diff options
Diffstat (limited to 'gn')
23 files changed, 6 insertions, 1509 deletions
diff --git a/gn/packages/mail.scm b/gn/packages/mail.scm index 1e3b888..dc2f2a3 100644 --- a/gn/packages/mail.scm +++ b/gn/packages/mail.scm @@ -3,6 +3,7 @@ #:use-module (guix gexp) #:use-module (guix packages) #:use-module (guix utils) + #:use-module (gnu packages) #:use-module (gnu packages mail)) (define-public opensmtpd-patched @@ -12,8 +13,7 @@ (source (origin (inherit (package-source opensmtpd)) - (patches - (list (local-file "patches/opensmtpd-gn-fixes.patch"))))) + (patches (search-patches "opensmtpd-gn-fixes.patch")))) (synopsis "Lightweight SMTP daemon (with GN patches)") (description "OpenSMTPD with patches for missing grp.h include, TLS option diff --git a/gn/packages/pangenome-rust.scm b/gn/packages/pangenome-rust.scm index 9f5ba8e..78bd6d3 100644 --- a/gn/packages/pangenome-rust.scm +++ b/gn/packages/pangenome-rust.scm @@ -1548,7 +1548,7 @@ (file-name (git-file-name "rust-spoa-rs" "0.1.0.6f4f102")) (sha256 (base32 "13hmxqk70c0728v8l44qap25qla4w86im3kwfmay7jwwg9lk7lfg")) (patches - (list (local-file "patches/do-not-build-cplusplus-spoa.patch"))))) + (search-patches "do-not-build-cplusplus-spoa.patch")))) (define rust-stable-deref-trait-1.2.1 (crate-source "stable_deref_trait" "1.2.1" diff --git a/gn/packages/pangenome.scm b/gn/packages/pangenome.scm index 87a1c07..b82845e 100644 --- a/gn/packages/pangenome.scm +++ b/gn/packages/pangenome.scm @@ -14,6 +14,7 @@ #:use-module (guix build-system gnu) #:use-module (guix build-system go) #:use-module (guix build-system trivial) + #:use-module (gnu packages) #:use-module (gnu packages base) #:use-module (gnu packages bioinformatics) #:use-module (gnu packages boost) @@ -543,8 +544,8 @@ graph model, as well as algorithms for pangenome analysis.") (sha256 (base32 "18wsrvqf0nsfk29v3ggdq2r4q15d4n4sq8v228qq1jsybbjlkgsa")) (patches - (list (local-file "patches/seqwish-paryfor-riscv.patch") - (local-file "patches/seqwish-shared-library.patch"))) + (search-patches "seqwish-paryfor-riscv.patch" + "seqwish-shared-library.patch")) (snippet #~(begin (use-modules (guix build utils)) diff --git a/gn/packages/patches/arrayfire-lapack-detection.patch b/gn/packages/patches/arrayfire-lapack-detection.patch deleted file mode 100644 index 1925122..0000000 --- a/gn/packages/patches/arrayfire-lapack-detection.patch +++ /dev/null @@ -1,277 +0,0 @@ -https://sources.debian.org/data/main/a/arrayfire/3.3.2+dfsg1-4/debian/patches/Fix-LAPACKE-detection.patch - -From: Ghislain Antony Vaillant <ghisvail@gmail.com> -Date: Wed, 2 Mar 2016 10:46:50 +0000 -Subject: Fix LAPACKE detection. - ---- - CMakeModules/FindLAPACKE.cmake | 54 +++++++++++++++------------------------ - src/backend/cpu/CMakeLists.txt | 18 ++++++------- - src/backend/cuda/CMakeLists.txt | 11 ++++---- - src/backend/opencl/CMakeLists.txt | 19 +++++++------- - 4 files changed, 45 insertions(+), 57 deletions(-) - -diff --git a/CMakeModules/FindLAPACKE.cmake b/CMakeModules/FindLAPACKE.cmake -index 9251ee9..1a73632 100644 ---- a/CMakeModules/FindLAPACKE.cmake -+++ b/CMakeModules/FindLAPACKE.cmake -@@ -4,13 +4,13 @@ - # FIND_PACKAGE(LAPACKE [REQUIRED] [QUIET] ) - # - # It sets the following variables: --# LAPACK_FOUND ... true if LAPACKE is found on the system --# LAPACK_LIBRARIES ... full path to LAPACKE library --# LAPACK_INCLUDES ... LAPACKE include directory --# -+# LAPACKE_FOUND ... true if LAPACKE is found on the system -+# LAPACKE_INCLUDE_DIRS ... LAPACKE include directories -+# LAPACKE_LIBRARIES ... path to LAPACKE libraries -+# LAPACKE_LIBRARY_DIRS ... LAPACKE library directories - - SET(LAPACKE_ROOT_DIR CACHE STRING -- "Root directory for custom LAPACK implementation") -+ "Root directory for custom LAPACKE implementation") - - IF (NOT INTEL_MKL_ROOT_DIR) - SET(INTEL_MKL_ROOT_DIR $ENV{INTEL_MKL_ROOT}) -@@ -40,29 +40,20 @@ IF(PKG_CONFIG_FOUND AND NOT LAPACKE_ROOT_DIR) - ENDIF() - - IF(PC_LAPACKE_FOUND) -+ -+ # Verify sanity of LAPACKE pkg-config file. - FOREACH(PC_LIB ${PC_LAPACKE_LIBRARIES}) - FIND_LIBRARY(${PC_LIB}_LIBRARY NAMES ${PC_LIB} HINTS ${PC_LAPACKE_LIBRARY_DIRS} ) - IF (NOT ${PC_LIB}_LIBRARY) - MESSAGE(FATAL_ERROR "Something is wrong in your pkg-config file - lib ${PC_LIB} not found in ${PC_LAPACKE_LIBRARY_DIRS}") - ENDIF (NOT ${PC_LIB}_LIBRARY) -- LIST(APPEND LAPACKE_LIB ${${PC_LIB}_LIBRARY}) - ENDFOREACH(PC_LIB) - -- FIND_PATH( -- LAPACKE_INCLUDES -- NAMES "lapacke.h" -- PATHS -- ${PC_LAPACKE_INCLUDE_DIRS} -- ${INCLUDE_INSTALL_DIR} -- /usr/include -- /usr/local/include -- /sw/include -- /opt/local/include -- DOC "LAPACKE Include Directory" -- ) -+ set(LAPACKE_LIBRARIES ${PC_LAPACKE_LIBRARIES}) -+ set(LAPACKE_LIBRARY_DIRS ${PC_LAPACKE_LIBRARY_DIRS}) - -- FIND_PACKAGE_HANDLE_STANDARD_ARGS(LAPACKE DEFAULT_MSG LAPACKE_LIB) -- MARK_AS_ADVANCED(LAPACKE_INCLUDES LAPACKE_LIB) -+ FIND_PATH(LAPACKE_INCLUDE_DIRS NAMES "lapacke.h" -+ PATHS ${PC_LAPACKE_INCLUDE_DIRS}) - - ELSE(PC_LAPACKE_FOUND) - -@@ -97,7 +88,6 @@ ELSE(PC_LAPACKE_FOUND) - LAPACKE_LIB - NAMES "lapacke" "liblapacke" "openblas" "mkl_rt" - PATHS -- ${PC_LAPACKE_LIBRARY_DIRS} - ${LIB_INSTALL_DIR} - /opt/intel/mkl/lib/ia32 - /opt/intel/mkl/lib/intel64 -@@ -113,7 +103,6 @@ ELSE(PC_LAPACKE_FOUND) - LAPACK_LIB - NAMES "lapack" "liblapack" "openblas" "mkl_rt" - PATHS -- ${PC_LAPACKE_LIBRARY_DIRS} - ${LIB_INSTALL_DIR} - /opt/intel/mkl/lib/ia32 - /opt/intel/mkl/lib/intel64 -@@ -129,7 +118,6 @@ ELSE(PC_LAPACKE_FOUND) - LAPACKE_INCLUDES - NAMES "lapacke.h" "mkl_lapacke.h" - PATHS -- ${PC_LAPACKE_INCLUDE_DIRS} - ${INCLUDE_INSTALL_DIR} - /opt/intel/mkl/include - /usr/include -@@ -141,17 +129,15 @@ ELSE(PC_LAPACKE_FOUND) - lapacke - ) - ENDIF(LAPACKE_ROOT_DIR) -+ SET(LAPACKE_INCLUDE_DIRS ${LAPACKE_INCLUDES}) -+ SET(LAPACKE_LIBRARIES ${LAPACKE_LIB} ${LAPACK_LIB}) -+ MARK_AS_ADVANCED(LAPACKE_INCLUDES LAPACKE_LIB LAPACK_LIB) - ENDIF(PC_LAPACKE_FOUND) - --IF(LAPACKE_LIB AND LAPACK_LIB) -- SET(LAPACK_LIBRARIES ${LAPACKE_LIB} ${LAPACK_LIB}) --ENDIF() --IF(LAPACKE_INCLUDES) -- SET(LAPACK_INCLUDE_DIR ${LAPACKE_INCLUDES}) --ENDIF() -- - INCLUDE(FindPackageHandleStandardArgs) --FIND_PACKAGE_HANDLE_STANDARD_ARGS(LAPACK DEFAULT_MSG -- LAPACK_INCLUDE_DIR LAPACK_LIBRARIES) -- --MARK_AS_ADVANCED(LAPACK_INCLUDES LAPACK_LIBRARIES) -+FIND_PACKAGE_HANDLE_STANDARD_ARGS(LAPACKE DEFAULT_MSG -+ LAPACKE_LIBRARIES -+ LAPACKE_INCLUDE_DIRS) -+MARK_AS_ADVANCED(LAPACKE_LIBRARIES -+ LAPACKE_INCLUDE_DIRS -+ LAPACKE_LIBRARY_DIRS) -diff --git a/src/backend/cpu/CMakeLists.txt b/src/backend/cpu/CMakeLists.txt -index ea57269..efe50a0 100644 ---- a/src/backend/cpu/CMakeLists.txt -+++ b/src/backend/cpu/CMakeLists.txt -@@ -55,7 +55,7 @@ MESSAGE(STATUS "FFTW Library: ${FFTW_LIBRARIES}") - - IF(APPLE) - FIND_PACKAGE(LAPACKE QUIET) # For finding MKL -- IF(NOT LAPACK_FOUND) -+ IF(NOT LAPACKE_FOUND) - # UNSET THE VARIABLES FROM LAPACKE - UNSET(LAPACKE_LIB CACHE) - UNSET(LAPACK_LIB CACHE) -@@ -67,11 +67,10 @@ ELSE(APPLE) # Linux and Windows - FIND_PACKAGE(LAPACKE) - ENDIF(APPLE) - --IF(NOT LAPACK_FOUND) -- MESSAGE(WARNING "LAPACK not found. Functionality will be disabled") --ELSE(NOT LAPACK_FOUND) -+IF(NOT LAPACKE_FOUND) -+ MESSAGE(WARNING "LAPACKE not found. Functionality will be disabled") -+ELSE(NOT LAPACKE_FOUND) - ADD_DEFINITIONS(-DWITH_CPU_LINEAR_ALGEBRA) -- MESSAGE(STATUS "LAPACK libraries found: ${LAPACK_LIBRARIES}") - ENDIF() - - IF(NOT UNIX) -@@ -99,8 +98,9 @@ INCLUDE_DIRECTORIES( - ${CBLAS_INCLUDE_DIR} - ) - --IF(LAPACK_FOUND) -- INCLUDE_DIRECTORIES(${LAPACK_INCLUDE_DIR}) -+IF(LAPACKE_FOUND) -+ INCLUDE_DIRECTORIES(${LAPACKE_INCLUDE_DIRS}) -+ LINK_DIRECTORIES(${LAPACKE_LIBRARY_DIRS}) - ENDIF() - - FILE(GLOB cpu_headers -@@ -213,8 +213,8 @@ IF(FORGE_FOUND AND NOT USE_SYSTEM_FORGE) - ADD_DEPENDENCIES(afcpu forge) - ENDIF() - --IF(LAPACK_FOUND) -- TARGET_LINK_LIBRARIES(afcpu PRIVATE ${LAPACK_LIBRARIES}) -+IF(LAPACKE_FOUND) -+ TARGET_LINK_LIBRARIES(afcpu PRIVATE ${LAPACKE_LIBRARIES}) - ENDIF() - - IF(FORGE_FOUND) -diff --git a/src/backend/cuda/CMakeLists.txt b/src/backend/cuda/CMakeLists.txt -index 4efb427..24c6544 100644 ---- a/src/backend/cuda/CMakeLists.txt -+++ b/src/backend/cuda/CMakeLists.txt -@@ -105,7 +105,7 @@ ELSE(CUDA_cusolver_LIBRARY) - ## Try to use CPU side lapack - IF(APPLE) - FIND_PACKAGE(LAPACKE QUIET) # For finding MKL -- IF(NOT LAPACK_FOUND) -+ IF(NOT LAPACKE_FOUND) - # UNSET THE VARIABLES FROM LAPACKE - UNSET(LAPACKE_LIB CACHE) - UNSET(LAPACK_LIB CACHE) -@@ -117,9 +117,9 @@ ELSE(CUDA_cusolver_LIBRARY) - FIND_PACKAGE(LAPACKE) - ENDIF(APPLE) - -- IF(NOT LAPACK_FOUND) -+ IF(NOT LAPACKE_FOUND) - MESSAGE(STATUS "CUDA Version ${CUDA_VERSION_STRING} does not contain cusolver library. Linear Algebra will not be available.") -- ELSE(NOT LAPACK_FOUND) -+ ELSE(NOT LAPACKE_FOUND) - MESSAGE(STATUS "CUDA Version ${CUDA_VERSION_STRING} does not contain cusolver library. But CPU LAPACK libraries are available. Will fallback to using host side code.") - ADD_DEFINITIONS(-DWITH_CPU_LINEAR_ALGEBRA) - IF(USE_CUDA_MKL) # Manual MKL Setup -@@ -148,7 +148,8 @@ INCLUDE_DIRECTORIES( - ) - - IF(CUDA_LAPACK_CPU_FALLBACK) -- INCLUDE_DIRECTORIES(${LAPACK_INCLUDE_DIR}) -+ INCLUDE_DIRECTORIES(${LAPACKE_INCLUDE_DIRS}) -+ LINK_DIRECTORIES(${LAPACKE_LIBRARY_DIRS}) - ENDIF() - - FILE(GLOB cuda_headers -@@ -379,7 +380,7 @@ ENDIF() - IF(CUDA_cusolver_LIBRARY) - TARGET_LINK_LIBRARIES(afcuda PRIVATE ${CUDA_cusolver_LIBRARY}) - ELSEIF(CUDA_LAPACK_CPU_FALLBACK) -- TARGET_LINK_LIBRARIES(afcuda PRIVATE ${LAPACK_LIBRARIES}) -+ TARGET_LINK_LIBRARIES(afcuda PRIVATE ${LAPACKE_LIBRARIES}) - ENDIF() - - SET_TARGET_PROPERTIES(afcuda PROPERTIES -diff --git a/src/backend/opencl/CMakeLists.txt b/src/backend/opencl/CMakeLists.txt -index 71247ce..ded53bf 100644 ---- a/src/backend/opencl/CMakeLists.txt -+++ b/src/backend/opencl/CMakeLists.txt -@@ -12,7 +12,7 @@ ENDIF() - - IF(APPLE) - FIND_PACKAGE(LAPACKE QUIET) # For finding MKL -- IF(NOT LAPACK_FOUND) -+ IF(NOT LAPACKE_FOUND) - # UNSET THE VARIABLES FROM LAPACKE - UNSET(LAPACKE_LIB CACHE) - UNSET(LAPACK_LIB CACHE) -@@ -24,9 +24,9 @@ ELSE(APPLE) # Linux and Windows - FIND_PACKAGE(LAPACKE) - ENDIF(APPLE) - --IF(NOT LAPACK_FOUND) -- MESSAGE(WARNING "LAPACK not found. Functionality will be disabled") --ELSE(NOT LAPACK_FOUND) -+IF(NOT LAPACKE_FOUND) -+ MESSAGE(WARNING "LAPACKE not found. Functionality will be disabled") -+ELSE(NOT LAPACKE_FOUND) - ADD_DEFINITIONS(-DWITH_OPENCL_LINEAR_ALGEBRA) - - IF(NOT USE_OPENCL_MKL) -@@ -105,8 +105,9 @@ INCLUDE_DIRECTORIES( - ${BoostCompute_INCLUDE_DIRS} - ${CBLAS_INCLUDE_DIR} - ) --IF(LAPACK_FOUND) -- INCLUDE_DIRECTORIES(${LAPACK_INCLUDE_DIR}) -+IF(LAPACKE_FOUND) -+ INCLUDE_DIRECTORIES(${LAPACKE_INCLUDE_DIRS}) -+ LINK_DIRECTORIES(${LAPACKE_LIBRARY_DIRS}) - ENDIF() - - FILE(GLOB opencl_headers -@@ -163,7 +164,7 @@ source_group(backend\\opencl\\kernel\\convolve\\Sources FILES ${conv_ker_sources - source_group(backend\\opencl\\cpu\\Headers FILES ${cpu_headers}) - source_group(backend\\opencl\\cpu\\Sources FILES ${cpu_sources}) - --IF(LAPACK_FOUND) -+IF(LAPACKE_FOUND) - FILE(GLOB magma_sources - "magma/*.cpp") - -@@ -313,9 +314,9 @@ IF(FORGE_FOUND AND NOT USE_SYSTEM_FORGE) - ADD_DEPENDENCIES(afopencl forge) - ENDIF() - --IF(LAPACK_FOUND) -+IF(LAPACKE_FOUND) - TARGET_LINK_LIBRARIES(afopencl -- PRIVATE ${LAPACK_LIBRARIES} -+ PRIVATE ${LAPACKE_LIBRARIES} - PRIVATE ${CBLAS_LIBRARIES}) - ENDIF() - diff --git a/gn/packages/patches/arrayfire-newer-boost-compute.patch b/gn/packages/patches/arrayfire-newer-boost-compute.patch deleted file mode 100644 index b08c121..0000000 --- a/gn/packages/patches/arrayfire-newer-boost-compute.patch +++ /dev/null @@ -1,33 +0,0 @@ -https://sources.debian.org/data/main/a/arrayfire/3.3.2+dfsg1-4/debian/patches/Use-compute-library-from-Boost-1.61.patch - -From: Ghislain Antony Vaillant <ghisvail@gmail.com> -Date: Fri, 12 Aug 2016 08:35:19 +0100 -Subject: Use compute library from Boost 1.61. - ---- - src/backend/opencl/CMakeLists.txt | 12 +++++++----- - 1 file changed, 7 insertions(+), 5 deletions(-) - -diff --git a/src/backend/opencl/CMakeLists.txt b/src/backend/opencl/CMakeLists.txt -index ded53bf..d7e3628 100644 ---- a/src/backend/opencl/CMakeLists.txt -+++ b/src/backend/opencl/CMakeLists.txt -@@ -84,11 +84,13 @@ ADD_DEFINITIONS( -DBOOST_ALL_NO_LIB ) - SET(Boost_USE_STATIC_LIBS OFF) - FIND_PACKAGE(Boost 1.48 REQUIRED) - --OPTION(USE_SYSTEM_BOOST_COMPUTE "Use system BoostCompute" OFF) --IF(USE_SYSTEM_BOOST_COMPUTE) -- FIND_PACKAGE(BoostCompute REQUIRED) --ELSE() -- INCLUDE("${CMAKE_MODULE_PATH}/build_boost_compute.cmake") -+IF(Boost_VERSION VERSION_LESS "1.61") -+ OPTION(USE_SYSTEM_BOOST_COMPUTE "Use system BoostCompute" OFF) -+ IF(USE_SYSTEM_BOOST_COMPUTE) -+ FIND_PACKAGE(BoostCompute REQUIRED) -+ ELSE() -+ INCLUDE("${CMAKE_MODULE_PATH}/build_boost_compute.cmake") -+ ENDIF() - ENDIF() - - SET( cl_kernel_headers diff --git a/gn/packages/patches/blist-stopiteration.patch b/gn/packages/patches/blist-stopiteration.patch deleted file mode 100644 index 198bef4..0000000 --- a/gn/packages/patches/blist-stopiteration.patch +++ /dev/null @@ -1,36 +0,0 @@ -From: Andrej Shadura <andrew.shadura@collabora.co.uk> -Date: Sun, 8 Jul 2018 09:00:16 +0200 -Subject: Catch StopIteration in a generator and return instead, per PEP 479 - -Signed-off-by: Andrej Shadura <andrew.shadura@collabora.co.uk> - -Forwarded: https://github.com/DanielStutzbach/blist/pull/92 -Bug-Debian: https://bugs.debian.org/902757 ---- - blist/_sortedlist.py | 13 ++++++++----- - 1 file changed, 8 insertions(+), 5 deletions(-) - -diff --git a/blist/_sortedlist.py b/blist/_sortedlist.py -index b34f69e..1f77170 100644 ---- a/blist/_sortedlist.py -+++ b/blist/_sortedlist.py -@@ -420,11 +420,14 @@ class _setmixin(object): - def __iter__(self): - it = super(_setmixin, self).__iter__() - while True: -- item = next(it) -- n = len(self) -- yield item -- if n != len(self): -- raise RuntimeError('Set changed size during iteration') -+ try: -+ item = next(it) -+ n = len(self) -+ yield item -+ if n != len(self): -+ raise RuntimeError('Set changed size during iteration') -+ except StopIteration: -+ return - - def safe_cmp(f): - def g(self, other): diff --git a/gn/packages/patches/delly-use-system-libraries.patch b/gn/packages/patches/delly-use-system-libraries.patch deleted file mode 100644 index 3ce817f..0000000 --- a/gn/packages/patches/delly-use-system-libraries.patch +++ /dev/null @@ -1,65 +0,0 @@ -This patch let's Delly use the system versions of htslib and boost. - -Patch by Roel Janssen <roel@gnu.org> ---- a/Makefile 2016-03-16 13:08:49.936706607 +0100 -+++ b/Makefile 2016-03-16 13:09:12.351706212 +0100 -@@ -9,8 +9,8 @@ - - # Flags - CXX=g++ --CXXFLAGS += -isystem ${SEQTK_ROOT} -isystem ${BOOST_ROOT} -pedantic -W -Wall -Wno-unknown-pragmas --LDFLAGS += -L${SEQTK_ROOT} -L${BOOST_ROOT}/stage/lib -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time -+CXXFLAGS += -pedantic -W -Wall -Wno-unknown-pragmas -+LDFLAGS += -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time - - # Additional flags for release/debug - ifeq (${PARALLEL}, 1) -@@ -23,7 +23,7 @@ - ifeq (${STATIC}, 1) - LDFLAGS += -static -static-libgcc -pthread -lhts -lz - else -- LDFLAGS += -lhts -lz -Wl,-rpath,${SEQTK_ROOT},-rpath,${BOOST_ROOT}/stage/lib -+ LDFLAGS += -lhts -lz - endif - ifeq (${DEBUG}, 1) - CXXFLAGS += -g -O0 -fno-inline -DDEBUG -@@ -41,32 +41,24 @@ - DELLYSOURCES = $(wildcard src/*.h) $(wildcard src/*.cpp) - - # Targets --TARGETS = .htslib .boost src/delly src/extract src/cov src/iover src/stats -+TARGETS = src/delly src/extract src/cov src/iover src/stats - - all: $(TARGETS) - --.htslib: $(HTSLIBSOURCES) -- cd src/htslib && make && make lib-static && cd ../../ && touch .htslib -- --.boost: $(BOOSTSOURCES) -- cd src/modular-boost && ./bootstrap.sh --prefix=${PWD}/src/modular-boost --without-icu --with-libraries=iostreams,filesystem,system,program_options,date_time && ./b2 && ./b2 headers && cd ../../ && touch .boost -- --src/delly: .htslib .boost $(DELLYSOURCES) -+src/delly: $(DELLYSOURCES) - $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS) - --src/extract: .htslib .boost $(DELLYSOURCES) -+src/extract: $(DELLYSOURCES) - $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS) - --src/cov: .htslib .boost $(DELLYSOURCES) -+src/cov: $(DELLYSOURCES) - $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS) - --src/iover: .htslib .boost $(DELLYSOURCES) -+src/iover: $(DELLYSOURCES) - $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS) - --src/stats: .htslib .boost $(DELLYSOURCES) -+src/stats: $(DELLYSOURCES) - $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS) - - clean: -- cd src/htslib && make clean -- cd src/modular-boost && ./b2 --clean-all -- rm -f $(TARGETS) $(TARGETS:=.o) .htslib .boost -+ rm -f $(TARGETS) $(TARGETS:=.o) diff --git a/gn/packages/patches/do-not-build-cplusplus-spoa.patch b/gn/packages/patches/do-not-build-cplusplus-spoa.patch deleted file mode 100644 index b9afb9a..0000000 --- a/gn/packages/patches/do-not-build-cplusplus-spoa.patch +++ /dev/null @@ -1,19 +0,0 @@ -diff --git a/build.rs b/build.rs -index 3f0566a..a607d9d 100644 ---- a/build.rs -+++ b/build.rs -@@ -3,14 +3,6 @@ use std::fs::canonicalize; - use std::path::PathBuf; - - fn main() { -- let out_dir = cmake::Config::new("spoa") -- //.uses_cxx11() // Deprecated -- .define("spoa_install", "OFF") -- .define("spoa_build_exe", "OFF") -- .define("spoa_build_tests", "OFF") -- .build_target("spoa") -- .build(); -- - println!( - "cargo:rustc-link-search=native={}/build/lib", - out_dir.display() diff --git a/gn/packages/patches/gnulib-gets.patch b/gn/packages/patches/gnulib-gets.patch deleted file mode 100644 index cccb55a..0000000 --- a/gn/packages/patches/gnulib-gets.patch +++ /dev/null @@ -1,60 +0,0 @@ -Minimally modified from upstream -only first change set from lib/stdio.in.h taken -s@lib/stdio@libgnu/stdio@g run on the 'diff' line. - -From: Eric Blake <eblake@redhat.com> -Date: Thu, 29 Mar 2012 19:30:41 +0000 (-0600) -Subject: stdio: don't assume gets any more -X-Git-Tag: v0.1~799 -X-Git-Url: https://git.savannah.gnu.org/gitweb/?p=gnulib.git;a=commitdiff_plain;h=66712c23388e93e5c518ebc8515140fa0c807348 - -stdio: don't assume gets any more - -Gnulib intentionally does not have a gets module, and now that C11 -and glibc have dropped it, we should be more proactive about warning -any user on a platform that still has a declaration of this dangerous -interface. - -* m4/stdio_h.m4 (gl_STDIO_H, gl_STDIO_H_DEFAULTS): Drop gets -support. -* modules/stdio (Makefile.am): Likewise. -* gnu/stdio-read.c (gets): Likewise. -* tests/test-stdio-c++.cc: Likewise. -* m4/warn-on-use.m4 (gl_WARN_ON_USE_PREPARE): Fix comment. -* gnu/stdio.in.h (gets): Make warning occur in more places. -* doc/posix-functions/gets.texi (gets): Update documentation. -Reported by Christer Solskogen. - -Signed-off-by: Eric Blake <eblake@redhat.com> ---- -diff --git a/libgnu/stdio.in.h b/libgnu/stdio.in.h -index aa7b599..c377b6e 100644 ---- a/libgnu/stdio.in.h -+++ b/libgnu/stdio.in.h -@@ -698,22 +698,11 @@ _GL_WARN_ON_USE (getline, "getline is unportable - " - # endif - #endif - --#if @GNULIB_GETS@ --# if @REPLACE_STDIO_READ_FUNCS@ && @GNULIB_STDIO_H_NONBLOCKING@ --# if !(defined __cplusplus && defined GNULIB_NAMESPACE) --# undef gets --# define gets rpl_gets --# endif --_GL_FUNCDECL_RPL (gets, char *, (char *s) _GL_ARG_NONNULL ((1))); --_GL_CXXALIAS_RPL (gets, char *, (char *s)); --# else --_GL_CXXALIAS_SYS (gets, char *, (char *s)); --# undef gets --# endif --_GL_CXXALIASWARN (gets); - /* It is very rare that the developer ever has full control of stdin, -- so any use of gets warrants an unconditional warning. Assume it is -- always declared, since it is required by C89. */ -+ so any use of gets warrants an unconditional warning; besides, C11 -+ removed it. */ -+#undef gets -+#if HAVE_RAW_DECL_GETS - _GL_WARN_ON_USE (gets, "gets is a security hole - use fgets instead"); - #endif - diff --git a/gn/packages/patches/octave-nested-class.patch b/gn/packages/patches/octave-nested-class.patch deleted file mode 100644 index 6d835cb..0000000 --- a/gn/packages/patches/octave-nested-class.patch +++ /dev/null @@ -1,39 +0,0 @@ -https://hg.savannah.gnu.org/hgweb/octave/raw-rev/7ffd2a0791ef - -# HG changeset patch -# User John W. Eaton <jwe@octave.org> -# Date 1325958274 18000 -# Node ID 7ffd2a0791ef389474bb52228e9b046a3721ab3f -# Parent 906eecd4bf43b0146c50019ee41acac2dc83c935 -fix name lookup problem with static nested class - -* oct-inttypes.h (octave_int_arith_base<T,false>::mul): -Tag truncate_int with octave_int_base<T>::. -(octave_int_arith_base<T,true>::mul): Likewise. - -diff --git a/liboctave/oct-inttypes.h b/liboctave/oct-inttypes.h ---- a/liboctave/oct-inttypes.h -+++ b/liboctave/oct-inttypes.h -@@ -366,8 +366,8 @@ - { - // Promotion type for multiplication (if exists). - typedef typename query_integer_type<2*sizeof (T), false>::type mptype; -- return truncate_int (static_cast<mptype> (x) -- * static_cast<mptype> (y)); -+ return octave_int_base<T>::truncate_int (static_cast<mptype> (x) -+ * static_cast<mptype> (y)); - } - - // Division with rounding to nearest. Note that / and % are probably -@@ -621,8 +621,8 @@ - { - // Promotion type for multiplication (if exists). - typedef typename query_integer_type<2*sizeof (T), true>::type mptype; -- return truncate_int (static_cast<mptype> (x) -- * static_cast<mptype> (y)); -+ return octave_int_base<T>::truncate_int (static_cast<mptype> (x) -+ * static_cast<mptype> (y)); - } - - // Division. - diff --git a/gn/packages/patches/opensmtpd-gn-fixes.patch b/gn/packages/patches/opensmtpd-gn-fixes.patch deleted file mode 100644 index e310bbe..0000000 --- a/gn/packages/patches/opensmtpd-gn-fixes.patch +++ /dev/null @@ -1,48 +0,0 @@ -diff -ruN opensmtpd-7.7.0p0.orig/usr.sbin/smtpd/smtpc.c opensmtpd-7.7.0p0/usr.sbin/smtpd/smtpc.c ---- opensmtpd-7.7.0p0.orig/usr.sbin/smtpd/smtpc.c 2026-04-17 10:19:15.152524476 +0000 -+++ opensmtpd-7.7.0p0/usr.sbin/smtpd/smtpc.c 2026-04-17 10:19:41.936756962 +0000 -@@ -114,8 +114,8 @@ - servname = value; - break; - case -1: -- if (suboptarg) -- fatalx("invalid TLS option \"%s\"", suboptarg); -+ //if (suboptarg) -+ // fatalx("invalid TLS option \"%s\"", suboptarg); - fatalx("missing TLS option"); - } - } -diff -ruN opensmtpd-7.7.0p0.orig/usr.sbin/smtpd/smtpctl.c opensmtpd-7.7.0p0/usr.sbin/smtpd/smtpctl.c ---- opensmtpd-7.7.0p0.orig/usr.sbin/smtpd/smtpctl.c 2026-04-17 10:19:15.156524511 +0000 -+++ opensmtpd-7.7.0p0/usr.sbin/smtpd/smtpctl.c 2026-04-17 10:19:15.212525001 +0000 -@@ -54,6 +54,8 @@ - #endif - #include <limits.h> - -+#include <grp.h> -+ - #include "smtpd.h" - #include "parser.h" - #include "log.h" -diff -ruN opensmtpd-7.7.0p0.orig/usr.sbin/smtpd/to.c opensmtpd-7.7.0p0/usr.sbin/smtpd/to.c ---- opensmtpd-7.7.0p0.orig/usr.sbin/smtpd/to.c 2026-04-17 10:19:15.156524511 +0000 -+++ opensmtpd-7.7.0p0/usr.sbin/smtpd/to.c 2026-04-17 10:19:15.252525351 +0000 -@@ -152,7 +152,7 @@ - time_to_text(time_t when) - { - struct tm *lt; -- static char buf[40]; -+ static char buf[50]; - const char *day[] = {"Sun", "Mon", "Tue", "Wed", "Thu", "Fri", "Sat"}; - const char *month[] = {"Jan","Feb","Mar","Apr","May","Jun", - "Jul","Aug","Sep","Oct","Nov","Dec"}; -@@ -169,6 +169,9 @@ - #elif defined HAVE_DECL_ALTZONE && defined HAVE_DECL_TIMEZONE - offset = lt->tm_isdst > 0 ? altzone : timezone; - tz = lt->tm_isdst > 0 ? tzname[1] : tzname[0]; -+#else -+ offset = 0; -+ tz = "GMT"; - #endif - - /* We do not use strftime because it is subject to locale substitution*/ diff --git a/gn/packages/patches/plink-ng-Makefile-zlib.patch b/gn/packages/patches/plink-ng-Makefile-zlib.patch deleted file mode 100644 index f3bb269..0000000 --- a/gn/packages/patches/plink-ng-Makefile-zlib.patch +++ /dev/null @@ -1,126 +0,0 @@ -diff --git a/Makefile.std b/Makefile.std -index 95b0940..30206be 100644 ---- a/Makefile.std -+++ b/Makefile.std -@@ -1,62 +1,22 @@ - # General-purpose Makefile for PLINK 1.90 - # --# Compilation options: --# Do not link to LAPACK NO_LAPACK - --# Leave blank after "=" to disable; put "= 1" to enable --# (when enabled, "#define NOLAPACK" must be uncommented in plink_common.h) --NO_LAPACK = -- -- --# should autodetect system --SYS = UNIX --ifdef SystemRoot -- SYS = WIN --else -- UNAME := $(shell uname) -- ifeq ($(UNAME), Darwin) -- SYS = MAC -- endif --endif -- --CFLAGS=-Wall -O2 --BLASFLAGS=-L/usr/lib64/atlas -llapack -lcblas -latlas --LINKFLAGS=-lm -lpthread --ZLIB=zlib-1.2.8/libz.so.1.2.8 -- --ifeq ($(SYS), MAC) -- GCC_GTEQ_43 := $(shell expr `g++ -dumpversion | sed -e 's/\.\([0-9][0-9]\)/\1/g' -e 's/\.\([0-9]\)/0\1/g' -e 's/^[0-9]\{3,4\}$$/&00/'` \>= 40300) -- ifeq "$(GCC_GTEQ_43)" "1" -- CFLAGS=-Wall -O2 -flax-vector-conversions -- endif -- BLASFLAGS=-framework Accelerate -- LINKFLAGS= -- ZLIB=zlib-1.2.8/libz.1.2.8.dylib --endif -- --ifeq ($(SYS), WIN) --# Note that, unlike the Linux and Mac build processes, this STATICALLY links --# LAPACK, since we have not gotten around to trying dynamically-linked LAPACK --# on Windows. --# If you don't already have LAPACK built, you'll probably want to turn on --# NO_LAPACK. -- BLASFLAGS=-L. lapack/liblapack.a -L. lapack/librefblas.a -- LINKFLAGS=-lm -static-libgcc -- ZLIB=zlib-1.2.8/libz.a --endif -- --ifdef NO_LAPACK -- BLASFLAGS= --endif -+# CFLAGS=-Wall -O2 -+# BLASFLAGS=-lblas -llapack -latlas -+LINKFLAGS=-lm -lpthread -lopenblas -llapack -latlas -lstdc++ -+ZLIB=-lz - - SRC = plink.c plink_assoc.c plink_calc.c plink_cluster.c plink_cnv.c plink_common.c plink_data.c plink_dosage.c plink_family.c plink_filter.c plink_glm.c plink_help.c plink_homozyg.c plink_lasso.c plink_ld.c plink_matrix.c plink_misc.c plink_set.c plink_stats.c SFMT.c dcdflib.c pigz.c yarn.c - -+OBJ = plink.o plink_assoc.o plink_calc.o plink_cluster.o plink_cnv.o plink_common.o plink_data.o plink_dosage.o plink_family.o plink_filter.o plink_glm.o plink_help.o plink_homozyg.o plink_lasso.o plink_ld.o plink_matrix.o plink_misc.o plink_set.o plink_stats.o SFMT.o dcdflib.o pigz.o yarn.o -+ - # In the likely event that you are concurrently using PLINK 1.07, we suggest - # either renaming that binary to "plink1" or this one to "plink2". - --plink: $(SRC) -- g++ $(CFLAGS) $(SRC) -o plink $(BLASFLAGS) $(LINKFLAGS) -L. $(ZLIB) -+# plink: $(SRC) -+# g++ $(CFLAGS) $(SRC) -o plink $(BLASFLAGS) $(LINKFLAGS) -L. $(ZLIB) - --plinkw: $(SRC) -+plink: $(SRC) - g++ $(CFLAGS) $(SRC) -c -- gfortran -O2 $(OBJ) -o plink -Wl,-Bstatic $(BLASFLAGS) $(LINKFLAGS) -L. $(ZLIB) -+ gfortran $(OBJ) -o plink2 $(BLASFLAGS) $(LINKFLAGS) -L. $(ZLIB) -+ # gfortran $^ -o plink2 -Wl,-Bstatic $(BLASFLAGS) $(LINKFLAGS) -L. $(ZLIB) -diff --git a/dose2plink.c b/dose2plink.c -index dc1f33a..ca2d31c 100644 ---- a/dose2plink.c -+++ b/dose2plink.c -@@ -96,7 +96,7 @@ - #endif - #endif - --#include "zlib-1.2.8/zlib.h" -+#include "zlib.h" - - #ifdef __APPLE__ - #include <sys/sysctl.h> -diff --git a/pigz.c b/pigz.c -index 6605925..3f4ca54 100644 ---- a/pigz.c -+++ b/pigz.c -@@ -303,7 +303,7 @@ - #include <stdio.h> - #include <stdlib.h> - #include <windows.h> --#include "zlib-1.2.8/zlib.h" -+#include "zlib.h" - - void pigz_init(uint32_t setprocs) { - return; -@@ -383,7 +383,7 @@ void parallel_compress(char* out_fname, uint32_t do_append, uint32_t(* emitn)(ui - # include <sys/pstat.h> - #endif - --#include "zlib-1.2.8/zlib.h" /* deflateInit2(), deflateReset(), deflate(), */ -+#include "zlib.h" /* deflateInit2(), deflateReset(), deflate(), */ - /* deflateEnd(), deflateSetDictionary(), crc32(), - inflateBackInit(), inflateBack(), inflateBackEnd(), - Z_DEFAULT_COMPRESSION, Z_DEFAULT_STRATEGY, -diff --git a/plink_common.h b/plink_common.h -index 5dd77e8..4da9371 100644 ---- a/plink_common.h -+++ b/plink_common.h -@@ -139,7 +139,7 @@ - - #endif // __LP64__ - --#include "zlib-1.2.8/zlib.h" -+#include "zlib.h" - #include "SFMT.h" - - // 64MB of non-workspace memory guaranteed for now diff --git a/gn/packages/patches/python-twint-mentions.patch b/gn/packages/patches/python-twint-mentions.patch deleted file mode 100644 index f792786..0000000 --- a/gn/packages/patches/python-twint-mentions.patch +++ /dev/null @@ -1,16 +0,0 @@ -diff --git a/twint/format.py b/twint/format.py -index 334b43a..3eeb8c2 100644 ---- a/twint/format.py -+++ b/twint/format.py -@@ -29,7 +29,10 @@ def Tweet(config, t): - output = output.replace("{quote_url}", t.quote_url) - output = output.replace("{near}", t.near) - output = output.replace("{geo}", t.geo) -- output = output.replace("{mentions}", ",".join(t.mentions)) -+ output = output.replace("{mentions}", -+ ",".join(map(lambda x: x.get("screen_name", -+ None), -+ t.mentions))) - output = output.replace("{translate}", t.translate) - output = output.replace("{trans_src}", t.trans_src) - output = output.replace("{trans_dest}", t.trans_dest) diff --git a/gn/packages/patches/python-twint-token.patch b/gn/packages/patches/python-twint-token.patch deleted file mode 100644 index 570ca8b..0000000 --- a/gn/packages/patches/python-twint-token.patch +++ /dev/null @@ -1,11 +0,0 @@ -diff --git a/twint/token.py b/twint/token.py -index 0eeb0dc..63b637a 100644 ---- a/twint/token.py -+++ b/twint/token.py -@@ -20,0 +21,6 @@ class Token: -+ self._session.headers.update( -+ {'User-Agent': -+ ('Mozilla/5.0 ' -+ '(Windows NT 10.0;' -+ ' Win64; x64; rv:78.0)' -+ ' Gecko/20100101 Firefox/78.0')}) diff --git a/gn/packages/patches/python-twint-userlist.patch b/gn/packages/patches/python-twint-userlist.patch deleted file mode 100644 index 1d5b860..0000000 --- a/gn/packages/patches/python-twint-userlist.patch +++ /dev/null @@ -1,19 +0,0 @@ -diff --git a/twint/cli.py b/twint/cli.py -index f463d68..68244c9 100644 ---- a/twint/cli.py -+++ b/twint/cli.py -@@ -69,10 +69,10 @@ def loadUserList(ul, _type): - else: - userlist = ul.split(",") - if _type == "search": -- un = "" -- for user in userlist: -- un += "%20OR%20from%3A" + user -- return un[15:] -+ un = userlist[0] -+ for user in userlist[1:]: -+ un += " OR from:" + user -+ return un - return userlist - - diff --git a/gn/packages/patches/python-unittest2-python3-compat.patch b/gn/packages/patches/python-unittest2-python3-compat.patch deleted file mode 100644 index 68fbcca..0000000 --- a/gn/packages/patches/python-unittest2-python3-compat.patch +++ /dev/null @@ -1,46 +0,0 @@ -Skip tests that fail with newer versions of Python. - -Patch copied from Gentoo: - -https://gitweb.gentoo.org/repo/gentoo.git/tree/dev-python/unittest2/files/unittest2-1.1.0-python3.5-test.patch - -diff --git a/unittest2/test/test_loader.py b/unittest2/test/test_loader.py -index 683f662..347eea5 100644 ---- a/unittest2/test/test_loader.py -+++ b/unittest2/test/test_loader.py -@@ -509,6 +509,7 @@ class Test_TestLoader(unittest2.TestCase): - # - # What happens when an impossible name is given, relative to the provided - # `module`? -+ @unittest.skipIf(sys.version_info[:2] >= (3, 5), "python 3.5 has problems here") - def test_loadTestsFromName__relative_malformed_name(self): - loader = unittest.TestLoader() - -@@ -811,6 +812,7 @@ class Test_TestLoader(unittest2.TestCase): - # TestCase or TestSuite instance." - # - # What happens when presented with an impossible module name? -+ @unittest.skipIf(sys.version_info[:2] >= (3, 5), "python 3.5 has problems here") - def test_loadTestsFromNames__malformed_name(self): - loader = unittest2.TestLoader() - -@@ -918,6 +920,7 @@ class Test_TestLoader(unittest2.TestCase): - # "The method optionally resolves name relative to the given module" - # - # What happens when presented with an impossible attribute name? -+ @unittest.skipIf(sys.version_info[:2] >= (3, 5), "python 3.5 has problems here") - def test_loadTestsFromNames__relative_malformed_name(self): - loader = unittest.TestLoader() - -diff --git a/unittest2/compatibility.py b/unittest2/compatibility.py -index 9e5f1a5..2d20c19 100644 ---- a/unittest2/compatibility.py -+++ b/unittest2/compatibility.py -@@ -140,6 +140,6 @@ except ImportError: - ### ChainMap (helper for configparser and string.Template) - ######################################################################## - --class ChainMap(collections.MutableMapping): -+class ChainMap(collections.abc.MutableMapping): - ''' A ChainMap groups multiple dicts (or other mappings) together - to create a single, updateable view. diff --git a/gn/packages/patches/python-unittest2-remove-argparse.patch b/gn/packages/patches/python-unittest2-remove-argparse.patch deleted file mode 100644 index c967387..0000000 --- a/gn/packages/patches/python-unittest2-remove-argparse.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- a/setup.py 2017-09-12 01:22:06.273997788 +0200 -+++ b/setup.py 2017-09-12 01:22:14.297918757 +0200 -@@ -57,7 +57,7 @@ - # Both install and setup requires - because we read VERSION from within the - # package, and the package also exports all the APIs. - # six for compat helpers --REQUIRES = ['argparse', 'six>=1.4', 'traceback2'], -+REQUIRES = ['six>=1.4', 'traceback2'], - - params = dict( - name=NAME, diff --git a/gn/packages/patches/python2-htmlgen-Applied-Deb-patch.patch b/gn/packages/patches/python2-htmlgen-Applied-Deb-patch.patch deleted file mode 100644 index d6a957c..0000000 --- a/gn/packages/patches/python2-htmlgen-Applied-Deb-patch.patch +++ /dev/null @@ -1,263 +0,0 @@ -From c0b16bbad9b8e396bdb64c638a3540547acfa3a5 Mon Sep 17 00:00:00 2001 -From: Pjotr Prins <pjotr.public01@thebird.nl> -Date: Sat, 13 Feb 2016 13:39:03 +0100 -Subject: [PATCH 1/2] Applied Deb patch - ---- - Formtools.py | 1 - - HTMLcalendar.py | 9 ++++----- - HTMLgen.py | 6 +++--- - HTMLtest.py | 12 ++++++------ - HTMLutil.py | 19 +++++++++---------- - ImagePaletteH.py | 2 +- - Makefile | 10 ++++++++++ - NavLinks.py | 1 - - barchart.py | 1 - - colorcube.py | 1 - - 10 files changed, 33 insertions(+), 29 deletions(-) - -diff --git a/Formtools.py b/Formtools.py -index bb598f4..1dabccd 100644 ---- a/Formtools.py -+++ b/Formtools.py -@@ -1,4 +1,3 @@ --#! /usr/bin/env python - "Provide some supporting classes to simplify Input Forms with HTMLgen" - #'$Id: Formtools.py,v 1.1 1999/04/19 23:45:36 friedric Exp friedric $' - # COPYRIGHT (C) 1999 ROBIN FRIEDRICH email: Robin.Friedrich@pdq.net -diff --git a/HTMLcalendar.py b/HTMLcalendar.py -index 3a03915..35edf27 100644 ---- a/HTMLcalendar.py -+++ b/HTMLcalendar.py -@@ -1,4 +1,3 @@ --#!/usr/bin/env python - # COPYRIGHT (C) 1997 ROBIN FRIEDRICH - # Permission to use, copy, modify, and distribute this software and its - # documentation for any purpose and without fee is hereby granted, -@@ -212,12 +211,12 @@ def makeint(value): - return value - else: - raise TypeError, ('cannot convert to int', value) --import regex --datepat = regex.compile('^ *\([0-9*][0-9]?\)[/-]' #first 2 char date field -+import re -+datepat = re.compile('^ *\([0-9*][0-9]?\)[/-]' #first 2 char date field - '\([0-9][0-9]?\)[/-]?' #second 2 char date field - '\([12][0-9][0-9][0-9]\)?[ \t]*:') #optional year field --daypat = regex.compile('^ *\('+string.join(day_name,'\|')+'\)') --timepat = regex.compile('\([0-9][0-9]?\):\([0-9][0-9]\)') -+daypat = re.compile('^ *\('+string.join(day_name,'\|')+'\)') -+timepat = re.compile('\([0-9][0-9]?\):\([0-9][0-9]\)') - - def read_appt_file(filename): - """Parsing function. -diff --git a/HTMLgen.py b/HTMLgen.py -index 10ecd28..dbdbd81 100644 ---- a/HTMLgen.py -+++ b/HTMLgen.py -@@ -284,7 +284,7 @@ class SimpleDocument(BasicDocument): - if self.meta: s.append(str(self.meta)) - if self.base: s.append(str(self.base)) - if self.stylesheet: -- s.append('\n <LINK rel=stylesheet href="%s" type=text/css title="%s">\n' \ -+ s.append('\n <LINK rel=stylesheet href="%s" type="text/css" title="%s">\n' \ - % (self.stylesheet, self.stylesheet)) - if self.style: - s.append('\n<STYLE>\n<!--\n%s\n-->\n</style>\n' % self.style) -@@ -1083,7 +1083,7 @@ class List(UserList.UserList): - - Overloaded by child classes to represent other list styles. - """ -- return '%s<LI>%s\n' % (self.pad*self.lvl, item) -+ return '%s<LI>%s</LI>\n' % (self.pad*self.lvl, item) - - def start_element(self): - """Generic creator for the HTML element opening tag. -@@ -2463,7 +2463,7 @@ class URL: - import urlparse - self.unparse = urlparse.urlunparse - self.proto, self.node, self.path, self.params, self.query, self.fragment = \ -- urlparse(url) -+ urlparse.urlparse(url) - self.dir, self.file = self.split(self.path) - - def split(self, p): -diff --git a/HTMLtest.py b/HTMLtest.py -index 5850a04..283233f 100755 ---- a/HTMLtest.py -+++ b/HTMLtest.py -@@ -1,8 +1,8 @@ --#!/bin/env python -+#!/usr/bin/env python - - """Test script which generates the online documentation for HTMLgen. - """ --import string, regex, regsub, os, time, glob -+import string, re, os, time, glob - from HTMLcolors import * - from HTMLgen import * - import HTMLgen #only so I can pick off the __version__ -@@ -232,11 +232,11 @@ def sample1(filename, aft=None, fore=None, top=None, home=None): - doc.email = 'jefferson@montecello.virginia.gov' - doc.logo = ('../image/eagle21.gif', 64, 54) - # parse Declaration of Independence -- re_hline = regex.compile('^--+$') -- re_title = regex.compile('^Title:\(.*$\)') -+ re_hline = re.compile('^--+$') -+ re_title = re.compile('^Title:\(.*$\)') - font2 = Font(size='+2') - s = open(os.path.join(datadir, 'DoI.txt')).read() -- paragraphs = regsub.split(s, '\n\([\t ]*\n\)+') -+ paragraphs = re.split(s, '\n\([\t ]*\n\)+') - for para in paragraphs: - if not para: continue - if re_title.search(para) > -1: -@@ -263,7 +263,7 @@ def sample2(filename, aft=None, fore=None, top=None, home=None): - #Ok parse that file - f = open(mpath(os.path.join(datadir, 'parrot.txt'))) - line = f.readline() -- re_dialog = regex.compile('\(^[OC].*:\)\(.*\)') -+ re_dialog = re.compile('\(^[OC].*:\)\(.*\)') - while line: - if re_dialog.search(line) > -1: - role, prose = re_dialog.group(1,2) -diff --git a/HTMLutil.py b/HTMLutil.py -index 2baf168..9a877e5 100755 ---- a/HTMLutil.py -+++ b/HTMLutil.py -@@ -1,4 +1,3 @@ --#!/usr/bin/env python - """This module provides utility functions/classes associated with HTMLgen. - - This is functionality use by HTMLgen script writers rather than by HTMLgen -@@ -19,7 +18,7 @@ itself. (i.e. HTMLgen.py is not dependant on this module.) - # OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR - # PERFORMANCE OF THIS SOFTWARE. - __version__ = '$Id: HTMLutil.py,v 1.3 1998/05/28 20:14:52 friedric Exp $' --import string, regex, os -+import string, re, os - import HTMLgen, HTMLcolors - from types import * - -@@ -79,7 +78,7 @@ def been_marked(text): - """Determine if the text have been marked by a previous gsub. - (ugly hack but it works) - """ -- if regex.search('\(</?FONT\)\|\(</?STRONG\)', text) > -1: -+ if re.search('\(</?FONT\)\|\(</?STRONG\)', text) > -1: - return 1 - else: - return 0 -@@ -125,13 +124,13 @@ def global_substitute(search_func, repl_func, s): - not_backslash = "[^\\\\]" - triple_single = "'''" - triple_double = '"""' --_doc_start_re = regex.compile( -+_doc_start_re = re.compile( - "\(^\|" + not_backslash + "\)" # bol or not backslash - + "\(" + triple_single + "\|" + triple_double + "\)" ) - single_re = not_backslash + triple_single - double_re = not_backslash + triple_double --_triple_re = { triple_single : regex.compile(single_re), -- triple_double : regex.compile(double_re) } -+_triple_re = { triple_single : re.compile(single_re), -+ triple_double : re.compile(double_re) } - - del not_backslash, triple_single, triple_double, \ - single_re, double_re -@@ -150,13 +149,13 @@ def find_docstring( s, begin=0): - return (None, None) - return startquote, quotefinder.regs[0][1] - --string_re = regex.compile('\(\(\'[^\'\n]*\'\)\|\("[^"\n]"\)\)') -+string_re = re.compile('\(\(\'[^\'\n]*\'\)\|\("[^"\n]"\)\)') - def find_string_literal( s, begin=0 ): - if string_re.search(s, begin) > -1: - return string_re.regs[1] - return (None, None) - --comment_re = regex.compile('#.*$') -+comment_re = re.compile('#.*$') - def find_comment( s, begin=0 ): - while comment_re.search(s, begin) > -1: - if been_marked(comment_re.group(0)): -@@ -166,13 +165,13 @@ def find_comment( s, begin=0 ): - return (None, None) - - Name = '[a-zA-Z_][a-zA-Z0-9_]*' --func_re = regex.compile('\(^[ \t]*def[ \t]+' +Name+ '\)[ \t]*(') -+func_re = re.compile('\(^[ \t]*def[ \t]+' +Name+ '\)[ \t]*(') - def find_function( s, begin=0 ): - if func_re.search(s, begin) > -1: - return func_re.regs[1] - return (None, None) - --class_re = regex.compile('\(^[ \t]*class[ \t]+' +Name+ '\)[ \t]*[(:]') -+class_re = re.compile('\(^[ \t]*class[ \t]+' +Name+ '\)[ \t]*[(:]') - def find_class( s, begin=0 ): - if class_re.search(s, begin) > -1: - return class_re.regs[1] -diff --git a/ImagePaletteH.py b/ImagePaletteH.py -index 83bb867..e723847 100644 ---- a/ImagePaletteH.py -+++ b/ImagePaletteH.py -@@ -70,7 +70,7 @@ def negative(mode = "RGB"): - return ImagePalette(mode, palette * len(mode)) - - def random(mode = "RGB"): -- from whrandom import randint -+# from whrandom import randint - palette = map(lambda a: randint(0, 255), [0]*256*len(mode)) - return ImagePalette(mode, palette) - -diff --git a/Makefile b/Makefile -index 1788fa6..e1ec846 100644 ---- a/Makefile -+++ b/Makefile -@@ -62,6 +62,16 @@ install: compileall - python installp.py -f $(MODULES) $(MODULESC) $(PIL) $(PILC) - @echo Installation of $(PACKAGE) done. - -+debinstall: -+ if [ -z "$(PYLIBDIR)" ]; then \ -+ echo "Unset PYLIBDIR."; \ -+ exit 1; \ -+ fi; \ -+ for f in $(MODULES) $(PIL); do \ -+ install -m 644 $$f $(PYLIBDIR)/; \ -+ done -+ @echo Installation of $(PACKAGE) done. -+ - checkin: - ci -u $(MODULES) $(PIL) $(EXTRAS) $(TEST) Makefile - -diff --git a/NavLinks.py b/NavLinks.py -index fcecbb3..51ef774 100644 ---- a/NavLinks.py -+++ b/NavLinks.py -@@ -1,4 +1,3 @@ --#!/usr/bin/env python - #'$Id: NavLinks.py,v 1.1 1999/02/04 04:54:29 friedric Exp friedric $' - # COPYRIGHT (C) 1999 ROBIN FRIEDRICH email:Robin.Friedrich@pdq.net - # Permission to use, copy, modify, and distribute this software and -diff --git a/barchart.py b/barchart.py -index 882cde5..a901fe4 100755 ---- a/barchart.py -+++ b/barchart.py -@@ -1,4 +1,3 @@ --#!/usr/bin/env python - - """Provides BarChart class which creates HTML 1D bar charts, - and StackedBarChart class to deal with multiple data plotting -diff --git a/colorcube.py b/colorcube.py -index be91154..94fa7dd 100644 ---- a/colorcube.py -+++ b/colorcube.py -@@ -1,4 +1,3 @@ --#!/usr/bin/env python - - """Utility to generate a table of browser safe colors. - """ --- -2.1.4 - diff --git a/gn/packages/patches/python2-htmlgen-Fix-test-for-random.patch b/gn/packages/patches/python2-htmlgen-Fix-test-for-random.patch deleted file mode 100644 index 279a82f..0000000 --- a/gn/packages/patches/python2-htmlgen-Fix-test-for-random.patch +++ /dev/null @@ -1,25 +0,0 @@ -From c9ca65d39ca1185cebf5be86a10ba0ceea171249 Mon Sep 17 00:00:00 2001 -From: Pjotr Prins <pjotr.public01@thebird.nl> -Date: Sat, 13 Feb 2016 13:40:46 +0100 -Subject: [PATCH 2/2] Fix test for random - ---- - HTMLgen.py | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/HTMLgen.py b/HTMLgen.py -index dbdbd81..034f672 100644 ---- a/HTMLgen.py -+++ b/HTMLgen.py -@@ -924,7 +924,7 @@ class MailTo: - def antispam(self, address): - """Process a string with HTML encodings to defeat address spiders. - """ -- from whrandom import choice -+ from random import choice - buffer = map(None, address) - for i in range(0, len(address), choice((2,3,4))): - buffer[i] = '&#%d;' % ord(buffer[i]) --- -2.1.4 - diff --git a/gn/packages/patches/quast.patch b/gn/packages/patches/quast.patch deleted file mode 100644 index 31e5460..0000000 --- a/gn/packages/patches/quast.patch +++ /dev/null @@ -1,88 +0,0 @@ -This patch is mostly adapted from the Debian patches -https://salsa.debian.org/med-team/quast/-/tree/master/debian/patches - -diff --git a/setup.py b/setup.py -index a982a430..24ab2f5f 100755 ---- a/setup.py -+++ b/setup.py -@@ -35,10 +35,10 @@ except: - exit_with_code=1) - - from quast_libs.glimmer import compile_glimmer --from quast_libs.run_busco import download_augustus, download_all_db --from quast_libs.search_references_meta import download_blast_binaries, download_blastdb -+from quast_libs.run_busco import download_all_db -+from quast_libs.search_references_meta import download_blastdb - from quast_libs.ca_utils.misc import compile_aligner --from quast_libs.ra_utils.misc import compile_reads_analyzer_tools, compile_bwa, compile_bedtools, download_gridss -+from quast_libs.ra_utils.misc import compile_reads_analyzer_tools, download_gridss - - name = 'quast' - quast_package = qconfig.PACKAGE_NAME -@@ -60,8 +60,6 @@ if cmd_in(['clean', 'sdist']): - logger.info('Cleaning up binary files...') - compile_aligner(logger, only_clean=True) - compile_glimmer(logger, only_clean=True) -- compile_bwa(logger, only_clean=True) -- compile_bedtools(logger, only_clean=True) - for fpath in [fn for fn in glob(join(quast_package, '*.pyc'))]: os.remove(fpath) - for fpath in [fn for fn in glob(join(quast_package, 'html_saver', '*.pyc'))]: os.remove(fpath) - for fpath in [fn for fn in glob(join(quast_package, 'site_packages', '*', '*.pyc'))]: os.remove(fpath) -@@ -74,10 +72,7 @@ if cmd_in(['clean', 'sdist']): - if isdir(name + '.egg-info'): - shutil.rmtree(name + '.egg-info') - download_gridss(logger, only_clean=True) -- download_blast_binaries(logger, only_clean=True) -- download_blastdb(logger, only_clean=True) - if qconfig.platform_name != 'macosx': -- download_augustus(logger, only_clean=True) - download_all_db(logger, only_clean=True) - logger.info('Done.') - sys.exit() -@@ -168,9 +163,6 @@ if cmd_in(['install', 'develop', 'build', 'build_ext']): - logger.info('* Downloading GRIDSS *') - if not download_gridss(logger): - modules_failed_to_install.append('GRIDSS (affects -1/--reads1 and -2/--reads2 options)') -- logger.info('* Downloading BLAST *') -- if not download_blast_binaries(logger): -- modules_failed_to_install.append('BLAST (affects metaquast.py in without references mode and --find-conserved-genes option)') - logger.info('* Downloading SILVA 16S rRNA gene database *') - if not download_blastdb(logger): - modules_failed_to_install.append('SILVA 16S rRNA gene database (affects metaquast.py in without references mode)') -@@ -186,20 +178,8 @@ if cmd_in(['install', 'develop', 'build', 'build_ext']): - logger.info('') - - --if qconfig.platform_name == 'macosx': -- sambamba_files = [join('sambamba', 'sambamba_osx')] --else: -- sambamba_files = [join('sambamba', 'sambamba_linux')] -- --minimap_files = find_package_files('minimap2') --bwa_files = [ -- join('bwa', fp) for fp in os.listdir(join(quast_package, 'bwa')) -- if isfile(join(quast_package, 'bwa', fp)) and fp.startswith('bwa')] --bedtools_files = [join('bedtools', 'bin', '*')] - full_install_tools = ( -- find_package_files('gridss') + -- find_package_files('blast') + -- [join(quast_package, 'busco', 'hmmsearch')] -+ find_package_files('gridss') - ) - - setup( -@@ -229,14 +209,10 @@ The tool accepts multiple assemblies, thus is suitable for comparison.''', - 'manual.html', - ] + - find_package_files('html_saver') + -- minimap_files + - find_package_files('genemark/' + qconfig.platform_name) + - find_package_files('genemark-es/' + qconfig.platform_name) + - find_package_files('genemark-es/lib') + - find_package_files('glimmer') + -- bwa_files + -- bedtools_files + -- sambamba_files + - (full_install_tools if install_full else []) - }, - include_package_data=True, diff --git a/gn/packages/patches/seqwish-paryfor-riscv.patch b/gn/packages/patches/seqwish-paryfor-riscv.patch deleted file mode 100644 index cecf806..0000000 --- a/gn/packages/patches/seqwish-paryfor-riscv.patch +++ /dev/null @@ -1,20 +0,0 @@ -diff --git a/deps/paryfor/paryfor.hpp b/deps/paryfor/paryfor.hpp -index b8ced09..0536580 100644 ---- a/deps/paryfor/paryfor.hpp -+++ b/deps/paryfor/paryfor.hpp -@@ -51,6 +51,15 @@ static inline void spin_loop_pause() noexcept { - } - } // namespace atomic_queue - } // namespace paryfor -+#elif defined(__riscv) && (__riscv_xlen == 64) -+namespace paryfor { -+namespace atomic_queue { -+constexpr int CACHE_LINE_SIZE = 64; -+static inline void spin_loop_pause() noexcept { -+ asm volatile ("nop" ::: "memory"); -+} -+} -+} - #else - #error "Unknown CPU architecture." - #endif diff --git a/gn/packages/patches/seqwish-shared-library.patch b/gn/packages/patches/seqwish-shared-library.patch deleted file mode 100644 index be982de..0000000 --- a/gn/packages/patches/seqwish-shared-library.patch +++ /dev/null @@ -1,195 +0,0 @@ -diff --git a/CMakeLists.txt b/CMakeLists.txt -index 09eafb5..a39f90f 100644 ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -7,6 +7,8 @@ project(seqwish) - # We build using c++14 - set(CMAKE_CXX_STANDARD 14) - -+include(GNUInstallDirs) -+ - set(THREADS_PREFER_PTHREAD_FLAG ON) - find_package(Threads REQUIRED) - -@@ -26,6 +28,8 @@ if(NOT DEFINED EXTRA_FLAGS) - "Extra compilation flags for C and CXX." FORCE) - endif() - -+set(SEQWISH_LINK_SHARED_LIBRARY OFF CACHE BOOL "Do not link against the libseqwish shared library") -+ - if (${CMAKE_BUILD_TYPE} MATCHES Release) - set(EXTRA_FLAGS "-Ofast ${EXTRA_FLAGS}") - set(CMAKE_CXX_FLAGS_RELEASE "-DNDEBUG") # reset CXX_FLAGS to replace -O3 with -Ofast -@@ -82,7 +86,7 @@ include(${CMAKE_ROOT}/Modules/ExternalProject.cmake) - # sdsl-lite (full build using its cmake config) - ExternalProject_Add(sdsl-lite - SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/sdsl-lite" -- CMAKE_ARGS "${CMAKE_ARGS};-DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>" -+ CMAKE_ARGS "${CMAKE_ARGS};-DCMAKE_CXX_FLAGS=-fPIC;-DCMAKE_C_FLAGS=-fPIC;-DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>" - UPDATE_COMMAND "" - INSTALL_COMMAND "") - ExternalProject_Get_property(sdsl-lite INSTALL_DIR) -@@ -203,27 +207,125 @@ set(mio_INCLUDE "${SOURCE_DIR}/include") - #set(CMAKE_BUILD_TYPE Debug) - set(CMAKE_BUILD_TYPE Release) - -+# set up our target libraries and specify its dependencies and includes -+add_library( libseqwish_static -+ ${CMAKE_SOURCE_DIR}/src/utils.cpp -+ ${CMAKE_SOURCE_DIR}/src/tempfile.cpp -+ ${CMAKE_SOURCE_DIR}/src/main.cpp -+ ${CMAKE_SOURCE_DIR}/src/seqindex.cpp -+ ${CMAKE_SOURCE_DIR}/src/paf.cpp -+ ${CMAKE_SOURCE_DIR}/src/sxs.cpp -+ ${CMAKE_SOURCE_DIR}/src/cigar.cpp -+ ${CMAKE_SOURCE_DIR}/src/alignments.cpp -+ ${CMAKE_SOURCE_DIR}/src/pos.cpp -+ ${CMAKE_SOURCE_DIR}/src/match.cpp -+ ${CMAKE_SOURCE_DIR}/src/transclosure.cpp -+ ${CMAKE_SOURCE_DIR}/src/links.cpp -+ ${CMAKE_SOURCE_DIR}/src/compact.cpp -+ ${CMAKE_SOURCE_DIR}/src/dna.cpp -+ ${CMAKE_SOURCE_DIR}/src/gfa.cpp -+ ${CMAKE_SOURCE_DIR}/src/vgp.cpp -+ ${CMAKE_SOURCE_DIR}/src/exists.cpp -+ ${CMAKE_SOURCE_DIR}/src/time.cpp -+ ${CMAKE_SOURCE_DIR}/src/mmap.cpp -+ ) -+add_dependencies(libseqwish_static tayweeargs) -+add_dependencies(libseqwish_static sdsl-lite) -+add_dependencies(libseqwish_static gzipreader) -+add_dependencies(libseqwish_static mmmulti) -+add_dependencies(libseqwish_static iitii) -+add_dependencies(libseqwish_static ips4o) -+add_dependencies(libseqwish_static bbhash) -+add_dependencies(libseqwish_static atomicbitvector) -+add_dependencies(libseqwish_static atomicqueue) -+add_dependencies(libseqwish_static ska) -+add_dependencies(libseqwish_static paryfor) -+add_dependencies(libseqwish_static mio) -+target_include_directories(libseqwish_static PUBLIC -+ "${sdsl-lite_INCLUDE}" -+ "${sdsl-lite-divsufsort_INCLUDE}" -+ "${tayweeargs_INCLUDE}" -+ "${gzipreader_INCLUDE}" -+ "${ips4o_INCLUDE}" -+ "${mmmulti_INCLUDE}" -+ "${iitii_INCLUDE}" -+ "${bbhash_INCLUDE}" -+ "${atomicbitvector_INCLUDE}" -+ "${atomicqueue_INCLUDE}" -+ "${ska_INCLUDE}" -+ "${paryfor_INCLUDE}" -+ "${mio_INCLUDE}") -+target_link_libraries(libseqwish_static -+ "${sdsl-lite_LIB}/libsdsl.a" -+ "${sdsl-lite-divsufsort_LIB}/libdivsufsort.a" -+ "${sdsl-lite-divsufsort_LIB}/libdivsufsort64.a" -+ "-latomic" -+ Threads::Threads -+ jemalloc -+ z) -+set_target_properties(libseqwish_static PROPERTIES OUTPUT_NAME "seqwish") -+ -+add_library( libseqwish SHARED -+ ${CMAKE_SOURCE_DIR}/src/utils.cpp -+ ${CMAKE_SOURCE_DIR}/src/tempfile.cpp -+ ${CMAKE_SOURCE_DIR}/src/main.cpp -+ ${CMAKE_SOURCE_DIR}/src/seqindex.cpp -+ ${CMAKE_SOURCE_DIR}/src/paf.cpp -+ ${CMAKE_SOURCE_DIR}/src/sxs.cpp -+ ${CMAKE_SOURCE_DIR}/src/cigar.cpp -+ ${CMAKE_SOURCE_DIR}/src/alignments.cpp -+ ${CMAKE_SOURCE_DIR}/src/pos.cpp -+ ${CMAKE_SOURCE_DIR}/src/match.cpp -+ ${CMAKE_SOURCE_DIR}/src/transclosure.cpp -+ ${CMAKE_SOURCE_DIR}/src/links.cpp -+ ${CMAKE_SOURCE_DIR}/src/compact.cpp -+ ${CMAKE_SOURCE_DIR}/src/dna.cpp -+ ${CMAKE_SOURCE_DIR}/src/gfa.cpp -+ ${CMAKE_SOURCE_DIR}/src/vgp.cpp -+ ${CMAKE_SOURCE_DIR}/src/exists.cpp -+ ${CMAKE_SOURCE_DIR}/src/time.cpp -+ ${CMAKE_SOURCE_DIR}/src/mmap.cpp -+ ${CMAKE_SOURCE_DIR}/src/version.cpp -+ ) -+add_dependencies(libseqwish tayweeargs) -+add_dependencies(libseqwish sdsl-lite) -+add_dependencies(libseqwish gzipreader) -+add_dependencies(libseqwish mmmulti) -+add_dependencies(libseqwish iitii) -+add_dependencies(libseqwish ips4o) -+add_dependencies(libseqwish bbhash) -+add_dependencies(libseqwish atomicbitvector) -+add_dependencies(libseqwish atomicqueue) -+add_dependencies(libseqwish ska) -+add_dependencies(libseqwish paryfor) -+add_dependencies(libseqwish mio) -+target_include_directories(libseqwish PUBLIC -+ "${sdsl-lite_INCLUDE}" -+ "${sdsl-lite-divsufsort_INCLUDE}" -+ "${tayweeargs_INCLUDE}" -+ "${gzipreader_INCLUDE}" -+ "${ips4o_INCLUDE}" -+ "${mmmulti_INCLUDE}" -+ "${iitii_INCLUDE}" -+ "${bbhash_INCLUDE}" -+ "${atomicbitvector_INCLUDE}" -+ "${atomicqueue_INCLUDE}" -+ "${ska_INCLUDE}" -+ "${paryfor_INCLUDE}" -+ "${mio_INCLUDE}") -+target_link_libraries(libseqwish -+ "${sdsl-lite_LIB}/libsdsl.a" -+ "${sdsl-lite-divsufsort_LIB}/libdivsufsort.a" -+ "${sdsl-lite-divsufsort_LIB}/libdivsufsort64.a" -+ "-latomic" -+ Threads::Threads -+ jemalloc -+ z) -+set_target_properties(libseqwish PROPERTIES OUTPUT_NAME "seqwish") -+ - # set up our target executable and specify its dependencies and includes - add_executable(seqwish -- ${CMAKE_SOURCE_DIR}/src/utils.cpp -- ${CMAKE_SOURCE_DIR}/src/tempfile.cpp - ${CMAKE_SOURCE_DIR}/src/main.cpp -- ${CMAKE_SOURCE_DIR}/src/seqindex.cpp -- ${CMAKE_SOURCE_DIR}/src/paf.cpp -- ${CMAKE_SOURCE_DIR}/src/sxs.cpp -- ${CMAKE_SOURCE_DIR}/src/cigar.cpp -- ${CMAKE_SOURCE_DIR}/src/alignments.cpp -- ${CMAKE_SOURCE_DIR}/src/pos.cpp -- ${CMAKE_SOURCE_DIR}/src/match.cpp -- ${CMAKE_SOURCE_DIR}/src/transclosure.cpp -- ${CMAKE_SOURCE_DIR}/src/links.cpp -- ${CMAKE_SOURCE_DIR}/src/compact.cpp -- ${CMAKE_SOURCE_DIR}/src/dna.cpp -- ${CMAKE_SOURCE_DIR}/src/gfa.cpp -- ${CMAKE_SOURCE_DIR}/src/vgp.cpp -- ${CMAKE_SOURCE_DIR}/src/exists.cpp -- ${CMAKE_SOURCE_DIR}/src/time.cpp -- ${CMAKE_SOURCE_DIR}/src/mmap.cpp - ${CMAKE_SOURCE_DIR}/src/version.cpp - ) - add_dependencies(seqwish tayweeargs) -@@ -252,6 +354,11 @@ target_include_directories(seqwish PUBLIC - "${ska_INCLUDE}" - "${paryfor_INCLUDE}" - "${mio_INCLUDE}") -+if( SEQWISH_LINK_SHARED_LIBRARY ) -+ target_link_libraries( seqwish libseqwish ) -+else() -+ target_link_libraries( seqwish libseqwish_static ) -+endif() - target_link_libraries(seqwish - "${sdsl-lite_LIB}/libsdsl.a" - "${sdsl-lite-divsufsort_LIB}/libdivsufsort.a" -@@ -269,4 +376,6 @@ endif() - file(MAKE_DIRECTORY ${CMAKE_SOURCE_DIR}/include) - execute_process(COMMAND bash ${CMAKE_SOURCE_DIR}/scripts/generate_git_version.sh ${CMAKE_SOURCE_DIR}/include) - --install(TARGETS seqwish DESTINATION bin) -+install(TARGETS seqwish DESTINATION "${CMAKE_INSTALL_BIDIR}") -+install(TARGETS libseqwish LIBRARY DESTINATION "${CMAKE_INSTALL_LIBDIR}") -+install(TARGETS libseqwish_static ARCHIVE DESTINATION "${CMAKE_INSTALL_LIBDIR}") diff --git a/gn/packages/patches/vcflib-use-system-fastahack-smithwaterman.patch b/gn/packages/patches/vcflib-use-system-fastahack-smithwaterman.patch deleted file mode 100644 index 91f372c..0000000 --- a/gn/packages/patches/vcflib-use-system-fastahack-smithwaterman.patch +++ /dev/null @@ -1,107 +0,0 @@ -diff --git a/CMakeLists.txt b/CMakeLists.txt -index af3fe67..f237563 100644 ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -63,8 +63,10 @@ set_package_properties(ZLIB PROPERTIES TYPE REQUIRED) - find_package(Threads) - set_package_properties(Threads PROPERTIES TYPE REQUIRED) - --pkg_check_modules(htslib IMPORTED_TARGET htslib) # Optionally builds from contrib/ --pkg_check_modules(tabixpp IMPORTED_TARGET tabixpp) # Optionally builds from contrib/ -+pkg_check_modules(htslib IMPORTED_TARGET htslib) # Optionally builds from contrib/ -+pkg_check_modules(tabixpp IMPORTED_TARGET tabixpp) # Optionally builds from contrib/ -+pkg_check_modules(fastahack IMPORTED_TARGET fastahack) # Optionally builds from contrib/ -+pkg_check_modules(smithwaterman IMPORTED_TARGET smithwaterman) # Optionally builds from contrib/ - - # ---- Build switches - set(CMAKE_INTERPROCEDURAL_OPTIMIZATION ${ipo_supported}) -@@ -113,12 +115,20 @@ endif(ZIG) - # ---- Include files - - include_directories(include) --include_directories(contrib/fastahack) - include_directories(contrib/intervaltree) --include_directories(contrib/smithwaterman) - include_directories(contrib/filevercmp) - include_directories(contrib/c-progress-bar) - -+if(NOT fastahack_FOUND) -+ message(STATUS "Using included fastahack") -+ include_directories(contrib/fastahack) -+endif() -+ -+if(NOT smithwaterman_FOUND) -+ message(STATUS "Using included smithwaterman") -+ include_directories(contrib/smithwaterman) -+endif() -+ - if(NOT htslib_FOUND) - message(STATUS "Using included htslib") - include(FindCURL) # for htslib -@@ -142,11 +152,19 @@ endif() - file(GLOB INCLUDES - src/*.h* - contrib/intervaltree/*.h* -- contrib/smithwaterman/*.h* -- contrib/fastahack/*.h* - contrib/filevercmp/*.h* - ) - -+if(NOT fastahack_FOUND) -+ file(GLOB FASTAHACK_INCLUDES contrib/fastahack/*.h*) -+ list(APPEND INCLUDES ${FASTAHACK_INCLUDES}) -+endif() -+ -+if(NOT smithwaterman_FOUND) -+ file(GLOB SW_INCLUDES contrib/smithwaterman/*.h*) -+ list(APPEND INCLUDES ${SW_INCLUDES}) -+endif() -+ - set(vcfwfa_SOURCE - src/legacy.cpp # introduces a WFA dependency - src/vcf-wfa.cpp -@@ -170,16 +188,24 @@ set(vcflib_SOURCE - src/LeftAlign.cpp - src/cigar.cpp - src/allele.cpp -- contrib/fastahack/Fasta.cpp -+ contrib/fsom/fsom.c -+ contrib/filevercmp/filevercmp.c -+ contrib/c-progress-bar/progress.c -+) -+ -+if(NOT fastahack_FOUND) -+ list(APPEND vcflib_SOURCE contrib/fastahack/Fasta.cpp) -+endif() -+ -+if(NOT smithwaterman_FOUND) -+ list(APPEND vcflib_SOURCE - contrib/smithwaterman/SmithWatermanGotoh.cpp - contrib/smithwaterman/Repeats.cpp - contrib/smithwaterman/IndelAllele.cpp - contrib/smithwaterman/disorder.cpp - contrib/smithwaterman/LeftAlign.cpp -- contrib/fsom/fsom.c -- contrib/filevercmp/filevercmp.c -- contrib/c-progress-bar/progress.c --) -+ ) -+endif() - - if (tabixpp_LOCAL) # add the tabixpp source file - list(APPEND vcflib_SOURCE ${tabixpp_SOURCE}) -@@ -440,6 +466,14 @@ if (NOT tabixpp_LOCAL) - target_link_libraries(vcflib PkgConfig::tabixpp) - endif() - -+if(fastahack_FOUND) -+ target_link_libraries(vcflib PkgConfig::fastahack) -+endif() -+ -+if(smithwaterman_FOUND) -+ target_link_libraries(vcflib PkgConfig::smithwaterman) -+endif() -+ - if(OPENMP) - target_link_libraries(vcflib OpenMP::OpenMP_CXX) - endif() |