diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 457 |
1 files changed, 312 insertions, 145 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a034bf134e..f2de09aa32 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1656,7 +1656,27 @@ package provides command line tools using the Bio++ library.") ;; Remove useless msbuild directory (delete-file-recursively "c++/src/build-system/project_tree_builder/msbuild") - #t)))) + + ;; Build reproducibly. + ;; Do not record the kernel version + (substitute* "c++/src/build-system/configure" + (("kver=.*") "kver=\"\"")) + ;; Do not generate random numbers. + (substitute* "c++/scripts/common/impl/define_random_macros.sh" + (("#define NCBI_RANDOM_VALUE_MAX 0xffffffffu" m) + (string-append m " +#define NCBI_RANDOM_VALUE_0 2845495105u +#define NCBI_RANDOM_VALUE_1 2158634051u +#define NCBI_RANDOM_VALUE_2 4072202242u +#define NCBI_RANDOM_VALUE_3 902228395u +#define NCBI_RANDOM_VALUE_4 1353323915u +#define NCBI_RANDOM_VALUE_5 574823513u +#define NCBI_RANDOM_VALUE_6 4119501261u +#define NCBI_RANDOM_VALUE_7 2477640938u +#define NCBI_RANDOM_VALUE_8 2776595395u +#define NCBI_RANDOM_VALUE_9 270550684u +")) + (("cksum") "cksum >/dev/null")))))) (build-system gnu-build-system) (arguments `(;; There are two(!) tests for this massive library, and both fail with @@ -2409,26 +2429,27 @@ are not included due to their size.") (define-public cd-hit (package (name "cd-hit") - (version "4.6.8") + (version "4.8.1") (source (origin (method url-fetch) (uri (string-append "https://github.com/weizhongli/cdhit" "/releases/download/V" version "/cd-hit-v" version - "-2017-0621-source.tar.gz")) + "-2019-0228.tar.gz")) (sha256 (base32 - "1b4mwm2520ixjbw57sil20f9iixzw4bkdqqwgg1fc3pzm6rz4zmn")))) + "1phmfhgcpyfd6kj7jwzw976613lcpv1wc2pzfdfaxla062x2s5r6")))) (build-system gnu-build-system) (arguments - `(#:tests? #f ; there are no tests - #:make-flags - ;; Executables are copied directly to the PREFIX. - ,#~(list (string-append "PREFIX=" #$output "/bin") - ;; Support longer sequences (e.g. Pacbio sequences) - "MAX_SEQ=60000000") - #:phases - (modify-phases %standard-phases + (list + #:tests? #f ; there are no tests + #:make-flags + ;; Executables are copied directly to the PREFIX. + #~(list (string-append "PREFIX=" #$output "/bin") + ;; Support longer sequences (e.g. Pacbio sequences) + "MAX_SEQ=60000000") + #:phases + '(modify-phases %standard-phases ;; No "configure" script (delete 'configure) ;; Remove sources of non-determinism @@ -2438,15 +2459,13 @@ are not included due to their size.") ((" \\(built on \" __DATE__ \"\\)") "")) (substitute* "cdhit-common.c++" (("__DATE__") "\"0\"") - (("\", %s, \" __TIME__ \"\\\\n\", date") "")) - #t)) + (("\", %s, \" __TIME__ \"\\\\n\", date") "")))) ;; The "install" target does not create the target directory. (add-before 'install 'create-target-dir (lambda* (#:key outputs #:allow-other-keys) - (mkdir-p (string-append (assoc-ref outputs "out") "/bin")) - #t))))) + (mkdir-p (string-append (assoc-ref outputs "out") "/bin"))))))) (inputs - (list perl)) + (list perl zlib)) (home-page "http://weizhongli-lab.org/cd-hit/") (synopsis "Cluster and compare protein or nucleotide sequences") (description @@ -2457,6 +2476,26 @@ databases.") ;; version 2 (GPLv2)." (license license:gpl2))) +(define-public cd-hit-auxtools + (package + (inherit cd-hit) + (name "cd-hit-auxtools") + (arguments + (list + #:tests? #f ; there are no tests + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'chdir (lambda _ (chdir "cd-hit-auxtools"))) + ;; No "configure" script + (delete 'configure) + ;; There is no install target. + (replace 'install + (lambda _ + (for-each (lambda (file) + (install-file file (string-append #$output "/bin"))) + '("cd-hit-dup" "cd-hit-lap" "read-linker"))))))) + (inputs '()))) + (define-public clipper (package (name "clipper") @@ -4825,7 +4864,7 @@ data.") (define-public kaiju (package (name "kaiju") - (version "1.6.3") + (version "1.9.0") (source (origin (method git-fetch) (uri (git-reference @@ -4834,24 +4873,45 @@ data.") (file-name (git-file-name name version)) (sha256 (base32 - "119pzi0ddzv9mjg4wwa6han0cwr3k3ssn7kirvsjfcq05mi5ka0x")))) + "1hfmadkfs6jjd7l3byly5xxb0ifm3dm1wis11sjbqfcv6l89snmg")))) (build-system gnu-build-system) (arguments - `(#:tests? #f ; There are no tests. - #:phases - (modify-phases %standard-phases - (delete 'configure) - (add-before 'build 'move-to-src-dir - (lambda _ (chdir "src") #t)) - (replace 'install - (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) - (mkdir-p bin) - (chdir "..") - (copy-recursively "bin" bin)) - #t))))) + (list + #:tests? #f ; There are no tests. + #:phases + #~(modify-phases %standard-phases + (delete 'configure) + (add-before 'build 'move-to-src-dir + (lambda _ (chdir "src"))) + (replace 'install + (lambda _ + (let ((bin (string-append #$output "/bin"))) + (mkdir-p bin) + (copy-recursively "../bin" bin) + (let ((path (search-path-as-list '("bin") + '#$(match (package-inputs this-package) + (((_ pkg) ...) pkg))))) + (for-each (lambda (script) + (let ((exe (string-append bin "/" script))) + (chmod exe #o555) + (wrap-script exe + #:guile #$(file-append guile-3.0 "/bin/guile") + `("PATH" ":" prefix ,path)))) + (list "kaiju-convertMAR.py" + "kaiju-gbk2faa.pl" + "kaiju-makedb"))))))))) (inputs - (list perl zlib)) + (list bzip2 + coreutils + curl + gawk + guile-3.0 ;for wrap-script + gzip + perl + python-wrapper + tar + wget + zlib)) (home-page "http://kaiju.binf.ku.dk/") (synopsis "Fast and sensitive taxonomic classification for metagenomics") (description "Kaiju is a program for sensitive taxonomic classification @@ -6236,7 +6296,7 @@ accessed/downloaded on demand across HTTP.") (origin (method url-fetch) (uri (string-append - "http://pngu.mgh.harvard.edu/~purcell/plink/dist/plink-" + "https://zzz.bwh.harvard.edu/plink/dist/plink-" version "-src.zip")) (sha256 (base32 "0as8gxm4pjyc8dxmm1sl873rrd7wn5qs0l29nqfnl31x8i467xaa")) @@ -8444,6 +8504,46 @@ BLAST, KEGG, GenBank, MEDLINE and GO.") ;; (LGPLv2.1+) and scripts in samples (which have GPL2 and GPL2+) (license (list license:ruby license:lgpl2.1+ license:gpl2+ )))) +(define-public centrifuge + (package + (name "centrifuge") + (version "1.0.4") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/DaehwanKimLab/centrifuge.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "167610gbz1rrh6ir3j7jcmhzg3x5msn7x7a3dpv7wmwdndnnqvg0")))) + (build-system gnu-build-system) + (arguments + (list + #:tests? #false ; no check target + #:make-flags + #~(list (string-append "prefix=" #$output)) + #:phases + '(modify-phases %standard-phases + (delete 'configure)))) + (inputs (list python-wrapper)) + (native-inputs + (list pandoc perl ;for documentation + which)) + (home-page "https://github.com/DaehwanKimLab/centrifuge/") + (synopsis "Classifier for metagenomic sequences") + (description "Centrifuge is a microbial classification engine that enables +rapid, accurate and sensitive labeling of reads and quantification of species +on desktop computers. The system uses an indexing scheme based on the +@dfn{Burrows-Wheeler transform} (BWT) and the @dfn{Ferragina-Manzini} (FM) +index, optimized specifically for the metagenomic classification problem. +Centrifuge requires a relatively small index (4.7 GB for all complete +bacterial and viral genomes plus the human genome) and classifies sequences at +very high speed, allowing it to process the millions of reads from a typical +high-throughput DNA sequencing run within a few minutes.") + (license license:gpl3+))) + (define-public bio-vcf (package (name "bio-vcf") @@ -10236,7 +10336,7 @@ The following file formats are supported: (define-public salmon (package (name "salmon") - (version "1.6.0") + (version "1.9.0") (source (origin (method git-fetch) (uri (git-reference @@ -10245,104 +10345,112 @@ The following file formats are supported: (file-name (git-file-name name version)) (sha256 (base32 - "1wb5wl0rc77svbwq6zvak5h7pf9acw3di0vz5i3gqyhg5l6qd736")) + "1370ry3jpj05gplzyny44mqg77a29a6gp8ijmjz135d2igf956r8")) (modules '((guix build utils))) (snippet ;; Delete bundled headers for eigen3. '(delete-file-recursively "include/eigen3/")))) (build-system cmake-build-system) (arguments - `(#:configure-flags - ,#~(list (string-append "-Dlibgff_DIR=" - #$(this-package-input "libgff") "/lib") - "-DCMAKE_CXX_FLAGS=\"-DHAVE_NUMERIC_LIMITS128=1\"" - "-Dlibgff_FOUND=TRUE" - "-DTBB_FOUND=TRUE" - #$(string-append "-DTBB_VERSION=" (package-version tbb-2020)) - "-DTBB_LIBRARIES=tbb -ltbbmalloc" - "-DFETCHED_PUFFERFISH=TRUE" - "-DUSE_SHARED_LIBS=TRUE") + (list + #:configure-flags + #~(list (string-append "-Dlibgff_DIR=" + #$(this-package-input "libgff") "/lib") + "-DCMAKE_CXX_FLAGS=\"-DHAVE_NUMERIC_LIMITS128=1\"" + "-Dlibgff_FOUND=TRUE" + "-DTBB_FOUND=TRUE" + #$(string-append "-DTBB_VERSION=" (package-version tbb)) + "-DFETCHED_PUFFERFISH=TRUE" + "-DUSE_SHARED_LIBS=TRUE") #:phases - (modify-phases %standard-phases - (add-after 'unpack 'prepare-pufferfish - (lambda* (#:key inputs #:allow-other-keys) - (copy-recursively (assoc-ref inputs "pufferfish") - "external/pufferfish") - ;; This test isn't working correctly, so compilation aborts. - (substitute* "external/pufferfish/include/string_view.hpp" - (("#if __has_include\\(<string_view>\\)") - "#if 0")) - (let ((headers "external/install/pufferfish/include/pufferfish") - (source "external/install/src/pufferfish")) - (mkdir-p headers) - (mkdir-p source) - (for-each (lambda (file) - (install-file (string-append "external/pufferfish/include/" file) - headers)) - (list "ProgOpts.hpp" "BooPHF.hpp" "SpinLock.hpp" - "Kmer.hpp" "CanonicalKmer.hpp" "string_view.hpp" - "CanonicalKmerIterator.hpp" - "PufferfishBaseIndex.hpp" - "PufferfishIndex.hpp" - "PufferfishSparseIndex.hpp" - "PufferfishLossyIndex.hpp" - "PufferfishTypes.hpp" - "rank9b.hpp" "rank9sel.hpp" "macros.hpp" - "select.hpp" "Util.hpp" - "PairedAlignmentFormatter.hpp" - "SelectiveAlignmentUtils.hpp" - "PuffAligner.hpp" "MemCollector.hpp" - "MemChainer.hpp" "CommonTypes.hpp" - "SAMWriter.hpp" "PufferfishConfig.hpp" - "BulkChunk.hpp" "BinWriter.hpp")) - (for-each (lambda (dir) - (copy-recursively - (string-append "external/pufferfish/include/" dir) - (string-append headers "/" dir))) - (list "libdivide" - "ksw2pp" - "compact_vector" - "metro" - "chobo" - "sparsepp" - "simde" - "tsl")) - (copy-recursively - (string-append "external/pufferfish/src/metro/") - (string-append source "/metro")) - (install-file - (string-append "external/pufferfish/src/rank9b.cpp") - source) - - ;; Do not complain about not having built libtbb - (substitute* "external/pufferfish/external/twopaco/CMakeLists.txt" - (("add_dependencies.*") ""))))) - (add-after 'unpack 'do-not-phone-home - (lambda _ - (substitute* "src/Salmon.cpp" - (("getVersionMessage\\(\\)") "\"\"")))) - (add-after 'unpack 'use-system-libraries - (lambda* (#:key inputs #:allow-other-keys) - ;; Ensure that all headers can be found - (setenv "CPLUS_INCLUDE_PATH" - (string-append (or (getenv "CPLUS_INCLUDE_PATH") "") - ":" - (getcwd) "/external/install/pufferfish/include:" - (assoc-ref inputs "eigen") - "/include/eigen3")))) - (add-after 'unpack 'fix-error-message-in-tests - (lambda _ - (substitute* "cmake/TestSalmonQuasi.cmake" - (("SALMON_QUASI_INDEX_COMMAND") - "SALMON_QUASI_INDEX_CMD"))))))) + '(modify-phases %standard-phases + (add-after 'unpack 'prepare-pufferfish + (lambda* (#:key inputs #:allow-other-keys) + (copy-recursively (assoc-ref inputs "pufferfish") + "external/pufferfish") + ;; This test isn't working correctly, so compilation aborts. + (substitute* "external/pufferfish/include/string_view.hpp" + (("#if __has_include\\(<string_view>\\)") + "#if 0")) + (let ((headers "external/install/pufferfish/include/pufferfish") + (source "external/install/src/pufferfish")) + (mkdir-p headers) + (mkdir-p source) + (for-each (lambda (file) + (install-file (string-append "external/pufferfish/include/" file) + headers)) + (list "ProgOpts.hpp" "BooPHF.hpp" "SpinLock.hpp" + "Kmer.hpp" "CanonicalKmer.hpp" "string_view.hpp" + "CanonicalKmerIterator.hpp" + "PufferfishBaseIndex.hpp" + "PufferfishIndex.hpp" + "PufferfishSparseIndex.hpp" + "PufferfishLossyIndex.hpp" + "PufferfishTypes.hpp" + "rank9b.hpp" "rank9sel.hpp" "macros.hpp" + "select.hpp" "Util.hpp" + "PairedAlignmentFormatter.hpp" + "SelectiveAlignmentUtils.hpp" + "PuffAligner.hpp" "MemCollector.hpp" + "MemChainer.hpp" "CommonTypes.hpp" + "SAMWriter.hpp" "PufferfishConfig.hpp" + "BulkChunk.hpp" "BinWriter.hpp")) + + (for-each (lambda (dir) + (copy-recursively + (string-append "external/pufferfish/include/" dir) + (string-append headers "/" dir))) + (list "libdivide" + "ksw2pp" + "compact_vector" + "itlib" + "metro" + "chobo" + "sparsepp" + "simde" + "tsl")) + (copy-recursively + (string-append "external/pufferfish/src/metro/") + (string-append source "/metro")) + (install-file + (string-append "external/pufferfish/src/rank9b.cpp") + source) + + ;; Do not complain about not having built libtbb + (substitute* "external/pufferfish/external/twopaco/CMakeLists.txt" + (("add_dependencies.*") ""))))) + (add-after 'unpack 'do-not-phone-home + (lambda _ + (substitute* "src/Salmon.cpp" + (("getVersionMessage\\(\\)") "\"\"")))) + (add-after 'unpack 'use-system-libraries + (lambda* (#:key inputs #:allow-other-keys) + ;; Ensure that all headers can be found + (setenv "CPLUS_INCLUDE_PATH" + (string-append (or (getenv "CPLUS_INCLUDE_PATH") "") + ":" + (getcwd) "/external/install/pufferfish/include:" + (assoc-ref inputs "eigen") + "/include/eigen3")))) + (add-after 'unpack 'fix-error-message-in-tests + (lambda _ + (substitute* "cmake/TestSalmonQuasi.cmake" + (("SALMON_QUASI_INDEX_COMMAND") + "SALMON_QUASI_INDEX_CMD"))))))) (inputs - `(("boost" ,boost) - ("bzip2" ,bzip2) - ("cereal" ,cereal-1.3.0) - ("curl" ,curl) - ("eigen" ,eigen) - ("jemalloc" ,jemalloc) - ("libgff" ,libgff) + (list boost + bzip2 + cereal-1.3.0 + curl + eigen + jemalloc + libgff + tbb + libstadenio-for-salmon + xz + zlib)) + (native-inputs + `(("pkg-config" ,pkg-config) ("pufferfish" ,(origin (method git-fetch) (uri (git-reference @@ -10351,13 +10459,7 @@ The following file formats are supported: (file-name (git-file-name "pufferfish" version)) (sha256 (base32 - "0jakgpbanl6cs23x3g26iab54p7zylcf9v8vc32ps57smp8wql52")))) - ("tbb" ,tbb-2020) - ("libstadenio-for-salmon" ,libstadenio-for-salmon) - ("xz" ,xz) - ("zlib" ,zlib))) - (native-inputs - (list pkg-config)) + "048a006mc2d0h78ym58mv67hl1pj480ilc5ifq0rlzfdyyfs1b8i")))))) (home-page "https://github.com/COMBINE-lab/salmon") (synopsis "Quantification from RNA-seq reads using lightweight alignments") (description "Salmon is a program to produce highly-accurate, @@ -11304,7 +11406,7 @@ based methods.") (define-public pigx-sars-cov-2 (package (name "pigx-sars-cov-2") - (version "0.0.7") + (version "0.0.8") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_sars-cov-2" @@ -11312,24 +11414,51 @@ based methods.") "/pigx_sars-cov-2-" version ".tar.gz")) (sha256 (base32 - "1bqm03ypf7l8lrkjkydxzn7vy0qlps3v9c5cpz2wb008zw44bi3k")))) + "1yf1y25asnhxz80dajs54wrhr0wyi9fldk7lxsnqrh7gpqp2dvcs")))) (build-system gnu-build-system) (arguments - `(#:tests? #f ;requires huge kraken database - #:phases - (modify-phases %standard-phases - (add-before 'bootstrap 'autoreconf - (lambda _ - ;; https://github.com/BIMSBbioinfo/pigx_sars-cov-2/issues/123 - (substitute* "m4/ax_r_package.m4" - (("if\\(is.na\\(packageDescription\\(\"PKG\"\\)\\)\\)") - "if(system.file(package=\"PKG\") == \"\")")) - (invoke "autoreconf" "-vif"))) + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'unpack-databases + (lambda* (#:key inputs #:allow-other-keys) + ;; The tests need to be able to write caches to HOME. + ;; They also default to reading the databases from there. + (setenv "HOME" "/tmp") + ;; Unpack the three databases in the expected location. + (let ((root "/tmp/.local/share/pigx/databases") + (use-underscore (lambda (c) (if (equal? c #\-) #\_ c)))) + (for-each (lambda (db) + (let ((where (string-append root "/" + (string-map use-underscore db)))) + (mkdir-p where) + (invoke "tar" "-C" where + "-xf" (assoc-ref inputs db)))) + '("kraken-db" "krona-db" "vep-db"))))) (add-before 'configure 'set-PYTHONPATH (lambda _ (setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH"))))))) (native-inputs - (list automake autoconf)) + (let ((bimsb-origin + (lambda (name hash) + (origin + (method url-fetch) + (uri + (string-append "https://bimsbstatic.mdc-berlin.de/akalin/AAkalin_pathogenomics" + "/databases_small-20221006/" name)) + (sha256 (base32 hash)))))) + `(("kraken-db" + ,(bimsb-origin + "kraken_db.tar.gz" + "0sdm4xh5npg6c3y2pz8xgphim4qpglm8wdid6rlaaqsn6iikv0mz")) + ("krona-db" + ,(bimsb-origin + "krona_db.tar.gz" + "1rwy4gd3vw1gdjldrgf44c1xaa3vq8i3pgisjhrac81yx63x8f2h")) + ("vep-db" + ,(bimsb-origin + "vep_db.tar.gz" + "0d8hhi43zsw3wqm7gd0z0gpcdsc6h6ra0imn87hifl9a64jxqzxz"))))) (inputs (list bash-minimal bedtools @@ -11345,10 +11474,16 @@ based methods.") python-pyyaml python-wrapper r-base64url + r-data-table + r-deconvr r-dplyr r-dt r-ggplot2 + r-htmltools + r-jsonlite + r-knitr r-magrittr + r-mass r-minimal r-plotly r-qpcr @@ -16229,6 +16364,38 @@ BigWig files, as well as efficient region coverage summary over intervals from both types of files.") (license license:expat))) +(define-public megahit + (package + (name "megahit") + (version "1.2.9") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/voutcn/megahit.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1r5d9nkdmgjsbrpj43q9hy3s8jwsabaz3ji561v18hy47v58923c")))) + (build-system cmake-build-system) + (arguments + (list + #:test-target "simple_test" + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'fix-tests + (lambda _ + (substitute* "src/megahit" + (("os.path.join\\(script_path, '..'\\)") + "os.path.join(script_path, '../source')"))))))) + (inputs (list python-wrapper zlib)) + (home-page "https://www.ncbi.nlm.nih.gov/pubmed/25609793") + (synopsis "Meta-genome assembler") + (description "Megahit is a fast and memory-efficient NGS assembler. It is +optimized for metagenomes, but also works well on generic single genome +assembly (small or mammalian size) and single-cell assembly.") + (license license:gpl3))) + (define-public mudskipper (package (name "mudskipper") |