diff options
| -rw-r--r-- | gn/packages/bioinformatics.scm | 119 |
1 files changed, 113 insertions, 6 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 5058535..8f98b8e 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -33,6 +33,7 @@ #:use-module (gnu packages bioinformatics) #:use-module (gnu packages boost) #:use-module (gnu packages bootstrap) + #:use-module (gnu packages c) #:use-module (gnu packages check) #:use-module (gnu packages cmake) #:use-module (gnu packages compression) @@ -511,6 +512,98 @@ reads.") collapses them into a non-redundant graph structure.") (license license:expat))) +(define-public agc-for-pgr-tk + (let ((commit "453c0afdc54b4aa00fa8e97a63f196931fdb81c4") ; April 26, 2022 + (revision "1")) + (package + (name "agc") + (version (git-version "2.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/cschin/agc") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1v5s79rl38dcyy5h1lykbp6clcbqq9winn533j54y49q1jp8chix")) + (snippet + #~(begin + (use-modules (guix build utils)) + ;; Copy the two radul files we can't find a replacement for: + ;; https://github.com/refresh-bio/RADULS + (mkdir "keep-libs") + (rename-file "libs/raduls.h" "keep-libs/raduls.h") + (rename-file "libs/libraduls.a" "keep-libs/libraduls.a") + (delete-file-recursively "libs") + (rename-file "keep-libs" "libs") + + (delete-file-recursively "py_agc_api/pybind11-2.8.1") + (substitute* '("makefile" "makefile.release") + (("-mavx") "") + (("-m64") "") + (("\\$\\(AGC_LIBS_DIR)\\/mimalloc/\\$\\(LIB_ALLOC\\)") + "$(pkg-config --cflags --libs mimalloc) /usr/lib/libmimalloc.so") + (("\\$\\(AGC_LIBS_DIR)\\/\\$\\(LIB_ZLIB\\)") + "$(pkg-config --cflags --libs zlib) /usr/lib/libz.so") + (("\\$\\(AGC_LIBS_DIR)\\/\\$\\(LIB_ZSTD\\)") + "$(pkg-config --cflags --libs libzstd) /usr/lib/libzstd.so") + (("^PYBIND11_LIB = .*") "PYBIND11_LIB = /usr/include/pybind11") + (("\\$\\(PYBIND11_LIB\\)/include") "$(PYBIND11_LIB)")) + (substitute* (find-files "src" "\\.(h|cpp)$") + (("../../libs/ketopt.h") "ketopt.h") + (("../../libs/zlib.h") "zlib.h") + (("../../libs/zstd.h") "zstd.h")))))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; No tests. + #:phases + (modify-phases %standard-phases + (delete 'configure) ; No configure script. + (add-after 'unpack 'adjust-sources + (lambda* (#:key inputs #:allow-other-keys) + (let ((mimalloc (assoc-ref inputs "mimalloc"))) + (substitute* '("makefile" "makefile.release") + (("/usr/include/pybind11") + (search-input-directory inputs "/include/pybind11")) + (("/usr/lib/libmimalloc.so") + (search-input-file inputs "/lib/libmimalloc.so")) + (("/usr/lib/libz.so") + (search-input-file inputs "/lib/libz.so")) + (("/usr/lib/libzstd.so") + (search-input-file inputs "/lib/libzstd.so")) + (("pkg-config") ,(pkg-config-for-target)))))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (include (string-append out "/include/"))) + (install-file "agc" (string-append out "/bin")) + (install-file "libagc.so" (string-append out "/lib")) + (mkdir-p (string-append include "app")) + (mkdir-p (string-append include "core")) + (mkdir-p (string-append include "lib-cxx")) + (with-directory-excursion "src" + (for-each + (lambda (file) + (copy-file file (string-append include file))) + (find-files "." "\\.h$"))))))))) + (native-inputs + (list minimap2 ; for ketopt.h + pkg-config)) + (inputs + (list mimalloc + python + pybind11 + zlib + (list zstd "lib"))) + (home-page "https://github.com/cschin/agc") + (synopsis "Assembled Genomes Compressor") + (description + "@acronym{Assembled Genomes Compressor, AGC} is a tool designed to +compress collections of de-novo assembled genomes. It can be used for various +types of datasets: short genomes (viruses) as well as long (humans).") + (license license:expat)))) + (define-public pgr-tk (package (name "pgr-tk") @@ -520,11 +613,10 @@ collapses them into a non-redundant graph structure.") (method git-fetch) (uri (git-reference (url "https://github.com/Sema4-Research/pgr-tk") - (commit (string-append "v" version)) - (recursive? #t))) ; agc, WFA + (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "160ngqbi8cbgaafq8crhfqv039mxr9jgl8hxxpwz0fh8mrh4003y")) + (base32 "0vm1k63v91zd0pfbg2zmwskajylz8xg83m63qxwaiwny5f4y6f1j")) (snippet #~(begin (use-modules (guix build utils)) @@ -570,7 +662,7 @@ collapses them into a non-redundant graph structure.") (copy-recursively (assoc-ref inputs "wfa-src") "rs-wfa/WFA"))) (add-after 'unpack 'adjust-source - (lambda _ + (lambda* (#:key inputs #:allow-other-keys) (substitute* '("pgr-bin/build.rs" "pgr-db/build.rs" "pgr-tk/build.rs") @@ -579,7 +671,17 @@ collapses them into a non-redundant graph structure.") ;; Build with zlib, not zlib-ng (substitute* '("pgr-bin/Cargo.toml" "pgr-db/Cargo.toml") - (("zlib-ng-compat") "zlib")))) + (("zlib-ng-compat") "zlib")) + ;; Don't look for agc to be bundled. + (substitute* "pgr-db/wrapper.h" + (("../agc/src/lib-cxx/agc-api.h") "lib-cxx/agc-api.h")) + (substitute* "pgr-db/build.rs" + ((".*panic!\\(\"Error.*") "")) + (mkdir-p "target/release") + (symlink (search-input-file inputs "/bin/agc") + "target/release/agc") + (symlink (search-input-file inputs "/lib/libagc.so") + "target/release/libagc"))) (replace 'install (lambda* (#:key outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out"))) @@ -593,7 +695,12 @@ collapses them into a non-redundant graph structure.") "pgr-multifilter" "pgr-probe-match" "pgr-shmmr-pair-count"))))))))) - (inputs (list clang python zlib)) + (inputs + (list agc-for-pgr-tk + clang + python + zlib + (list zstd "lib"))) (native-inputs `(("pkg-config" ,pkg-config) ("wfa-src" |