diff options
| -rw-r--r-- | gn/packages/bioinformatics.scm | 226 |
1 files changed, 226 insertions, 0 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 9d65d6f..9e63a26 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -35,6 +35,7 @@ #:use-module (gnu packages gcc) #:use-module (gnu packages ghostscript) #:use-module (gnu packages gtk) + #:use-module (gnu packages guile) #:use-module (gnu packages image) #:use-module (gnu packages imagemagick) #:use-module (gnu packages jemalloc) @@ -54,6 +55,7 @@ #:use-module (gnu packages readline) #:use-module (gnu packages rsync) #:use-module (gnu packages ruby) + #:use-module (gnu packages serialization) #:use-module (gnu packages shells) #:use-module (gnu packages statistics) #:use-module (gnu packages tcl) @@ -1972,3 +1974,227 @@ cases include: divergence below ~15%. @end enumerate\n") (license license:expat))) + +(define-public hap.py + (package + (name "hap.py") + (version "0.3.14") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Illumina/hap.py") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1bnm7s86651p3zf6wahz5pic7n8416fx677kj47lwckr3syp2x1h")) + (modules '((guix build utils))) + (snippet + '(begin + (delete-file-recursively "external/bcftools.tar.gz") + (delete-file-recursively "external/boost_subset_1_58_0.tar.bz2") + (delete-file-recursively "external/htslib.tar.gz") + ;; TODO: Unbundle jsoncpp. + ;(delete-file-recursively "external/jsoncpp") + ;(delete-file-recursively "external/klib") + (delete-file-recursively "external/samtools.tar.gz") + (delete-file-recursively "external/virtualenv-12.0.7.tar.gz") + (delete-file-recursively "external/zlib-1.2.8.tar.gz") + #t)))) + (build-system cmake-build-system) + (arguments + `(#:configure-flags (list "-DBUILD_VCFEVAL=ON") + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'set-package-version + (lambda _ + (substitute* "CMakeLists.txt" + (("git describe --tags --always") + (string-append "echo " ,version))) + #t)) + ;; A shared library conflicts with boost-static. + ;; Not using boost-static causes linking errors. + ;(add-after 'unpack 'build-dynamic-library + ; (lambda _ + ; (substitute* "src/c++/lib/CMakeLists.txt" + ; (("STATIC") "SHARED")) + ; #t)) + (add-after 'unpack 'fix-build + (lambda* (#:key inputs #:allow-other-keys) + (let ((zlib (assoc-ref inputs "zlib")) + (bcftools (assoc-ref inputs "bcftools")) + (boost (assoc-ref inputs "boost")) + (htslib (assoc-ref inputs "htslib")) + (samtools (assoc-ref inputs "samtools"))) + (mkdir-p "external/bin") + (mkdir-p "external/lib") + (mkdir-p "external/include") + (mkdir-p "external/scratch/lib") + + (substitute* "external/make_dependencies.sh" + (("zlib-1\\.2\\.8/libz\\.a") "lib/libz.so")) + (substitute* "src/cmake/FindHTSLib.cmake" + (("libhts\\.a") "libhts.so")) + (substitute* "CMakeLists.txt" + (("ZLIB_LIBRARIES .*\\)") + (string-append "ZLIB_LIBRARIES \"" zlib "/lib/libz.so\")"))) + + (setenv "BOOST_ROOT" boost) + (setenv "LDFLAGS" + (string-append "-L" (assoc-ref %build-inputs "htslib") "/lib")) + + (symlink (string-append zlib "/lib/libz.so") + "external/scratch/lib/libz.so") + + (symlink (string-append htslib "/include/htslib") + "external/include/htslib") + (symlink (string-append htslib "/lib/libhts.so") + "external/lib/libhts.so") + (symlink (string-append htslib "/lib/libhts.so") + "external/lib/libhts.so.3") + + (symlink (string-append bcftools "/bin/bcftools") + "external/bin/bcftools") + (symlink (string-append samtools "/bin/samtools") + "external/bin/samtools") + #t))) + (add-after 'fix-build 'insert-rtg-tools + (lambda* (#:key inputs #:allow-other-keys) + (let ((rtg-tools (assoc-ref inputs "rtg-tools"))) + (mkdir "external/libexec") + (invoke "unzip" "-j" rtg-tools + "rtg-tools-3.12.1/rtg" + "rtg-tools-3.12.1/RTG.jar" + "rtg-tools-3.12.1/README.txt" + "rtg-tools-3.12.1/LICENSE.txt" + "rtg-tools-3.12.1/third-party/gzipfix.jar" + "-d" "external/libexec/rtg-tools-install") + (mkdir "external/libexec/rtg-tools-install/third-party") + (rename-file "external/libexec/rtg-tools-install/gzipfix.jar" + "external/libexec/rtg-tools-install/third-party/gzipfix.jar") + (copy-file "external/rtg.cfg" + "external/libexec/rtg-tools-install/rtg.cfg") + #t))) + (replace 'configure + (lambda* (#:key outputs (configure-flags '()) (out-of-source? #t) + build-type target + #:allow-other-keys) + "Configure the given package." + (let* ((out (assoc-ref outputs "out")) + (abs-srcdir (getcwd)) + (srcdir (if out-of-source? + (string-append "../" (basename abs-srcdir)) + "."))) + (format #t "source directory: ~s (relative from build: ~s)~%" + abs-srcdir srcdir) + (when out-of-source? + (mkdir "../build") + + ;; Extra code added here!! + (copy-recursively "external/scratch" "../build/scratch") + (copy-recursively "external/libexec" "../build/libexec") + (copy-recursively "external/lib" "../build/lib") + (copy-recursively "external/bin" "../build/bin") + (copy-recursively "external/include" "../build/include") + + (chdir "../build")) + (format #t "build directory: ~s~%" (getcwd)) + + (let ((args `(,srcdir + ,@(if build-type + (list (string-append "-DCMAKE_BUILD_TYPE=" + build-type)) + '()) + ,(string-append "-DCMAKE_INSTALL_PREFIX=" out) + ;; ensure that the libraries are installed into /lib + "-DCMAKE_INSTALL_LIBDIR=lib" + ;; add input libraries to rpath + "-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=TRUE" + ;; add (other) libraries of the project itself to rpath + ,(string-append "-DCMAKE_INSTALL_RPATH=" out "/lib") + ;; enable verbose output from builds + "-DCMAKE_VERBOSE_MAKEFILE=ON" + + ;; Cross-build + ,@(if target + (list (string-append "-DCMAKE_C_COMPILER=" + target "-gcc") + (string-append "-DCMAKE_CXX_COMPILER=" + target "-g++") + (if (string-contains target "mingw") + + "-DCMAKE_SYSTEM_NAME=Windows" + "-DCMAKE_SYSTEM_NAME=Linux")) + '()) + ,@configure-flags))) + (format #t "running 'cmake' with arguments ~s~%" args) + (apply invoke "cmake" args))))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "./bin/test_haplotypes")) + #t)) + (add-before 'install 'remove-extra-files + (lambda _ + (delete-file "bin/bcftools") + (delete-file "bin/samtools") + (delete-file "bin/test_haplotypes") + (delete-file "lib/libhts.so") + (delete-file "lib/libhts.so.3") + #t)) + (add-after 'install 'wrap-programs + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out")) + (bcftools (assoc-ref inputs "bcftools")) + (samtools (assoc-ref inputs "samtools"))) + (for-each + (lambda (file) + (wrap-script file + `("PYTHONPATH" ":" prefix (,(getenv "PYTHONPATH"))) + `("PATH" ":" prefix (,(string-append bcftools "/bin") + ,(string-append samtools "/bin"))))) + (find-files (string-append out "/bin") "\\.py$")) + #t)))))) + (native-inputs + `(("rtg-tools" + ;; When updating this package also update the insert-rtg-tools phase. + ;; This bundled software is bsd-2 licensed. + ,(origin + (method url-fetch) + (uri (string-append "https://github.com/RealTimeGenomics/rtg-tools" + "/releases/download/3.12.1" + "/rtg-tools-3.12.1-nojre.zip")) + (sha256 + (base32 "1an4axkrj28br09xpj9g0a6k5hrx1cx4wcldrryvj6a0ljqqrz2y")))) + ("unzip" ,unzip))) + (inputs + `(("bcftools" ,bcftools) + ("boost" ,boost-static) ; has to be boost-static + ("guile" ,guile-3.0) ; for wrap-script + ("htslib" ,htslib) + ;; The software specifically states python-2. + ("python" ,python-2) + ("python2-bx-python" ,python2-bx-python) + ("python2-numpy" ,python2-numpy) + ("python2-pandas" ,python2-pandas) + ("python2-pysam" ,python2-pysam) + ("python2-scipy" ,python2-scipy) + ("samtools" ,samtools) + ("zlib" ,zlib))) + (home-page "https://github.com/Illumina/hap.py") + (synopsis "Haplotype VCF comparison tools") + (description + "This is a set of programs based on htslib to benchmark variant calls +against gold standard truth datasets. + +The main two tools are @code{hap.py} (diploid precision/recall evaluation) and +@code{som.py} (somatic precision/recall evaluation -- this ignores the GT and +just checks for presence of alleles). Other tools are @code{qfy.py} (which just +executes the quantification step of the analysis pipeline, this requires a +GA4GH-intermediate VCF file), and @code{pre.py}, which is @code{hap.py}'s input +cleaning and variant normalisation step. + +To run the bundled rtg-tools software you will also need java. The +@code{icedtea:jdk} output should work nicely.") + (license (list license:expat ; bundled jsoncpp, klib + license:bsd-2)))) |