diff options
| -rw-r--r-- | gn/packages/bioinformatics.scm | 199 |
1 files changed, 199 insertions, 0 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index a362b73..dc1ff65 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -45,6 +45,7 @@ #:use-module (gnu packages guile) #:use-module (gnu packages image) #:use-module (gnu packages imagemagick) + #:use-module (gnu packages java) #:use-module (gnu packages jemalloc) #:use-module (gnu packages linux) #:use-module (gnu packages machine-learning) @@ -2600,3 +2601,201 @@ protein alignments and syntenic genomic alignments.") (license (license:non-copyleft "https://opensource.org/licenses/artistic-license-1.0" "Artistic-license-1.0")))) + +(define-public sepp + (package + (name "sepp") + (version "4.5.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/smirarab/sepp") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1bw5gjhymq0a4slkk7pr5dl4jb9bnwv4qpn26mvwp8fx3aszvmij")) + (modules '((guix build utils))) + (snippet + '(begin + (delete-file-recursively "tools/bundled") + (mkdir-p "tools/bundled/Linux") + (for-each (lambda (file) + (with-output-to-file + (string-append "tools/bundled/Linux/" file) + (lambda _ + (format #t "")))) + '("guppy-32" "guppy-64" + "hmmalign-32" "hmmalign-64" + "hmmbuild-32" "hmmbuild-64" + "hmmsearch-32" "hmmsearch-64" + "pplacer-32" "pplacer-64")) + ;; TODO: Rebuild java blob. + ;(delete-file-recursively "tools/merge/lib") + ;(delete-file "tools/merge/seppJsonMerger.jar") + ;; This is a circular reference to the top directory ... + (delete-file-recursively "sepp-package/sepp"))))) + (build-system python-build-system) + (arguments + `(#:tests? #f ; Test suite hangs. + #:phases + (modify-phases %standard-phases + (add-before 'check 'pre-check + (lambda* (#:key tests? inputs outputs #:allow-other-keys) + (let ((hmmer (string-append (assoc-ref inputs "hmmer") "/bin/")) + (pplacer (string-append (assoc-ref inputs "pplacer") "/bin/")) + (tools "tools/bundled/Linux/")) + (for-each + (lambda (target package) + (delete-file (string-append tools target)) + (symlink (string-append package (string-drop-right target 3)) + (string-append tools target))) + (list "guppy-32" "guppy-64" + "hmmalign-32" "hmmalign-64" + "hmmbuild-32" "hmmbuild-64" + "hmmsearch-32" "hmmsearch-64" + "pplacer-32" "pplacer-64") + (list pplacer pplacer + hmmer hmmer + hmmer hmmer + hmmer hmmer + pplacer pplacer)) + #t))) + (replace 'check + (lambda* (#:key tests? inputs outputs #:allow-other-keys) + (when tests? + (add-installed-pythonpath inputs outputs) + ;; This test is upset we removed the Darwin binary. + (delete-file "test/unittest/testConfig.py") + ;; This test is missing its config file. + (delete-file "test/unittest/testUPP.py") + (invoke "nosetests" "-w" "test/unittest")))) + (replace 'build + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (home.path (string-append out "/share/sepp"))) + (setenv "HOME" home.path) + (mkdir-p (string-append home.path "/.sepp")) + ;; configure with '-c' so our pretend bundled + ;; libraries aren't actually installed. + (invoke "python" "setup.py" "config" "-c") + #t))) + (add-after 'install 'copy-home.path + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (home.path (string-append out "/share/sepp"))) + (with-output-to-file (string-append out "/home.path") + (lambda _ + (format #t "~a/.sepp" + home.path))) + (with-output-to-file (string-append home.path "/.sepp/main.config") + (lambda _ + (format #t "[pplacer]~@ + path=~a/bin/pplacer~@ + ~@ + [hmmalign]~@ + path=~a/bin/hmmalign~@ + ~@ + [hmmsearch]~@ + path=~a/bin/hmmsearch~@ + piped=False~@ + elim=10000~@ + filters=True~@ + ~@ + [hmmbuild]~@ + path=~a/bin/hmmbuild~@ + ~@ + [jsonmerger]~@ + path=~a/share/sepp/seppJsonMerger.jar~@ + ~@ + [exhaustive]~@ + strategy = centroid~@ + minsubsetsize = 2~@ + placementminsubsetsizefacotr = 4~@ + placer = pplacer~@ + weight_placement_by_alignment = True~%" + (assoc-ref inputs "pplacer") + (assoc-ref inputs "hmmer") + (assoc-ref inputs "hmmer") + (assoc-ref inputs "hmmer") + out))) + (install-file "tools/merge/seppJsonMerger.jar" + home.path) + (copy-file (string-append out "/home.path") + (string-append (site-packages inputs outputs) "/home.path")) + #t)))))) + (inputs + `(("hmmer" ,hmmer) + ("java" ,icedtea-8) + ("pplacer" ,pplacer) + ("python-dendropy" ,python-dendropy))) + (native-inputs + `(("python-nose" ,python-nose))) + (home-page "https://github.com/smirarab/sepp") + (synopsis "SATe enabled phylogenetic placement") + (description "SEPP operates by using a divide-and-conquer strategy adopted +from SATe-II (@url{Liu et al. (Systematic Biology 2012), +http://sysbio.oxfordjournals.org/content/61/1/90.full.pdf+html?sid=dd32838d-89dc-4bda-8008-6f948146341f} +and @url{Liu et. al. (Science 2009), +http://www.sciencemag.org/content/324/5934/1561.abstract}) to construct an +Ensemble of @acronym{HMMs, Hidden Markov Models} to represent the input +multiple sequence alignment `A`. It then computes the fit of each query +sequence in `X` to each HMM in the ensemble, and uses the highest scoring HMM to +add the sequence to the input tree `T`. This technique improves the accuracy of +the placements of the query sequences compared to using a single HMM to +represent the input alignment. SEPP uses tools in HMMER to construct HMMs, +compute the fit of sequences to HMMs, and add sequences to the alignment `A`. +SEPP uses @code{pplacer} to add query sequences to the input tree `T`, after +they are added to the alignment `A`. SEPP is also used in other software, +including @acronym{TIPP, taxonomic identical using phylogenetic placement} and +@acronym{UPP, ultra-large alignments using phylogeny-aware profiles}.") + (license license:gpl3+))) + +(define-public busco + (package + (name "busco") + (version "5.2.2") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.com/ezlab/busco") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0l5bxg5311svfszqysd5dkakq7zsdgrv9a1iiwjsvjdz66f7db1p")))) + (build-system python-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda* (#:key inputs outputs tests? #:allow-other-keys) + (when tests? + (begin (add-installed-pythonpath inputs outputs) + (invoke "python" "setup.py" "check"))))) + (add-after 'install 'wrap-binary + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (wrap-program (string-append out "/bin/busco") + `("PATH" ":" prefix + (,(string-append (assoc-ref inputs "augustus") "/bin") + ,(string-append (assoc-ref inputs "blast") "/bin") + ,(string-append (assoc-ref inputs "hmmer") "/bin") + ,(string-append (assoc-ref inputs "metaeuk") "/bin") + ,(string-append (assoc-ref inputs "prodigal") "/bin") + ,(string-append (assoc-ref inputs "r") "/bin") + ,(string-append (assoc-ref inputs "sepp") "/bin")))) + #t)))))) + (inputs + `(("augustus" ,augustus) + ("blast" ,blast+) + ("hmmer" ,hmmer) + ("metaeuk" ,metaeuk) + ("prodigal" ,prodigal) + ("python-biopython" ,python-biopython) + ("python-pandas" ,python-pandas) + ("r" ,r) + ("sepp" ,sepp))) + (home-page "https://busco.ezlab.org/") + (synopsis "Assess genome assembly and annotation completeness") + (description "Assess genome assembly and annotation completeness with +Benchmarking Universal Single-Copy Orthologs.") + (license license:expat))) |