diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 193 |
1 files changed, 191 insertions, 2 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4cd032abd4..dc5d84653c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7916,13 +7916,13 @@ as well as query and modify the browser state, such as the current viewport.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.34.7") + (version "1.34.8") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "100y8cx9xfglbn36k25y09y0qfwm0qpb4b01qhk367832rqz5dhz")))) + "1sxp86hdsg32l2c85jgic65gy92d8kxsm01264hrx6yikdhicjax")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) @@ -14555,3 +14555,192 @@ overlapping paired-ended reads into (longer) consensus sequences. Additionally, the AdapterRemoval may be used to recover a consensus adapter sequence for paired-ended data, for which this information is not available.") (license license:gpl3+))) + +(define-public pplacer + (let ((commit "807f6f3")) + (package + (name "pplacer") + ;; The commit should be updated with each version change. + (version "1.1.alpha19") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/matsen/pplacer.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "11ppbbbx20p2g9wj3ff64dhnarb12q79v7qh4rk0gj6lkbz4n7cn")))) + (build-system ocaml-build-system) + (arguments + `(#:modules ((guix build ocaml-build-system) + (guix build utils) + (ice-9 ftw)) + #:phases + (modify-phases %standard-phases + (delete 'configure) + (add-after 'unpack 'fix-build-with-latest-ocaml + (lambda _ + (substitute* "myocamlbuild.ml" + (("dep \\[\"c_pam\"\\]" m) + (string-append "flag [\"ocaml\"; \"compile\"] (A \"-unsafe-string\");\n" + m)) + (("let run_and_read" m) + (string-append " +let split s ch = + let x = ref [] in + let rec go s = + let pos = String.index s ch in + x := (String.before s pos)::!x; + go (String.after s (pos + 1)) + in + try go s + with Not_found -> !x +let split_nl s = split s '\\n' +let before_space s = + try String.before s (String.index s ' ') + with Not_found -> s + +" m)) + (("run_and_read \"ocamlfind list \\| cut -d' ' -f1\"" m) + (string-append "List.map before_space (split_nl & " m ")")) + ((" blank_sep_strings &") "") + ((" Lexing.from_string &") "")) + #t)) + (add-after 'unpack 'replace-bundled-cddlib + (lambda* (#:key inputs #:allow-other-keys) + (let* ((cddlib-src (assoc-ref inputs "cddlib-src")) + (local-dir "cddlib_guix")) + (mkdir local-dir) + (with-directory-excursion local-dir + (invoke "tar" "xvf" cddlib-src)) + (let ((cddlib-src-folder + (string-append local-dir "/" + (list-ref (scandir local-dir) 2) + "/lib-src"))) + (for-each make-file-writable (find-files "cdd_src" ".*")) + (for-each + (lambda (file) + (copy-file file + (string-append "cdd_src/" (basename file)))) + (find-files cddlib-src-folder ".*[ch]$"))) + #t))) + (add-after 'unpack 'fix-makefile + (lambda _ + ;; Remove system calls to 'git'. + (substitute* "Makefile" + (("^DESCRIPT:=pplacer-.*") + (string-append + "DESCRIPT:=pplacer-$(shell uname)-v" ,version "\n"))) + (substitute* "myocamlbuild.ml" + (("git describe --tags --long .*\\\" with") + (string-append + "echo -n v" ,version "-" ,commit "\" with"))) + #t)) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin"))) + (copy-recursively "bin" bin)) + #t))))) + (inputs + `(("zlib" ,zlib "static") + ("gsl" ,gsl) + ("ocaml-ounit" ,ocaml-ounit) + ("ocaml-batteries" ,ocaml-batteries) + ("ocaml-camlzip" ,camlzip) + ("ocaml-csv" ,ocaml-csv) + ("ocaml-sqlite3" ,ocaml-sqlite3) + ("ocaml-xmlm" ,ocaml-xmlm) + ("ocaml-mcl" ,ocaml-mcl) + ("ocaml-gsl" ,ocaml-gsl-1))) + (native-inputs + `(("cddlib-src" ,(package-source cddlib)) + ("ocamlbuild" ,ocamlbuild) + ("pkg-config" ,pkg-config))) + (propagated-inputs + `(("pplacer-scripts" ,pplacer-scripts))) + (synopsis "Phylogenetic placement of biological sequences") + (description + "Pplacer places query sequences on a fixed reference phylogenetic tree +to maximize phylogenetic likelihood or posterior probability according to a +reference alignment. Pplacer is designed to be fast, to give useful +information about uncertainty, and to offer advanced visualization and +downstream analysis.") + (home-page "http://matsen.fhcrc.org/pplacer") + (license license:gpl3)))) + +;; This package is installed alongside 'pplacer'. It is a separate package so +;; that it can use the python-build-system for the scripts that are +;; distributed alongside the main OCaml binaries. +(define pplacer-scripts + (package + (inherit pplacer) + (name "pplacer-scripts") + (build-system python-build-system) + (arguments + `(#:python ,python-2 + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'enter-scripts-dir + (lambda _ (chdir "scripts") #t)) + (replace 'check + (lambda _ (invoke "python" "-m" "unittest" "discover" "-v") #t)) + (add-after 'install 'wrap-executables + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin"))) + (let ((path (string-append + (assoc-ref inputs "hmmer") "/bin:" + (assoc-ref inputs "infernal") "/bin"))) + (display path) + (wrap-program (string-append bin "/refpkg_align.py") + `("PATH" ":" prefix (,path)))) + (let ((path (string-append + (assoc-ref inputs "hmmer") "/bin"))) + (wrap-program (string-append bin "/hrefpkg_query.py") + `("PATH" ":" prefix (,path))))) + #t))))) + (inputs + `(("infernal" ,infernal) + ("hmmer" ,hmmer))) + (propagated-inputs + `(("python-biopython" ,python2-biopython) + ("taxtastic" ,taxtastic))) + (synopsis "Pplacer Python scripts"))) + +(define-public python2-checkm-genome + (package + (name "python2-checkm-genome") + (version "1.0.13") + (source + (origin + (method url-fetch) + (uri (pypi-uri "checkm-genome" version)) + (sha256 + (base32 + "0bm8gpxjmzxsxxl8lzwqhgx8g1dlnmp6znz7wv3hgb0gdjbf9dzz")))) + (build-system python-build-system) + (arguments + `(#:python ,python-2 + #:tests? #f)) ; some tests are interactive + (propagated-inputs + `(("python-dendropy" ,python2-dendropy) + ("python-matplotlib" ,python2-matplotlib) + ("python-numpy" ,python2-numpy) + ("python-pysam" ,python2-pysam) + ("python-scipy" ,python2-scipy))) + (home-page "http://pypi.python.org/pypi/checkm/") + (synopsis "Assess the quality of putative genome bins") + (description + "CheckM provides a set of tools for assessing the quality of genomes +recovered from isolates, single cells, or metagenomes. It provides robust +estimates of genome completeness and contamination by using collocated sets of +genes that are ubiquitous and single-copy within a phylogenetic lineage. +Assessment of genome quality can also be examined using plots depicting key +genomic characteristics (e.g., GC, coding density) which highlight sequences +outside the expected distributions of a typical genome. CheckM also provides +tools for identifying genome bins that are likely candidates for merging based +on marker set compatibility, similarity in genomic characteristics, and +proximity within a reference genome.") + (license license:gpl3+))) |