aboutsummaryrefslogtreecommitdiff
path: root/gnu/packages/bioinformatics.scm
diff options
context:
space:
mode:
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
-rw-r--r--gnu/packages/bioinformatics.scm306
1 files changed, 134 insertions, 172 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 02cafb2358..5dc3945035 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -12,6 +12,7 @@
;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com>
;;; Copyright © 2018 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
+;;; Copyright © 2019 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -612,16 +613,22 @@ intended to behave exactly the same as the original BWK awk.")
(define-public python-pybedtools
(package
(name "python-pybedtools")
- (version "0.7.10")
+ (version "0.8.0")
(source (origin
(method url-fetch)
(uri (pypi-uri "pybedtools" version))
(sha256
(base32
- "0l2b2wrnj85azfqgr0zwr60f7j58vlla1hcgxvr9rwikpl8j72ji"))))
+ "1xl454ijvd4dzfvqgfahad49b49j7qy710fq9xh1rvk42z6x5ssf"))))
(build-system python-build-system)
(arguments
- `(#:phases
+ `(#:modules ((ice-9 ftw)
+ (srfi srfi-1)
+ (srfi srfi-26)
+ (guix build utils)
+ (guix build python-build-system))
+ ;; See https://github.com/daler/pybedtools/issues/192
+ #:phases
(modify-phases %standard-phases
;; See https://github.com/daler/pybedtools/issues/261
(add-after 'unpack 'disable-broken-tests
@@ -631,21 +638,59 @@ intended to behave exactly the same as the original BWK awk.")
(substitute* "pybedtools/test/test_scripts.py"
(("def test_venn_mpl")
"def _do_not_test_venn_mpl"))
- ;; Requires internet access.
(substitute* "pybedtools/test/test_helpers.py"
+ ;; Requires internet access.
(("def test_chromsizes")
- "def _do_not_test_chromsizes"))
- ;; FIXME: these two fail for no good reason.
- (substitute* "pybedtools/test/test1.py"
- (("def test_issue_157")
- "def _do_not_test_issue_157")
- (("def test_to_dataframe")
- "def _do_not_test_to_dataframe"))
- #t)))))
- (propagated-inputs
- ;; Tests don't pass with Bedtools 2.27.1.
- ;; See https://github.com/daler/pybedtools/issues/260
- `(("bedtools" ,bedtools-2.26)
+ "def _do_not_test_chromsizes")
+ ;; Broken as a result of the workaround used in the check phase
+ ;; (see: https://github.com/daler/pybedtools/issues/192).
+ (("def test_getting_example_beds")
+ "def _do_not_test_getting_example_beds"))
+ #t))
+ ;; TODO: Remove phase after it's part of PYTHON-BUILD-SYSTEM.
+ ;; build system.
+ ;; Force the Cythonization of C++ files to guard against compilation
+ ;; problems.
+ (add-after 'unpack 'remove-cython-generated-files
+ (lambda _
+ (let ((cython-sources (map (cut string-drop-right <> 4)
+ (find-files "." "\\.pyx$")))
+ (c/c++-files (find-files "." "\\.(c|cpp|cxx)$")))
+ (define (strip-extension filename)
+ (string-take filename (string-index-right filename #\.)))
+ (define (cythonized? c/c++-file)
+ (member (strip-extension c/c++-file) cython-sources))
+ (for-each delete-file (filter cythonized? c/c++-files))
+ #t)))
+ (add-after 'remove-cython-generated-files 'generate-cython-extensions
+ (lambda _
+ (invoke "python" "setup.py" "cythonize")))
+ (replace 'check
+ (lambda _
+ (let* ((cwd (getcwd))
+ (build-root-directory (string-append cwd "/build/"))
+ (build (string-append
+ build-root-directory
+ (find (cut string-prefix? "lib" <>)
+ (scandir (string-append
+ build-root-directory)))))
+ (scripts (string-append
+ build-root-directory
+ (find (cut string-prefix? "scripts" <>)
+ (scandir build-root-directory)))))
+ (setenv "PYTHONPATH"
+ (string-append build ":" (getenv "PYTHONPATH")))
+ ;; Executable scripts such as 'intron_exon_reads.py' must be
+ ;; available in the PATH.
+ (setenv "PATH"
+ (string-append scripts ":" (getenv "PATH"))))
+ ;; The tests need to be run from elsewhere...
+ (mkdir-p "/tmp/test")
+ (copy-recursively "pybedtools/test" "/tmp/test")
+ (with-directory-excursion "/tmp/test"
+ (invoke "pytest")))))))
+ (propagated-inputs
+ `(("bedtools" ,bedtools)
("samtools" ,samtools)
("python-matplotlib" ,python-matplotlib)
("python-pysam" ,python-pysam)
@@ -654,9 +699,11 @@ intended to behave exactly the same as the original BWK awk.")
`(("python-numpy" ,python-numpy)
("python-pandas" ,python-pandas)
("python-cython" ,python-cython)
- ("python-nose" ,python-nose)
- ("kentutils" ,kentutils) ; for bedGraphToBigWig
- ("python-six" ,python-six)))
+ ("kentutils" ,kentutils) ; for bedGraphToBigWig
+ ("python-six" ,python-six)
+ ;; For the test suite.
+ ("python-pytest" ,python-pytest)
+ ("python-psutil" ,python-psutil)))
(home-page "https://pythonhosted.org/pybedtools/")
(synopsis "Python wrapper for BEDtools programs")
(description
@@ -667,34 +714,7 @@ Python.")
(license license:gpl2+)))
(define-public python2-pybedtools
- (let ((pkg (package-with-python2 python-pybedtools)))
- (package (inherit pkg)
- (arguments
- `(#:modules ((ice-9 ftw)
- (srfi srfi-1)
- (srfi srfi-26)
- (guix build utils)
- (guix build python-build-system))
- ;; See https://github.com/daler/pybedtools/issues/192
- ,@(substitute-keyword-arguments (package-arguments pkg)
- ((#:phases phases)
- `(modify-phases ,phases
- (replace 'check
- (lambda _
- (let ((cwd (getcwd)))
- (setenv "PYTHONPATH"
- (string-append cwd "/build/"
- (find (cut string-prefix? "lib" <>)
- (scandir (string-append cwd "/build")))
- ":" (getenv "PYTHONPATH"))))
- ;; The tests need to be run from elsewhere...
- (mkdir-p "/tmp/test")
- (copy-recursively "pybedtools/test" "/tmp/test")
- (with-directory-excursion "/tmp/test"
- (invoke "nosetests"
- ;; This test fails for unknown reasons
- "--exclude=.*test_getting_example_beds"))
- #t))))))))))
+ (package-with-python2 python-pybedtools))
(define-public python-biom-format
(package
@@ -4345,130 +4365,6 @@ interrupted by stop codons. OrfM finds and prints these ORFs.")
(home-page "https://github.com/wwood/OrfM")
(license license:lgpl3+)))
-(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
- `(#:ocaml ,ocaml-4.01
- #:findlib ,ocaml4.01-findlib
- #:modules ((guix build ocaml-build-system)
- (guix build utils)
- (ice-9 ftw))
- #:phases
- (modify-phases %standard-phases
- (delete 'configure)
- (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)))))
- (native-inputs
- `(("zlib" ,zlib)
- ("gsl" ,gsl)
- ("ocaml-ounit" ,ocaml4.01-ounit)
- ("ocaml-batteries" ,ocaml4.01-batteries)
- ("ocaml-camlzip" ,ocaml4.01-camlzip)
- ("ocaml-csv" ,ocaml4.01-csv)
- ("ocaml-sqlite3" ,ocaml4.01-sqlite3)
- ("ocaml-xmlm" ,ocaml4.01-xmlm)
- ("ocaml-mcl" ,ocaml4.01-mcl)
- ("ocaml-gsl" ,ocaml4.01-gsl)
- ("cddlib-src" ,(package-source cddlib))))
- (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-pbcore
(package
(name "python2-pbcore")
@@ -11172,7 +11068,7 @@ droplet sequencing. It has been particularly tailored for Drop-seq.")
(native-inputs
`(("ldc" ,ldc)
("rdmd" ,rdmd)
- ("python" ,python-minimal)
+ ("python" ,python)
("biod"
,(let ((commit "4f1a7d2fb7ef3dfe962aa357d672f354ebfbe42e"))
(origin
@@ -14441,3 +14337,69 @@ Nanopolish can calculate an improved consensus sequence for a draft genome
assembly, detect base modifications, call SNPs (Single nucleotide
polymorphisms) and indels with respect to a reference genome and more.")
(license license:expat))))
+
+(define-public cnvkit
+ (package
+ (name "cnvkit")
+ (version "0.9.5")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/etal/cnvkit.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0g2f78k68yglmj4fsfmgs8idqv3di9aj53fg0ld0hqljg8chhh82"))))
+ (build-system python-build-system)
+ (propagated-inputs
+ `(("python-biopython" ,python-biopython)
+ ("python-future" ,python-future)
+ ("python-matplotlib" ,python-matplotlib)
+ ("python-numpy" ,python-numpy)
+ ("python-reportlab" ,python-reportlab)
+ ("python-pandas" ,python-pandas)
+ ("python-pysam" ,python-pysam)
+ ("python-pyfaidx" ,python-pyfaidx)
+ ("python-scipy" ,python-scipy)
+ ;; R packages
+ ("r-dnacopy" ,r-dnacopy)))
+ (home-page "https://cnvkit.readthedocs.org/")
+ (synopsis "Copy number variant detection from targeted DNA sequencing")
+ (description
+ "CNVkit is a Python library and command-line software toolkit to infer
+and visualize copy number from high-throughput DNA sequencing data. It is
+designed for use with hybrid capture, including both whole-exome and custom
+target panels, and short-read sequencing platforms such as Illumina and Ion
+Torrent.")
+ (license license:asl2.0)))
+
+(define-public python-pyfit-sne
+ (package
+ (name "python-pyfit-sne")
+ (version "1.0.1")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/KlugerLab/pyFIt-SNE.git")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "13wh3qkzs56azmmgnxib6xfr29g7xh09sxylzjpni5j0pp0rc5qw"))))
+ (build-system python-build-system)
+ (propagated-inputs
+ `(("python-numpy" ,python-numpy)))
+ (inputs
+ `(("fftw" ,fftw)))
+ (native-inputs
+ `(("python-cython" ,python-cython)))
+ (home-page "https://github.com/KlugerLab/pyFIt-SNE")
+ (synopsis "FFT-accelerated Interpolation-based t-SNE")
+ (description
+ "t-Stochastic Neighborhood Embedding (t-SNE) is a highly successful
+method for dimensionality reduction and visualization of high dimensional
+datasets. A popular implementation of t-SNE uses the Barnes-Hut algorithm to
+approximate the gradient at each iteration of gradient descent. This package
+is a Cython wrapper for FIt-SNE.")
+ (license license:bsd-4)))
generated by cgit v1.2.3 (git 2.45.0) at 2024-11-20 06:01:18 +0000