOOST_BUILD_LIBS} --prefix=<INSTALL_DIR> -- BUILD_COMMAND CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} ${CMAKE_CURRENT_SOURCE_DIR}/external/boost_1_66_0/b2 -d0 -j2 ${BOOST_LIB_SUBSET} toolset=${BOOST_TOOLSET} ${BOOST_EXTRA_FLAGS} cxxflags=${BOOST_CXX_FLAGS} link=static install -- BUILD_IN_SOURCE 1 -- INSTALL_COMMAND "" -- ) -- -- ## -- # After we've installed boost, -- ## -- SET( RECONFIG_FLAGS ${RECONFIG_FLAGS} -DBOOST_WILL_RECONFIGURE=FALSE -DBOOST_RECONFIGURE=TRUE -DFETCH_BOOST=FALSE) -- ExternalProject_Add_Step(libboost reconfigure -- COMMAND ${CMAKE_COMMAND} ${CMAKE_CURRENT_SOURCE_DIR} ${RECONFIG_FLAGS} -- DEPENDEES install -- ) -- set (FETCHED_BOOST TRUE) - endif() - --## --# If we're fetching boost and we need to have dummy paths for these variables --# so that CMake won't complain --## --if (BOOST_WILL_RECONFIGURE) -- message("Setting Temporary Boost paths") -- set(Boost_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install/include) -- set(Boost_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/include) -- set(Boost_LIBRARY_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/lib) -- set(Boost_FOUND TRUE) --endif() -- -- - message("BOOST INCLUDE DIR = ${Boost_INCLUDE_DIR}") - message("BOOST INCLUDE DIRS = ${Boost_INCLUDE_DIRS}") - message("BOOST LIB DIR = ${Boost_LIBRARY_DIRS}") -@@ -422,9 +331,9 @@ - include(ExternalProject) - ExternalProject_Add(libcereal - DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external -- DOWNLOAD_COMMAND curl -k -L https://github.com/USCiLab/cereal/archive/v1.2.2.tar.gz -o cereal-v1.2.2.tar.gz && -- ${SHASUM} 1921f26d2e1daf9132da3c432e2fd02093ecaedf846e65d7679ddf868c7289c4 cereal-v1.2.2.tar.gz && -- tar -xzvf cereal-v1.2.2.tar.gz -+ DOWNLOAD_COMMAND cp ../../../distdir/cereal-1.2.2.tar.gz . && -+ ${SHASUM} 1921f26d2e1daf9132da3c432e2fd02093ecaedf846e65d7679ddf868c7289c4 cereal-1.2.2.tar.gz && -+ tar -xzvf cereal-1.2.2.tar.gz - - ## - #URL https://github.com/USCiLab/cereal/archive/v1.2.2.tar.gz -@@ -455,12 +364,12 @@ - ExternalProject_Add(libbwa - DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external - #URL https://github.com/COMBINE-lab/bwa/archive/0.7.12.3.tar.gz -- #DOWNLOAD_NAME bwa-master.tar.gz -- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/bwa/archive/v0.7.12.5.tar.gz -o bwa-master.tar.gz && -- ${SHASUM} 1ac5661d9e12e9017a47f0264201a75d9128f28dbd9a26952925f7745ddf6036 bwa-master.tar.gz && -- mkdir -p bwa-master && -- tar -xzvf bwa-master.tar.gz --strip-components=1 -C bwa-master -- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/bwa-master -+ #DOWNLOAD_NAME bwa-0.7.12.5.tar.gz -+ DOWNLOAD_COMMAND cp ../../../distdir/bwa-0.7.12.5.tar.gz . && -+ ${SHASUM} 1ac5661d9e12e9017a47f0264201a75d9128f28dbd9a26952925f7745ddf6036 bwa-0.7.12.5.tar.gz && -+ mkdir -p bwa-0.7.12.5 && -+ tar -xzvf bwa-0.7.12.5.tar.gz --strip-components=1 -C bwa-0.7.12.5 -+ SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/bwa-0.7.12.5 - INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install - CONFIGURE_COMMAND "" - BUILD_COMMAND sh -c "make ${QUIET_MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}" -@@ -562,9 +471,9 @@ - message("==================================================================") - ExternalProject_Add(libgff - DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external -- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz -o libgff.tgz && -- ${SHASUM} 34597ecd3718e6d6e7a1dd4350220664be2c1cd992070d1218564a20d7aa5697 libgff.tgz && -- tar -xzvf libgff.tgz -+ DOWNLOAD_COMMAND cp ../../../distdir/libgff-1.1.tgz . && -+ ${SHASUM} 34597ecd3718e6d6e7a1dd4350220664be2c1cd992070d1218564a20d7aa5697 libgff-1.1.tgz && -+ tar -xzvf libgff-1.1.tgz - ## - #URL https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz - #DOWNLOAD_NAME libff.tgz -@@ -600,10 +509,10 @@ - message("==================================================================") - ExternalProject_Add(libstadenio - DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external -- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/staden-io_lib/archive/v1.14.8.1.tar.gz -o staden-io_lib-v1.14.8.tar.gz && -- ${SHASUM} f6f30eefa478cfb708f3109a35fb6ffa0e24951d9d971985df2cef5919dd0bc3 staden-io_lib-v1.14.8.tar.gz && -+ DOWNLOAD_COMMAND cp ../../../distdir/staden-io_lib-1.14.8.tar.gz . && -+ ${SHASUM} f6f30eefa478cfb708f3109a35fb6ffa0e24951d9d971985df2cef5919dd0bc3 staden-io_lib-1.14.8.tar.gz && - mkdir -p staden-io_lib-1.14.8 && -- tar -xzf staden-io_lib-v1.14.8.tar.gz --strip-components=1 -C staden-io_lib-1.14.8 && -+ tar -xzf staden-io_lib-1.14.8.tar.gz --strip-components=1 -C staden-io_lib-1.14.8 && - rm -fr staden-io_lib && - mv -f staden-io_lib-1.14.8 staden-io_lib - SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/staden-io_lib -@@ -620,9 +529,9 @@ - message("==================================================================") - ExternalProject_Add(libspdlog - DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external -- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/spdlog/archive/v0.16.1.tar.gz -o spdlog-v0.16.1.tar.gz && -- ${SHASUM} 733260e1fbdcf1b3dc307fc585e4476240026de8be28eb905731d2ab0942deae spdlog-v0.16.1.tar.gz && -- tar -xzf spdlog-v0.16.1.tar.gz -+ DOWNLOAD_COMMAND cp ../../../distdir/spdlog-0.16.1.tar.gz . && -+ ${SHASUM} 733260e1fbdcf1b3dc307fc585e4476240026de8be28eb905731d2ab0942deae spdlog-0.16.1.tar.gz && -+ tar -xzf spdlog-0.16.1.tar.gz - ## - #URL https://github.com/COMBINE-lab/spdlog/archive/v0.12.0.tar.gz - #DOWNLOAD_NAME spdlog-v0.12.0.tar.gz diff --git a/sci-biology/salmon/files/salmon-1.6.0-find-boost.patch b/sci-biology/salmon/files/salmon-1.6.0-find-boost.patch deleted file mode 100644 index 76ef25547..000000000 --- a/sci-biology/salmon/files/salmon-1.6.0-find-boost.patch +++ /dev/null @@ -1,116 +0,0 @@ -diff --git a/CMakeLists.txt b/CMakeLists.txt -index 1be02ab..48ffda2 100644 ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -428,9 +428,9 @@ endif() - ## - # Set the latest version and look for what we need - ## --set(Boost_ADDITIONAL_VERSIONS "1.59.0" "1.60.0" "1.61.0" "1.62.0" "1.63.0" "1.64.0" "1.65.0" "1.66.0" "1.67.0" "1.68.0" "1.69.0" "1.70.0" "1.71.0") -+set(Boost_ADDITIONAL_VERSIONS "1.59.0" "1.60.0" "1.61.0" "1.62.0" "1.63.0" "1.64.0" "1.65.0" "1.66.0" "1.67.0" "1.68.0" "1.69.0" "1.70.0" "1.71.0" "1.77.0" "1.78.0") - if (NOT BOOST_RECONFIGURE) --find_package(Boost 1.59.0 COMPONENTS iostreams filesystem system timer chrono program_options) -+find_package(Boost 1.59.0 COMPONENTS ALL) - message("BOOST_INCLUDEDIR = ${BOOST_INCLUDEDIR}") - message("BOOST_LIBRARYDIR = ${BOOST_LIBRARYDIR}") - message("Boost_FOUND = ${Boost_FOUND}") -@@ -610,7 +610,7 @@ if (NOT CEREAL_FOUND) - endif() - - ## Try and find TBB first --find_package(TBB 2019.0 COMPONENTS tbb tbbmalloc tbbmalloc_proxy) -+find_package(TBB) - - ## NOTE: we actually require at least 2019 U4 or greater - ## since we are using tbb::global_control. However, they -@@ -618,12 +618,8 @@ find_package(TBB 2019.0 COMPONENTS tbb tbbmalloc tbbmalloc_proxy) - ## source. Check before release if we can bump to the 2020 - ## version (requires having tbb 2020 for OSX). - if (${TBB_FOUND}) -- if (${TBB_VERSION} VERSION_GREATER_EQUAL 2019.0) - message("FOUND SUITABLE TBB VERSION : ${TBB_VERSION}") - set(TBB_TARGET_EXISTED TRUE) -- else() -- set(TBB_TARGET_EXISTED FALSE) -- endif() - else() - set(TBB_TARGET_EXISTED FALSE) - endif() -@@ -750,10 +746,6 @@ if(NOT libgff_FOUND) - message("Build system will compile libgff") - message("==================================================================") - externalproject_add(libgff -- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external -- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/libgff/archive/v2.0.0.tar.gz -o libgff.tgz && -- ${SHASUM} 7656b19459a7ca7d2fd0fcec4f2e0fd0deec1b4f39c703a114e8f4c22d82a99c libgff.tgz && -- tar -xzvf libgff.tgz - ## - #URL https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz - #DOWNLOAD_NAME libff.tgz -diff --git a/cmake/Modules/FindTBB.cmake b/cmake/Modules/FindTBB.cmake -index c8b3eb5..b4c23da 100644 ---- a/cmake/Modules/FindTBB.cmake -+++ b/cmake/Modules/FindTBB.cmake -@@ -184,7 +184,6 @@ if(NOT TBB_FOUND) - ################################## - - if(TBB_INCLUDE_DIRS) -- file(READ "${TBB_INCLUDE_DIRS}/tbb/tbb_stddef.h" _tbb_version_file) - string(REGEX REPLACE ".*#define TBB_VERSION_MAJOR ([0-9]+).*" "\\1" - TBB_VERSION_MAJOR "${_tbb_version_file}") - string(REGEX REPLACE ".*#define TBB_VERSION_MINOR ([0-9]+).*" "\\1" -diff --git a/scripts/fetchPufferfish.sh b/scripts/fetchPufferfish.sh -index d32e131..1b5cbf2 100755 ---- a/scripts/fetchPufferfish.sh -+++ b/scripts/fetchPufferfish.sh -@@ -10,18 +10,6 @@ CURR_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd ) - EXTERNAL_DIR=${CURR_DIR}/../external - INSTALL_DIR=${CURR_DIR}/../external/install - --if [ -d ${EXTERNAL_DIR}/pufferfish ] ; then -- rm -fr ${EXTERNAL_DIR}/pufferfish --fi -- --if [ -d ${INSTALL_DIR}/include/pufferfish ] ; then -- rm -fr ${INSTALL_DIR}/include/pufferfish --fi -- --if [ -d ${INSTALL_DIR}/src/pufferfish ] ; then -- rm -fr ${INSTALL_DIR}/src/pufferfish --fi -- - SVER=salmon-v1.6.0 - #SVER=develop - #SVER=sketch-mode -@@ -29,31 +17,6 @@ SVER=salmon-v1.6.0 - EXPECTED_SHA256=f71b3c08f254200fcdc2eb8fe3dcca8a8e9489e79ef5952a4958d8b9979831dc - - mkdir -p ${EXTERNAL_DIR} --curl -k -L https://github.com/COMBINE-lab/pufferfish/archive/${SVER}.zip -o ${EXTERNAL_DIR}/pufferfish.zip -- --hashcheck="" --if exists sha256sum; then -- hashcheck="sha256sum" --elif exists shasum; then -- hashcheck="shasum -a256" --else -- unset hashcheck --fi -- --if [ -z "${hashcheck-}" ]; then -- echo "Couldn't find shasum command; can't verify contents of downloaded pufferfish"; --else -- if [[ $SVER != develop ]]; then -- echo "${EXPECTED_SHA256} ${EXTERNAL_DIR}/pufferfish.zip" | ${hashcheck} -c - || { echo "pufferfish.zip did not match expected SHA1! Exiting."; exit 1; } -- else -- echo "not testing sha since pulling from develop" -- fi --fi -- -- --rm -fr ${EXTERNAL_DIR}/pufferfish --unzip ${EXTERNAL_DIR}/pufferfish.zip -d ${EXTERNAL_DIR} --mv ${EXTERNAL_DIR}/pufferfish-${SVER} ${EXTERNAL_DIR}/pufferfish - - mkdir -p ${INSTALL_DIR}/include/pufferfish - diff --git a/sci-biology/salmon/metadata.xml b/sci-biology/salmon/metadata.xml deleted file mode 100644 index 1907254d6..000000000 --- a/sci-biology/salmon/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biol...@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <maintainer type="person"> - <email>mschu....@gmail.com</email> - <name>Michael Schubert</name> - </maintainer> - <upstream> - <remote-id type="github">COMBINE-lab/salmon</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/salmon/salmon-0.10.2.ebuild b/sci-biology/salmon/salmon-0.10.2.ebuild deleted file mode 100644 index c3ef9e50a..000000000 --- a/sci-biology/salmon/salmon-0.10.2.ebuild +++ /dev/null @@ -1,73 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit cmake - -DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments" -HOMEPAGE="https://github.com/COMBINE-lab/salmon"; -SRC_URI="https://github.com/COMBINE-lab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz - https://github.com/COMBINE-lab/RapMap/archive/salmon-v0.10.2.zip -> ${P}_RapMap.zip - https://github.com/USCiLab/cereal/archive/v1.2.2.tar.gz -> cereal-1.2.2.tar.gz - https://github.com/COMBINE-lab/bwa/archive/v0.7.12.5.tar.gz -> bwa-0.7.12.5.tar.gz - https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz -> libgff-1.1.tgz - https://github.com/COMBINE-lab/staden-io_lib/archive/v1.14.8.1.tar.gz -> staden-io_lib-1.14.8.tar.gz - https://github.com/COMBINE-lab/spdlog/archive/v0.16.1.tar.gz -> spdlog-0.16.1.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -PATCHES=( "${FILESDIR}"/${P}-no-boost-static.patch - "${FILESDIR}"/salmon-0.10.2_remove_curl_call.patch - "${FILESDIR}"/salmon-0.10.2_remove_curl_calls.patch - "${FILESDIR}"/salmon-0.10.2_fix_lib_dir.patch - "${FILESDIR}"/salmon-0.10.2_fix_tests.patch - "${FILESDIR}"/salmon-0.10.2_TestSalmonQuasi.cmake.patch ) - -RDEPEND="${DEPEND}" -# budled copies of: -# sci-biology/bwa-0.7.12.5 -# sci-biology/jellyfish -# sci-biology/staden-1.14.8.1 -# sci-biology/gfftools -# -# libgff-1.1 from https://github.com/Kingsford-Group/libgff -# actually unreleased version from https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz -# https://github.com/Kingsford-Group/libgff/issues/1 -# -# dev-libs/spdlog-0.16.1 -# cereal-1.2.2 - -# see the many curl executions: -# salmon-0.10.2$ find . -type f | xargs grep curl 2>/dev/null -# -DEPEND=" - sys-libs/zlib - app-arch/bzip2 - app-arch/xz-utils - dev-libs/boost:0= - dev-libs/libdivsufsort - sci-biology/bwa - >=dev-libs/jemalloc-5.0.1 - >=dev-cpp/tbb-2018.20180312 -" -RDEPEND="${DEPEND}" -BDEPEND=" - net-misc/curl - app-arch/unzip -" - -src_prepare() { - # use system libs - sed -i \ - -e "s%\${GAT_SOURCE_DIR}/external/install/lib/libstaden-read.a%/usr/$(get_libdir)/libstaden-read.so%g" \ - -e "s%\${GAT_SOURCE_DIR}/external/install/lib/libdivsufsort.a%/usr/$(get_libdir)/libdivsufsort.so%g" \ - -e "s%\${GAT_SOURCE_DIR}/external/install/lib/libdivsufsort64.a%/usr/$(get_libdir)/libdivsufsort64.so%g" \ - -e "s%\${GAT_SOURCE_DIR}/external/install/lib/libbwa.a%/usr/$(get_libdir)/libbwa.so%g" \ - src/CMakeLists.txt || die - - cmake_src_prepare -} diff --git a/sci-biology/salmon/salmon-1.6.0.ebuild b/sci-biology/salmon/salmon-1.6.0.ebuild deleted file mode 100644 index 6c19ff58f..000000000 --- a/sci-biology/salmon/salmon-1.6.0.ebuild +++ /dev/null @@ -1,70 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -inherit cmake - -DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments" -HOMEPAGE="https://github.com/COMBINE-lab/salmon"; -SRC_URI=" - https://github.com/COMBINE-lab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz - https://github.com/COMBINE-lab/pufferfish/archive/salmon-v${PV}.tar.gz -> pufferfish-${P}.tar.gz - https://github.com/COMBINE-lab/libgff/archive/v2.0.0.tar.gz -> libgff-${P}.tar.gz -" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64" - -RDEPEND=" - dev-libs/boost:= - sys-libs/zlib -" - -DEPEND="${RDEPEND} - app-arch/bzip2 - app-arch/xz-utils - >=dev-libs/jemalloc-5.0.1 - >=dev-cpp/tbb-2018.20180312 - dev-libs/cereal - sci-libs/io_lib[static-libs] -" - -BDEPEND=" - app-arch/unzip - net-misc/curl -" - -PATCHES=( - "${FILESDIR}/${P}-find-boost.patch" -) - -src_unpack() { - default - mkdir -p "${S}/external/install/lib" || die - mv "${WORKDIR}/pufferfish-${PN}-v${PV}" "${S}/external/pufferfish" || die - mv "${WORKDIR}/libgff-2.0.0" "${S}/external/libgff-2.0.0" || die - ln -s "${EPREFIX}/usr/lib64/libtbb.so" "${S}/external/install/lib/libtbb.so" || die - ln -s "${EPREFIX}/usr/lib64/libtbbmalloc.so" "${S}/external/install/lib/libtbbmalloc.so" || die - ln -s "${EPREFIX}/usr/lib64/libtbbmalloc_proxy.so" "${S}/external/install/lib/libtbbmalloc_proxy.so" || die -} - -src_prepare() { - cmake_src_prepare - sed -e 's:tbb/mutex.h:oneapi/tbb/mutex.h:g' \ - -i external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.h \ - -i external/pufferfish/external/twopaco/common/streamfastaparser.h || die -} - -src_configure() { - local mycmakeargs=( - -DFETCH_BOOST=FALSE - -DBOOST_INCLUDEDIR="${EPREFIX}/usr/include/boost" - -DBOOST_LIBRARYDIR="${EPREFIX}/usr/lib64" - -DBoost_ALL_FOUND=TRUE - -Dboost_headers_FOUND=TRUE - -DBoost_FOUND=TRUE - ) - cmake_src_configure -} diff --git a/sci-biology/staden/files/staden-2.0.0_beta11-ldflags.patch b/sci-biology/staden/files/staden-2.0.0_beta11-ldflags.patch deleted file mode 100644 index 735feb315..000000000 --- a/sci-biology/staden/files/staden-2.0.0_beta11-ldflags.patch +++ /dev/null @@ -1,30 +0,0 @@ - abi/Makefile | 2 +- - alf/Makefile | 2 +- - 2 files changed, 2 insertions(+), 2 deletions(-) - -diff --git a/abi/Makefile b/abi/Makefile -index 3c1f8fb..58b4353 100644 ---- a/abi/Makefile -+++ b/abi/Makefile -@@ -23,7 +23,7 @@ getABISampleName: $(OBJSSN) - $(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSSN) $(LIBS) $(LIBSC) - - getABIdate: $(OBJSD) -- $(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSD) $(IOUTILS_LIB) $(MISC_LIB) $(LIBSC) -+ $(CLD) $(LDFLAGS) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSD) $(IOUTILS_LIB) $(MISC_LIB) $(LIBSC) - - getABIcomment: $(OBJSC) - $(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSC) $(LIBS) $(LIBSC) -diff --git a/alf/Makefile b/alf/Makefile -index 94b7480..ef41a26 100644 ---- a/alf/Makefile -+++ b/alf/Makefile -@@ -16,7 +16,7 @@ INCLUDES_E += $(MISC_INC) - ALFOBJ = alfsplit.o - - alfsplit: $(ALFOBJ) -- $(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(ALFOBJ) $(LIBSC) -+ $(CLD) $(LDFLAGS) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(ALFOBJ) $(LIBSC) - - RSOBJ = $(ALFBIN)/2rs.o - diff --git a/sci-biology/staden/metadata.xml b/sci-biology/staden/metadata.xml deleted file mode 100644 index 1ed1820a4..000000000 --- a/sci-biology/staden/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="person"> - <email>mmokr...@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biol...@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">staden</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/staden/staden-2.0.0_beta11.ebuild b/sci-biology/staden/staden-2.0.0_beta11.ebuild deleted file mode 100644 index a0f91720b..000000000 --- a/sci-biology/staden/staden-2.0.0_beta11.ebuild +++ /dev/null @@ -1,76 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit flag-o-matic fortran-2 - -DESCRIPTION="DNA sequence assembly (gap4, gap5), editing and analysis tools (Spin)" -HOMEPAGE="https://sourceforge.net/projects/staden"; -SRC_URI="https://downloads.sourceforge.net/staden/staden-${PV/_beta/b}-2016-src.tar.gz -> ${P}-src.tar.gz" - -LICENSE="staden" -SLOT="0" -KEYWORDS="~amd64" -IUSE="debug doc fortran png tcl tk X zlib" - -# either g77 or gfortran must be available -# edit src/mk/linux.mk accordingly -# -# this is a glibc-2.9 issue, see https://sourceforge.net/tracker/index.php?func=detail&aid=2629155&group_id=100316&atid=627058 -# -# -# - -DEPEND=" - app-arch/xz-utils - dev-lang/tk:0= - dev-tcltk/tklib - media-libs/libpng:0 - sci-biology/samtools:0 - >=sci-libs/io_lib-1.13.8 - sys-libs/zlib" -RDEPEND="${DEPEND} - >=dev-tcltk/iwidgets-4.0 - tcl? ( >=dev-tcltk/itcl-3.2 ) - tk? ( >=dev-tcltk/itk-3.2 ) - net-misc/curl - doc? ( sci-biology/staden_doc )" - -S="${WORKDIR}"/staden-${PV/_beta/b}-2016-src - -PATCHES=( - "${FILESDIR}/${P}-ldflags.patch" -) - -src_prepare() { - default - sed \ - -e 's:svnversion:false:' \ - -i configure.in || die -} - -src_configure(){ - use debug && append-cflags "-DCACHE_REF_DEBUG" - econf \ - $(use_enable X x) \ - $(use_enable amd64 64bit) \ - --with-tklib="/usr/$(get_libdir)/tklib" -} - -src_install() { - default - # install the LDPATH so that it appears in /etc/ld.so.conf after env-update - # subsequently, apps linked against /usr/lib/staden can be run because - # loader can find the library (I failed to use '-Wl,-rpath,/usr/lib/staden' - # somehow for gap2caf, for example - cat >> "${T}"/99staden <<- EOF - STADENROOT="${EPREFIX}"/usr/share/staden - LDPATH="${EPREFIX}/usr/$(get_libdir)/staden" - EOF - doenvd "${T}"/99staden -} - -pkg_postinst(){ - einfo "There is a tutorial at https://sourceforge.net/projects/staden/files/tutorials/1.1/course-1.1.tar.gz"; -} diff --git a/sci-biology/staden_doc/metadata.xml b/sci-biology/staden_doc/metadata.xml deleted file mode 100644 index 1ed1820a4..000000000 --- a/sci-biology/staden_doc/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="person"> - <email>mmokr...@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biol...@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">staden</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/staden_doc/staden_doc-2.0.0_beta11.ebuild b/sci-biology/staden_doc/staden_doc-2.0.0_beta11.ebuild deleted file mode 100644 index 5a70701b0..000000000 --- a/sci-biology/staden_doc/staden_doc-2.0.0_beta11.ebuild +++ /dev/null @@ -1,42 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="Documentation files for the staden package" -HOMEPAGE="https://sourceforge.net/projects/staden"; -SRC_URI="https://sourceforge.net/projects/staden/files/staden/${PV/_beta/b}/staden_doc-${PV/_beta/b}-src.tar.gz"; - -LICENSE="staden" -SLOT="0" -KEYWORDS="~amd64" - -DEPEND=" - dev-lang/perl - app-text/texlive - app-text/texi2html" -BDEPEND="app-editors/emacs" -RDEPEND="${DEPEND} ${BDEPEND}" - -S="${WORKDIR}"/staden_doc-${PV/_beta/b}-src - -# do not use texi2html-5 because it fails with: -# texi2html -menu -verbose -split_chapter -index_chars interface.htmlinfo -# Unknown option: index_char -# src_prepare(){ -# default -# # avoid running bundled texi2html code -# sed -e "s#./tools/texi2html#texi2html#" -i manual/Makefile || die -# } - -src_compile(){ - cd manual || die - emake -j1 spotless || die - cd .. || die - emake -j1 unix PAPER=A4 -} - -src_install(){ - emake -j1 install prefix="${D}"/usr - dodoc gkb547_gml.pdf -}
