diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 99 |
1 files changed, 94 insertions, 5 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f90a0bf90c..32b795948b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -79,6 +79,7 @@ #:use-module (gnu packages golang) #:use-module (gnu packages glib) #:use-module (gnu packages graph) + #:use-module (gnu packages graphviz) #:use-module (gnu packages groff) #:use-module (gnu packages gtk) #:use-module (gnu packages guile) @@ -4942,14 +4943,24 @@ files and writing bioinformatics applications.") "1agfz6zqa8nc6cw47yh0s3y14gkpa9wqazwcj7mwwj3ffnw39p3j")))) (build-system python-build-system) (arguments - `(#:python ,python-2)) ; requires Python 2.7 + `(#:python ,python-2 ; requires Python 2.7 + #:tests? #f ; test data are not included + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'use-weave + (lambda _ + (substitute* "warpedlmm/util/linalg.py" + (("from scipy import linalg, weave") + "from scipy import linalg\nimport weave")) + #t))))) (propagated-inputs `(("python-scipy" ,python2-scipy) ("python-numpy" ,python2-numpy) ("python-matplotlib" ,python2-matplotlib) ("python-fastlmm" ,python2-fastlmm) ("python-pandas" ,python2-pandas) - ("python-pysnptools" ,python2-pysnptools))) + ("python-pysnptools" ,python2-pysnptools) + ("python-weave" ,python2-weave))) (native-inputs `(("python-mock" ,python2-mock) ("python-nose" ,python2-nose) @@ -11984,7 +11995,8 @@ dependency like SeqAn.") ;; Ensure that Eigen headers can be found (setenv "CPLUS_INCLUDE_PATH" (string-append (assoc-ref inputs "eigen") - "/include/eigen3")) + "/include/eigen3:" + (or (getenv "CPLUS_INCLUDE_PATH") ""))) #t))))) (inputs `(("boost" ,boost) @@ -12162,8 +12174,8 @@ The following file formats are supported: (("lib/libdivsufsort.a") "/lib/libdivsufsort.so")) ;; Ensure that all headers can be found - (setenv "CPATH" - (string-append (getenv "CPATH") + (setenv "CPLUS_INCLUDE_PATH" + (string-append (or (getenv "CPLUS_INCLUDE_PATH") "") ":" (assoc-ref inputs "eigen") "/include/eigen3")) @@ -13302,6 +13314,42 @@ cases include: @end enumerate\n") (license license:expat))) +(define-public miniasm + (package + (name "miniasm") + (version "0.3") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/lh3/miniasm/archive/v" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0g89pa98dvh34idv7w1zv12bsbyr3a11c4qb1cdcz68gyda88s4v")))) + (build-system gnu-build-system) + (inputs + `(("zlib" ,zlib))) + (arguments + `(#:tests? #f ; There are no tests. + #:phases + (modify-phases %standard-phases + (delete 'configure) + (replace 'install + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) + (install-file "miniasm" bin) + (install-file "minidot" bin))))))) + (home-page "https://github.com/lh3/miniasm") + (synopsis "Ultrafast de novo assembly for long noisy reads") + (description "Miniasm is a very fast OLC-based de novo assembler for noisy +long reads. It takes all-vs-all read self-mappings (typically by minimap) as +input and outputs an assembly graph in the GFA format. Different from +mainstream assemblers, miniasm does not have a consensus step. It simply +concatenates pieces of read sequences to generate the final unitig sequences. +Thus the per-base error rate is similar to the raw input reads.") + (license license:expat))) + (define-public r-circus (package (name "r-circus") @@ -15807,3 +15855,44 @@ biological processes. SBML is useful for models of metabolism, cell signaling, and more. It continues to be evolved and expanded by an international community.") (license license:lgpl2.1+))) + +(define-public grocsvs + ;; The last release is out of date and new features have been added. + (let ((commit "ecd956a65093a0b2c41849050e4512d46fecea5d") + (revision "1")) + (package + (name "grocsvs") + (version (git-version "0.2.6.1" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/grocsvs/grocsvs") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "14505725gr7qxc17cxxf0k6lzcwmgi64pija4mwf29aw70qn35cc")) + (patches (search-patches "grocsvs-dont-use-admiral.patch")))) + (build-system python-build-system) + (arguments + `(#:tests? #f ; No test suite. + #:python ,python-2)) ; Only python-2 supported. + (inputs + `(("python2-h5py" ,python2-h5py) + ("python2-ipython-cluster-helper" ,python2-ipython-cluster-helper) + ("python2-networkx" ,python2-networkx) + ("python2-psutil" ,python2-psutil) + ("python2-pandas" ,python2-pandas) + ("python2-pybedtools" ,python2-pybedtools) + ("python2-pyfaidx" ,python2-pyfaidx) + ("python2-pygraphviz" ,python2-pygraphviz) + ("python2-pysam" ,python2-pysam) + ("python2-scipy" ,python2-scipy))) + (home-page "https://github.com/grocsvs/grocsvs") + (synopsis "Genome-wide reconstruction of complex structural variants") + (description + "@dfn{Genome-wide Reconstruction of Complex Structural Variants} +(GROC-SVs) is a software pipeline for identifying large-scale structural +variants, performing sequence assembly at the breakpoints, and reconstructing +the complex structural variants using the long-fragment information from the +10x Genomics platform.") + (license license:expat)))) |