diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 180 |
1 files changed, 172 insertions, 8 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b9d641ec34..3db67f5427 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -50,6 +50,7 @@ #:use-module (gnu packages cpio) #:use-module (gnu packages curl) #:use-module (gnu packages documentation) + #:use-module (gnu packages databases) #:use-module (gnu packages datastructures) #:use-module (gnu packages file) #:use-module (gnu packages flex) @@ -84,6 +85,7 @@ #:use-module (gnu packages readline) #:use-module (gnu packages ruby) #:use-module (gnu packages serialization) + #:use-module (gnu packages shells) #:use-module (gnu packages statistics) #:use-module (gnu packages swig) #:use-module (gnu packages tbb) @@ -96,7 +98,6 @@ #:use-module (gnu packages web) #:use-module (gnu packages xml) #:use-module (gnu packages xorg) - #:use-module (gnu packages zip) #:use-module (srfi srfi-1) #:use-module (srfi srfi-26)) @@ -1384,15 +1385,13 @@ well as many of the command line options.") (define-public python2-bx-python (package (name "python2-bx-python") - (version "0.7.2") + (version "0.7.3") (source (origin (method url-fetch) - (uri (string-append - "https://pypi.python.org/packages/source/b/bx-python/bx-python-" - version ".tar.gz")) + (uri (pypi-uri "bx-python" version)) (sha256 (base32 - "0ld49idhc5zjdvbhvjq1a2qmpjj7h5v58rqr25dzmfq7g34b50xh")) + "15z2w3bvnc0n4qmb9bd6d8ylc2h2nj883x2w9iixf4x3vki9b22i")) (modules '((guix build utils))) (snippet '(substitute* "setup.py" @@ -3697,7 +3696,7 @@ trimming, pruning, condensing, drawing (ASCII graphics or SVG).") (define-public orfm (package (name "orfm") - (version "0.6.1") + (version "0.7.1") (source (origin (method url-fetch) (uri (string-append @@ -3705,7 +3704,7 @@ trimming, pruning, condensing, drawing (ASCII graphics or SVG).") version "/orfm-" version ".tar.gz")) (sha256 (base32 - "19hwp13n82isdvk16710l9m35cmzf0q3fsrcn3r8c5r67biiz39s")))) + "16iigyr2gd8x0imzkk1dr3k5xsds9bpmwg31ayvjg0f4pir9rwqr")))) (build-system gnu-build-system) (inputs `(("zlib" ,zlib))) (native-inputs @@ -9540,3 +9539,168 @@ correct interaction matrices, identify and compare the so-called interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models.") (license license:gpl3+))) + +(define-public kentutils + (package + (name "kentutils") + ;; 302.1.0 is out, but the only difference is the inclusion of + ;; pre-built binaries. + (version "302.0.0") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/ENCODE-DCC/kentUtils/" + "archive/v" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "134aja3k1cj32kbk1nnw0q9gxjb2krr15q6sga8qldzvc0585rmm")) + (modules '((guix build utils) + (srfi srfi-26) + (ice-9 ftw))) + (snippet + '(begin + ;; Only the contents of the specified directories are free + ;; for all uses, so we remove the rest. "hg/autoSql" and + ;; "hg/autoXml" are nominally free, but they depend on a + ;; library that is built from the sources in "hg/lib", + ;; which is nonfree. + (let ((free (list "." ".." + "utils" "lib" "inc" "tagStorm" + "parasol" "htslib")) + (directory? (lambda (file) + (eq? 'directory (stat:type (stat file)))))) + (for-each (lambda (file) + (and (directory? file) + (delete-file-recursively file))) + (map (cut string-append "src/" <>) + (scandir "src" + (lambda (file) + (not (member file free))))))) + ;; Only make the utils target, not the userApps target, + ;; because that requires libraries we won't build. + (substitute* "Makefile" + ((" userApps") " utils")) + ;; Only build libraries that are free. + (substitute* "src/makefile" + (("DIRS =.*") "DIRS =\n") + (("cd jkOwnLib.*") "") + ((" hgLib") "") + (("cd hg.*") "")) + (substitute* "src/utils/makefile" + ;; These tools depend on "jkhgap.a", which is part of the + ;; nonfree "src/hg/lib" directory. + (("raSqlQuery") "") + (("pslLiftSubrangeBlat") "") + + ;; Do not build UCSC tools, which may require nonfree + ;; components. + (("ALL_APPS =.*") "ALL_APPS = $(UTILS_APPLIST)\n")) + #t)))) + (build-system gnu-build-system) + (arguments + `( ;; There is no global test target and the test target for + ;; individual tools depends on input files that are not + ;; included. + #:tests? #f + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-paths + (lambda _ + (substitute* "Makefile" + (("/bin/echo") (which "echo"))) + #t)) + (add-after 'unpack 'prepare-samtabix + (lambda* (#:key inputs #:allow-other-keys) + (copy-recursively (assoc-ref inputs "samtabix") + "samtabix") + #t)) + (delete 'configure) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") + "/bin"))) + (copy-recursively "bin" bin)) + #t))))) + (native-inputs + `(("samtabix" + ,(origin + (method git-fetch) + (uri (git-reference + (url "http://genome-source.cse.ucsc.edu/samtabix.git") + (commit "10fd107909c1ac4d679299908be4262a012965ba"))) + (sha256 + (base32 + "0c1nj64l42v395sa84n7az43xiap4i6f9n9dfz4058aqiwkhkmma")))))) + (inputs + `(("zlib" ,zlib) + ("tcsh" ,tcsh) + ("perl" ,perl) + ("libpng" ,libpng) + ("mysql" ,mysql) + ("openssl" ,openssl))) + (home-page "http://genome.cse.ucsc.edu/index.html") + (synopsis "Assorted bioinformatics utilities") + (description "This package provides the kentUtils, a selection of +bioinformatics utilities used in combination with the UCSC genome +browser.") + ;; Only a subset of the sources are released under a non-copyleft + ;; free software license. All other sources are removed in a + ;; snippet. See this bug report for an explanation of how the + ;; license statements apply: + ;; https://github.com/ENCODE-DCC/kentUtils/issues/12 + (license (license:non-copyleft + "http://genome.ucsc.edu/license/" + "The contents of this package are free for all uses.")))) + +(define-public f-seq + (let ((commit "6ccded34cff38cf432deed8503648b4a66953f9b") + (revision "1")) + (package + (name "f-seq") + (version (string-append "1.1-" revision "." commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/aboyle/F-seq.git") + (commit commit))) + (file-name (string-append name "-" version)) + (sha256 + (base32 + "1nk33k0yajg2id4g59bc4szr58r2q6pdq42vgcw054m8ip9wv26h")) + (modules '((guix build utils))) + ;; Remove bundled Java library archives. + (snippet + '(begin + (for-each delete-file (find-files "lib" ".*")) + #t)))) + (build-system ant-build-system) + (arguments + `(#:tests? #f ; no tests included + #:phases + (modify-phases %standard-phases + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((target (assoc-ref outputs "out")) + (doc (string-append target "/share/doc/f-seq/"))) + (mkdir-p target) + (mkdir-p doc) + (substitute* "bin/linux/fseq" + (("java") (which "java"))) + (install-file "README.txt" doc) + (install-file "bin/linux/fseq" (string-append target "/bin")) + (install-file "build~/fseq.jar" (string-append target "/lib")) + (copy-recursively "lib" (string-append target "/lib")) + #t)))))) + (inputs + `(("perl" ,perl) + ("java-commons-cli" ,java-commons-cli))) + (home-page "http://fureylab.web.unc.edu/software/fseq/") + (synopsis "Feature density estimator for high-throughput sequence tags") + (description + "F-Seq is a software package that generates a continuous tag sequence +density estimation allowing identification of biologically meaningful sites +such as transcription factor binding sites (ChIP-seq) or regions of open +chromatin (DNase-seq). Output can be displayed directly in the UCSC Genome +Browser.") + (license license:gpl3+)))) |