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-rw-r--r--gnu/packages/bioinformatics.scm180
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+))))