diff options
Diffstat (limited to 'gn/packages/bioinformatics.scm')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 370 |
1 files changed, 176 insertions, 194 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 397b38f..3f89abe 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -47,6 +47,7 @@ #:use-module (gnu packages databases) #:use-module (gnu packages datastructures) #:use-module (gnu packages digest) + #:use-module (gnu packages documentation) #:use-module (gnu packages elf) #:use-module (gnu packages fontutils) #:use-module (gnu packages gcc) @@ -1898,14 +1899,13 @@ The path-guided stochastic gradient descent based 1D sort implemented in (define-public graphaligner (package (name "graphaligner") - (version "1.0.19") + (version "1.0.20") (source (origin (method url-fetch) - (uri (string-append "https://github.com/maickrau/GraphAligner/files/" - "14037134/GraphAligner.tar.gz")) + (uri "https://github.com/user-attachments/files/17976913/GraphAligner.tar.gz") (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 "1z1rxvl2pmiqbh670phkx7vma36w90ylp27wyadlbzf32pa2cpdn")))) + (base32 "1gs6jds4lazljb1s7s8f1vp0l4j8jvqy6qhb9sck7x66z8157ndm")))) (build-system gnu-build-system) (arguments (list @@ -1917,16 +1917,17 @@ The path-guided stochastic gradient descent based 1D sort implemented in (delete 'configure) ; no configure phase (add-after 'unpack 'patch-source (lambda* (#:key inputs #:allow-other-keys) - (let ((concurrentqueue (assoc-ref inputs "concurrentqueue"))) - (delete-file-recursively "concurrentqueue") - (substitute* "makefile" - (("-Iconcurrentqueue") - (string-append "-I" concurrentqueue "/include/concurrentqueue")) - (("^JEMALLOCFLAGS.*") - "JEMALLOCFLAGS= `pkg-config --libs jemalloc`\n") - ;; No need to build statically. - (("-Wl,-Bstatic") "") - (("-static-libstdc\\+\\+") ""))))) + (delete-file-recursively "concurrentqueue") + (substitute* "makefile" + (("-Iconcurrentqueue") + (string-append "-I" (search-input-directory inputs "/include/concurrentqueue"))) + (("^JEMALLOCFLAGS.*") + "JEMALLOCFLAGS= `pkg-config --libs jemalloc`\n") + (("`pkg-config --cflags zlib`/bamtools") + (string-append "-I " (search-input-directory inputs "include/bamtools"))) + ;; No need to build statically. + (("-Wl,-Bstatic") "") + (("-static-libstdc\\+\\+") "")))) (replace 'install (lambda* (#:key outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out"))) @@ -1943,7 +1944,8 @@ The path-guided stochastic gradient descent based 1D sort implemented in pkg-config sparsehash)) (inputs - (list boost + (list bamtools + boost concurrentqueue jemalloc libdivsufsort @@ -2335,14 +2337,14 @@ in-memory footprint at the cost of packing and unpacking.") (define-public vg (package (name "vg") - (version "1.50.0") + (version "1.61.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/vgteam/vg/releases/download/v" version "/vg-v" version ".tar.gz")) (sha256 - (base32 "1n06fh6qvffhbxy7m096r8cy16wi0nm6gfgi3rsjy9zrb7g1jzhs")) + (base32 "1yb8ffqq65ma5di42qlj483x42viq5j4xyyg3vpww60gm15n1yxx")) (snippet #~(begin (use-modules (guix build utils)) @@ -2353,194 +2355,174 @@ in-memory footprint at the cost of packing and unpacking.") (("-mcx16") "")))))) (build-system gnu-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (delete 'configure) ; no configure script - (add-after 'unpack 'patch-source - (lambda* (#:key inputs #:allow-other-keys) - ;; Most of these are so that we can skip bootstrapping some of the sources. - (substitute* "Makefile" - ;; PKG_CONFIG_DEPS needs to be substituted to actually link to everything. - (("cairo libzstd") - "cairo htslib libzstd libdw libelf protobuf raptor2 sdsl-lite tabixpp vcflib fastahack libdeflate") - - ;; Skip the part where we link static libraries special. It doesn't like the changes we make - (("-Wl,-B.*") "\n") - - (("\\$\\(CWD\\)/\\$\\(LIB_DIR\\)/libtabixpp\\.a") "$(LIB_DIR)/libtabixpp.a") - ((" \\$\\(LIB_DIR\\)/libtabixpp\\.a") - (string-append " " (search-input-file inputs "/lib/libtabixpp.so"))) - (("\\$\\(LIB_DIR\\)/pkgconfig/tabixpp\\.pc") - (string-append " " (search-input-file inputs "/lib/pkgconfig/tabixpp.pc"))) - - (("\\$\\(CWD\\)/\\$\\(LIB_DIR\\)/libhts\\.a") "$(LIB_DIR)/libhts.a") - ((" \\$\\(LIB_DIR\\)/libhts\\.a") - (string-append " " (search-input-file inputs "/lib/libhts.so"))) - (("\\$\\(LIB_DIR\\)/pkgconfig/htslib\\.pc") - (string-append " " (search-input-file inputs "/lib/pkgconfig/htslib.pc"))) - - (("\\$\\(CWD\\)/\\$\\(LIB_DIR\\)/libdeflate\\.a") "$(LIB_DIR)/libdeflate.a") - ((" \\$\\(LIB_DIR\\)/libdeflate\\.a") - (string-append " " (search-input-file inputs "/lib/libdeflate.so"))) - - ((" \\$\\(LIB_DIR\\)/libvcflib.a") - (string-append " " (search-input-file inputs "/lib/libvcflib.so"))) - ((" \\$\\(BIN_DIR\\)/vcf2tsv") - (string-append " " (search-input-file inputs "/bin/vcf2tsv"))) - - ((" \\$\\(FASTAHACK_DIR\\)/fastahack") - (string-append " " (search-input-file inputs "/bin/fastahack"))) - (("\\+= \\$\\(OBJ_DIR\\)/Fasta\\.o") - (string-append "+= " (search-input-file inputs "/lib/libfastahack.so"))) - - ((" \\$\\(LIB_DIR\\)/libsnappy.a") - (string-append " " (search-input-file inputs "/lib/libsnappy.so"))) - - ;; Only link against the libraries in the elfutils package. - (("-ldwfl -ldw -ldwelf -lelf -lebl") "-ldw -lelf") - ((" \\$\\(LIB_DIR\\)/libelf.a") - (string-append " " (search-input-file inputs "/lib/libelf.so"))) - ((" \\$\\(LIB_DIR\\)/libdw.a") - (string-append " " (search-input-file inputs "/lib/libdw.so"))) - - ;; We need the Make.helper file in SDSL_DIR for gcsa2 - ;((" \\$\\(LIB_DIR\\)/libsdsl.a") - ; (string-append " " (search-input-file inputs "/lib/libsdsl.so"))) - - ((" \\$\\(LIB_DIR\\)/%divsufsort.a") - (string-append " " (dirname + (list + #:make-flags + #~(list (string-append "CC=" #$(cc-for-target)) + ;; Set rpath so the validate-runpath phase finds + ;; libhandlegraph.so. + (string-append "LDFLAGS=-Wl,-rpath=" #$output "/lib")) + #:phases + #~(modify-phases %standard-phases + (delete 'configure) ; no configure script + (add-after 'unpack 'patch-source + (lambda* (#:key inputs #:allow-other-keys) + ;; Most of these are so that we can skip bootstrapping some of the sources. + (substitute* "Makefile" + ;; PKG_CONFIG_DEPS needs to be substituted to actually link to everything. + (("cairo libzstd") + "cairo htslib libzstd libdw libelf protobuf raptor2 sdsl-lite tabixpp vcflib fastahack libdeflate") + + ;; Skip the part where we link static libraries special. It doesn't like the changes we make + (("-Wl,-B.*") "\n") + + (("\\$\\(CWD\\)/\\$\\(LIB_DIR\\)/libtabixpp\\.a") "$(LIB_DIR)/libtabixpp.a") + ((" \\$\\(LIB_DIR\\)/libtabixpp\\.a") + (string-append " " (search-input-file inputs "/lib/libtabixpp.so"))) + (("\\$\\(LIB_DIR\\)/pkgconfig/tabixpp\\.pc") + (string-append " " (search-input-file inputs "/lib/pkgconfig/tabixpp.pc"))) + + (("\\$\\(CWD\\)/\\$\\(LIB_DIR\\)/libhts\\.a") "$(LIB_DIR)/libhts.a") + ((" \\$\\(LIB_DIR\\)/libhts\\.a") + (string-append " " (search-input-file inputs "/lib/libhts.so"))) + (("\\$\\(LIB_DIR\\)/pkgconfig/htslib\\.pc") + (string-append " " (search-input-file inputs "/lib/pkgconfig/htslib.pc"))) + + (("\\$\\(CWD\\)/\\$\\(LIB_DIR\\)/libdeflate\\.a") "$(LIB_DIR)/libdeflate.a") + ((" \\$\\(LIB_DIR\\)/libdeflate\\.a") + (string-append " " (search-input-file inputs "/lib/libdeflate.so"))) + + ((" \\$\\(LIB_DIR\\)/libvcflib.a") + (string-append " " (search-input-file inputs "/lib/libvcflib.so"))) + ((" \\$\\(BIN_DIR\\)/vcf2tsv") + (string-append " " (search-input-file inputs "/bin/vcf2tsv"))) + + ((" \\$\\(FASTAHACK_DIR\\)/fastahack") + (string-append " " (search-input-file inputs "/bin/fastahack"))) + (("\\+= \\$\\(OBJ_DIR\\)/Fasta\\.o") + (string-append "+= " (search-input-file inputs "/lib/libfastahack.so"))) + + ((" \\$\\(LIB_DIR\\)/libsnappy.a") + (string-append " " (search-input-file inputs "/lib/libsnappy.so"))) + + ;; Only link against the libraries in the elfutils package. + (("-ldwfl -ldw -ldwelf -lelf -lebl") "-ldw -lelf") + ((" \\$\\(LIB_DIR\\)/libelf.a") + (string-append " " (search-input-file inputs "/lib/libelf.so"))) + ((" \\$\\(LIB_DIR\\)/libdw.a") + (string-append " " (search-input-file inputs "/lib/libdw.so"))) + + ((" \\$\\(LIB_DIR\\)/%divsufsort.a") + (string-append " " (dirname (search-input-file inputs "/lib/libdivsufsort.so")) - "%divsufsort.so")) - ((" \\$\\(LIB_DIR\\)/libdivsufsort.a") - (string-append " " (search-input-file inputs "/lib/libdivsufsort.so"))) - ((" \\$\\(LIB_DIR\\)/%divsufsort64.a") - (string-append " " (dirname + "%divsufsort.so")) + ((" \\$\\(LIB_DIR\\)/libdivsufsort.a") + (string-append " " (search-input-file inputs "/lib/libdivsufsort.so"))) + ((" \\$\\(LIB_DIR\\)/%divsufsort64.a") + (string-append " " (dirname (search-input-file inputs "/lib/libdivsufsort64.so")) - "%divsufsort64.so")) - ((" \\$\\(LIB_DIR\\)/libdivsufsort64.a") - (string-append " " (search-input-file inputs "/lib/libdivsufsort64.so"))) - - ((" \\$\\(LIB_DIR\\)/libjemalloc.a") - (string-append " " (search-input-file inputs "/lib/libjemalloc.a"))) - - ((" \\$\\(INC_DIR\\)/sparsehash") - (string-append " " (search-input-directory inputs "/include/sparsehash"))) - - ((" \\$\\(INC_DIR\\)/raptor2") - (string-append " " (search-input-directory inputs "/include/raptor2"))) - ((" \\$\\(LIB_DIR\\)/libraptor2.a") - (string-append " " (search-input-file inputs "/lib/libraptor2.so"))) - ((" \\$\\(BIN_DIR\\)/rapper") - (string-append " " (search-input-file inputs "/bin/rapper")))))) - (add-after 'unpack 'link-with-some-shared-libraries - (lambda* (#:key inputs #:allow-other-keys) - (substitute* '("deps/mmmultimap/CMakeLists.txt" - "deps/xg/CMakeLists.txt" - "deps/xg/deps/mmmulti/CMakeLists.txt") - (("\".*libsdsl\\.a\"") "\"-lsdsl\"") - (("\".*libdivsufsort\\.a\"") "\"-ldivsufsort\"") - (("\".*libdivsufsort64\\.a\"") "\"-ldivsufsort64\"") - (("\\$\\{sdsl-lite_INCLUDE\\}") - (search-input-directory inputs "/include/sdsl")) - (("\\$\\{sdsl-lite-divsufsort_INCLUDE\\}") - (dirname + "%divsufsort64.so")) + ((" \\$\\(LIB_DIR\\)/libdivsufsort64.a") + (string-append " " (search-input-file inputs "/lib/libdivsufsort64.so"))) + + ((" \\$\\(LIB_DIR\\)/libjemalloc.a") + (string-append " " (search-input-file inputs "/lib/libjemalloc.a"))) + + ((" \\$\\(INC_DIR\\)/sparsehash") + (string-append " " (search-input-directory inputs "/include/sparsehash"))) + + ((" \\$\\(INC_DIR\\)/raptor2") + (string-append " " (search-input-directory inputs "/include/raptor2"))) + ((" \\$\\(LIB_DIR\\)/libraptor2.a") + (string-append " " (search-input-file inputs "/lib/libraptor2.so"))) + ((" \\$\\(BIN_DIR\\)/rapper") + (string-append " " (search-input-file inputs "/bin/rapper")))) + ;; Create obj and lib directories. They do not exist in + ;; the release tarball. + (mkdir "deps/libbdsg/bdsg/obj") + (mkdir "deps/libbdsg/lib") + ;; Do not remove obj and lib directories in the clean + ;; target. + (substitute* "deps/libbdsg/Makefile" + (("\\[ ! -e \\$\\(OBJ_DIR\\) \\][^\n]*") "") + (("\\[ ! -e \\$\\(LIB_DIR\\) \\][^\n]*") "")))) + (add-after 'unpack 'link-with-some-shared-libraries + (lambda* (#:key inputs #:allow-other-keys) + (substitute* '("deps/mmmultimap/CMakeLists.txt" + "deps/xg/CMakeLists.txt" + "deps/xg/deps/mmmulti/CMakeLists.txt") + (("\".*libsdsl\\.a\"") "\"-lsdsl\"") + (("\".*libdivsufsort\\.a\"") "\"-ldivsufsort\"") + (("\".*libdivsufsort64\\.a\"") "\"-ldivsufsort64\"") + (("\\$\\{sdsl-lite_INCLUDE\\}") + (search-input-directory inputs "/include/sdsl")) + (("\\$\\{sdsl-lite-divsufsort_INCLUDE\\}") + (dirname (search-input-file inputs "/include/divsufsort.h")))))) - #; - (add-before 'patch-source 'use-shared-libvg - (lambda* (#:key inputs outputs #:allow-other-keys) - (substitute* "Makefile" - (("libvg\\.a") "libvg.so") - ;; Have the linker find the shared library. - (("\\$\\(LIB_DIR\\)/libvg.\\$\\(SHARED_SUFFIX\\) \\$\\(LDFLAGS\\)") - "-lvg $(LDFLAGS)") - (("\\$\\(LDFLAGS\\) \\$\\(LIB_DIR\\)/libvg.so") - "$(LDFLAGS) -lvg")) - (setenv "LDFLAGS" (string-append "-Wl,-rpath=" - (assoc-ref outputs "out") "/lib")) - - ;; We need to tell a number of dependencies to build with -fPIC. - (substitute* "Makefile" - (("^CXXFLAGS := -O3") - (string-append "CFLAGS := -fPIC\n" - "CXXFLAGS := -O3 -fPIC")) - (("^export CXXFLAGS") - (string-append "export CFLAGS\n" - "$(info CFLAGS are $(CFLAGS))\n" - "export CXXFLAGS")) - ((" \\$\\(LIB_DIR\\)/libjemalloc.a") - (string-append " " (assoc-ref inputs "jemalloc") - "/lib/libjemalloc_pic.a"))) - ;; We don't want to pull in all the global CXXFLAGS here. - (substitute* "deps/sublinear-Li-Stephens/makefile" - (("^CXXFLAGS:=") "CXXFLAGS:= -fPIC ")) - ;; CMAKE_CXX_FLAGS aren't set globally. - (substitute* "deps/kff-cpp-api/CMakeLists.txt" - (("CMAKE_CXX_FLAGS \"") "CMAKE_CXX_FLAGS \" -fPIC ")))) - (add-after 'unpack 'dont-build-shared-vgio - (lambda _ - ;; vg will link with libvgio and fail the 'validate-runpath phase. - (substitute* "deps/libvgio/CMakeLists.txt" - (("TARGETS vgio vgio_static") "TARGETS vgio_static")))) - (add-after 'unpack 'fix-fastahack-dependency - (lambda _ - (substitute* (append (list "src/aligner.hpp" - "src/vg.hpp") - (find-files "deps/vcflib/src" "\\.cpp$")) - (("Fasta.h") "fastahack/Fasta.h")) - (substitute* '("deps/vcflib/src/Variant.h" - "src/constructor.hpp" - "src/index_registry.cpp") - (("<Fasta.h>") "\"fastahack/Fasta.h\"")))) - (add-after 'unpack 'adjust-tests - (lambda* (#:key inputs #:allow-other-keys) - (let ((bash-tap (assoc-ref inputs "bash-tap"))) - (substitute* (find-files "test/t") - (("BASH_TAP_ROOT.*") - (string-append "BASH_TAP_ROOT=" bash-tap "/bin\n")) - ((".*bash-tap-bootstrap") - (string-append ". " bash-tap "/bin/bash-tap-bootstrap"))) - (substitute* "test/t/02_vg_construct.t" - (("../deps/fastahack/fastahack") (which "fastahack")) - (("../bin/vcf2tsv") (which "vcf2tsv"))) - ;; Lets skip the 9 failing tests for now. They fail with our - ;; bash-tap and the bundled one. - (substitute* "test/t/02_vg_construct.t" - ((".*self-inconsistent.*") "is $(true) \"\" \"\"\n")) - (substitute* "test/t/07_vg_map.t" - ;; Change in fasta's output - (("identity\\) 1 \"") "identity) 1.0 \"")) - (substitute* '("test/t/07_vg_map.t" - "test/t/33_vg_mpmap.t") - ((".*node id.*") "is $(true) \"\" \"\"\n")) - (substitute* "test/t/48_vg_convert.t" - (("true \"vg.*") "true \"true\"\n")) - (substitute* "test/t/50_vg_giraffe.t" - ((".*A long read can.*") "is $(true) \"\" \"\"\n") - ((".*A long read has.*") "is $(true) \"\" \"\"\n") - ((".*Long read minimizer.*") "is $(true) \"\" \"\"\n")) - ;; Don't test the docs, we're not providing npm - (substitute* "Makefile" - ((".*test-docs.*") ""))))) - (add-after 'build 'build-manpages - (lambda* (#:key inputs #:allow-other-keys) - (when (assoc-ref inputs "asciidoctor") - (invoke "make" "man")))) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (install-file "bin/vg" (string-append out "/bin")) - ;(install-file "lib/libvg.so" (string-append out "/lib")) - (for-each + (add-after 'unpack 'dont-build-shared-vgio + (lambda _ + ;; vg will link with libvgio and fail the 'validate-runpath phase. + (substitute* "deps/libvgio/CMakeLists.txt" + (("TARGETS vgio vgio_static") "TARGETS vgio_static")))) + (add-after 'unpack 'fix-fastahack-dependency + (lambda _ + (substitute* (append (list "src/aligner.hpp" + "src/vg.hpp") + (find-files "deps/vcflib/src" "\\.cpp$")) + (("Fasta.h") "fastahack/Fasta.h")) + (substitute* '("deps/vcflib/src/Variant.h" + "src/constructor.hpp" + "src/index_registry.cpp") + (("<Fasta.h>") "\"fastahack/Fasta.h\"")))) + (add-after 'unpack 'adjust-tests + (lambda* (#:key inputs #:allow-other-keys) + (let ((bash-tap (assoc-ref inputs "bash-tap"))) + (substitute* (find-files "test/t") + (("BASH_TAP_ROOT.*") + (string-append "BASH_TAP_ROOT=" bash-tap "/bin\n")) + ((".*bash-tap-bootstrap") + (string-append ". " bash-tap "/bin/bash-tap-bootstrap"))) + (substitute* "test/t/02_vg_construct.t" + (("../deps/fastahack/fastahack") (which "fastahack")) + (("../bin/vcf2tsv") (which "vcf2tsv"))) + ;; Lets skip the 9 failing tests for now. They fail with our + ;; bash-tap and the bundled one. + (substitute* "test/t/02_vg_construct.t" + ((".*self-inconsistent.*") "is $(true) \"\" \"\"\n")) + (substitute* "test/t/07_vg_map.t" + ;; Change in fasta's output + (("identity\\) 1 \"") "identity) 1.0 \"")) + (substitute* '("test/t/07_vg_map.t" + "test/t/33_vg_mpmap.t") + ((".*node id.*") "is $(true) \"\" \"\"\n")) + (substitute* "test/t/48_vg_convert.t" + (("true \"vg.*") "true \"true\"\n")) + (substitute* "test/t/50_vg_giraffe.t" + ((".*A long read can.*") "is $(true) \"\" \"\"\n") + ((".*A long read has.*") "is $(true) \"\" \"\"\n") + ((".*Long read minimizer.*") "is $(true) \"\" \"\"\n")) + ;; Don't test the docs, we're not providing npm + (substitute* "Makefile" + ((".*test-docs.*") ""))))) + (add-after 'build 'build-manpages + (lambda* (#:key inputs #:allow-other-keys) + (invoke "make" "man"))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (install-file "bin/vg" (string-append out "/bin")) + (install-file "lib/libhandlegraph.so" (string-append out "/lib")) + (for-each (lambda (file) (install-file file (string-append out "/share/man/man1"))) (find-files "doc/man" "\\.1$")))))) - #:test-target "test")) + #:test-target "test")) (native-inputs (append (if (supported-package? ruby-asciidoctor) (list ruby-asciidoctor) '()) - (list bash-tap + (list asciidoc + bash-tap bc cmake-minimal jq |