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authorEfraim Flashner2022-11-13 12:57:36 +0200
committerEfraim Flashner2022-11-13 12:57:36 +0200
commitdd9aab67b68cad7f2fa2c15626d73b1e25198dee (patch)
treedbdc1c92e571545d5450d38862b13d531b12e2ce
parent3c387a68ac8baec058352e0933f347ac4189019d (diff)
downloadguix-bioinformatics-dd9aab67b68cad7f2fa2c15626d73b1e25198dee.tar.gz
gn: pgr-tk: Unbundle agc.
-rw-r--r--gn/packages/bioinformatics.scm119
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"