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-rw-r--r--gnu/packages/bioinformatics.scm193
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+)))
generated by cgit v1.2.3 (git 2.25.4) at 2024-07-09 23:03:23 +0000