#:use-module (gnu packages linux)
#:use-module (gnu packages machine-learning)
#:use-module (gnu packages maths)
+ #:use-module (gnu packages mpi)
#:use-module (gnu packages ncurses)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
license:lgpl2.0+
license:asl2.0))))
+(define-public bless
+ (package
+ (name "bless")
+ (version "1p02")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "mirror://sourceforge/bless-ec/bless.v"
+ version ".tgz"))
+ (sha256
+ (base32
+ "0rm0gw2s18dqwzzpl3c2x1z05ni2v0xz5dmfk3d33j6g4cgrlrdd"))
+ (modules '((guix build utils)))
+ (snippet
+ `(begin
+ ;; Remove bundled boost, pigz, zlib, and .git directory
+ ;; FIXME: also remove bundled sources for google-sparsehash,
+ ;; murmurhash3, kmc once packaged.
+ (delete-file-recursively "boost")
+ (delete-file-recursively "pigz")
+ (delete-file-recursively "zlib")
+ (delete-file-recursively ".git")
+ #t))))
+ (build-system gnu-build-system)
+ (arguments
+ '(#:tests? #f ;no "check" target
+ #:make-flags
+ (list (string-append "ZLIB="
+ (assoc-ref %build-inputs "zlib")
+ "/lib/libz.a")
+ (string-append "LDFLAGS="
+ (string-join '("-lboost_filesystem"
+ "-lboost_system"
+ "-lboost_iostreams"
+ "-lz"
+ "-fopenmp"
+ "-std=c++11"))))
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'do-not-build-bundled-pigz
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (substitute* "Makefile"
+ (("cd pigz/pigz-2.3.3; make") ""))
+ #t))
+ (add-after 'unpack 'patch-paths-to-executables
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (substitute* "parse_args.cpp"
+ (("kmc_binary = .*")
+ (string-append "kmc_binary = \""
+ (assoc-ref outputs "out")
+ "/bin/kmc\";"))
+ (("pigz_binary = .*")
+ (string-append "pigz_binary = \""
+ (assoc-ref inputs "pigz")
+ "/bin/pigz\";")))
+ #t))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
+ (for-each (lambda (file)
+ (install-file file bin))
+ '("bless" "kmc/bin/kmc"))
+ #t)))
+ (delete 'configure))))
+ (native-inputs
+ `(("perl" ,perl)))
+ (inputs
+ `(("openmpi" ,openmpi)
+ ("boost" ,boost)
+ ("pigz" ,pigz)
+ ("zlib" ,zlib)))
+ (supported-systems '("x86_64-linux"))
+ (home-page "http://sourceforge.net/p/bless-ec/wiki/Home/")
+ (synopsis "Bloom-filter-based error correction tool for NGS reads")
+ (description
+ "@dfn{Bloom-filter-based error correction solution for high-throughput
+sequencing reads} (BLESS) uses a single minimum-sized bloom filter is a
+correction tool for genomic reads produced by @dfn{Next-generation
+sequencing} (NGS). BLESS produces accurate correction results with much less
+memory compared with previous solutions and is also able to tolerate a higher
+false-positive rate. BLESS can extend reads like DNA assemblers to correct
+errors at the end of reads.")
+ (license license:gpl3+)))
+
(define-public bowtie
(package
(name "bowtie")
ChIP-Seq, and analysis of metagenomic data.")
(license license:artistic2.0)))
+(define-public express-beta-diversity
+ (package
+ (name "express-beta-diversity")
+ (version "1.0.7")
+ (source (origin
+ (method url-fetch)
+ (uri
+ (string-append
+ "https://github.com/dparks1134/ExpressBetaDiversity/archive/v"
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1djvdlmqvjf6h0zq7w36y8cl5cli6rgj86x65znl48agnwmzxfxr"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (add-before 'build 'enter-source (lambda _ (chdir "source") #t))
+ (replace 'check
+ (lambda _ (zero? (system* "../bin/ExpressBetaDiversity"
+ "-u"))))
+ (add-after 'check 'exit-source (lambda _ (chdir "..") #t))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out")
+ "/bin")))
+ (mkdir-p bin)
+ (copy-file "scripts/convertToEBD.py"
+ (string-append bin "/convertToEBD.py"))
+ (copy-file "bin/ExpressBetaDiversity"
+ (string-append bin "/ExpressBetaDiversity"))
+ #t))))))
+ (inputs
+ `(("python" ,python-2)))
+ (home-page "http://kiwi.cs.dal.ca/Software/ExpressBetaDiversity")
+ (synopsis "Taxon- and phylogenetic-based beta diversity measures")
+ (description
+ "Express Beta Diversity (EBD) calculates ecological beta diversity
+(dissimilarity) measures between biological communities. EBD implements a
+variety of diversity measures including those that make use of phylogenetic
+similarity of community members.")
+ (license license:gpl3+)))
+
(define-public fasttree
(package
(name "fasttree")
`(("perl" ,perl)
("python" ,python)
("zlib" ,zlib)))
+ ;; Non-portable SSE instructions are used so building fails on platforms
+ ;; other than x86_64.
+ (supported-systems '("x86_64-linux"))
(home-page "http://ccb.jhu.edu/software/hisat/index.shtml")
(synopsis "Hierarchical indexing for spliced alignment of transcripts")
(description
"1i85ppf2j2lj12m0x690qq5nn17xxk23pbbx2c83r8ayb5wngzwv"))))
(build-system python-build-system)
(arguments `(#:python ,python-2)) ; only Python 2 is supported
- (inputs
- `(("python-numpy" ,python2-numpy)
- ("python-setuptools" ,python2-setuptools)))
+ ;; Numpy needs to be propagated when htseq is used as a Python library.
+ (propagated-inputs
+ `(("python-numpy" ,python2-numpy)))
+ (native-inputs
+ `(("python-setuptools" ,python2-setuptools)))
(home-page "http://www-huber.embl.de/users/anders/HTSeq/")
(synopsis "Analysing high-throughput sequencing data with Python")
(description
(inputs
`(("perl" ,perl)
("zlib" ,zlib)))
+ (supported-systems '("x86_64-linux"))
(home-page "https://code.google.com/p/mosaik-aligner/")
(synopsis "Map nucleotide sequence reads to reference genomes")
(description
(define-public ngs-sdk
(package
(name "ngs-sdk")
- (version "1.1.1")
+ (version "1.2.2")
(source
(origin
(method url-fetch)
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "1x58gpm574n0xmk2a98gmikbgycq78ia0bvnb42k5ck34fmd5v8y"))))
+ "0rvq61zfw2h9jcz6a33b9xrl20r7s5a9rldvv6rs2qy42khpmf5j"))))
(build-system gnu-build-system)
(arguments
`(#:parallel-build? #f ; not supported
(srfi srfi-26))
,@(package-arguments ngs-sdk))
((#:phases phases)
- `(alist-cons-after
- 'enter-dir 'fix-java-symlink-installation
- (lambda _
- ;; Only replace the version suffix, not the version number in
- ;; the directory name. Reported here:
- ;; https://github.com/ncbi/ngs/pull/4
- (substitute* "Makefile.java"
- (((string-append "\\$\\(subst "
- "(\\$\\(VERSION[^\\)]*\\)),"
- "(\\$\\([^\\)]+\\)),"
- "(\\$\\([^\\)]+\\)|\\$\\@)"
- "\\)")
- _ pattern replacement target)
- (string-append "$(patsubst "
- "%" pattern ","
- "%" replacement ","
- target ")"))))
- (alist-replace
- 'enter-dir (lambda _ (chdir "ngs-java") #t)
- ,phases))))))
+ `(modify-phases ,phases
+ (replace 'enter-dir (lambda _ (chdir "ngs-java") #t)))))))
(inputs
`(("jdk" ,icedtea6 "jdk")
("ngs-sdk" ,ngs-sdk)))
(define-public ncbi-vdb
(package
(name "ncbi-vdb")
- (version "2.4.5-5")
+ (version "2.5.4")
(source
(origin
(method url-fetch)
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "1cj8nk6if8sqagv20vx36v566fdvhcaadf0x1ycnbgql6chbs6vy"))))
+ "1rcnyc4xkdfcjww2i0s0qrbapys0cxbjcx2sy3qkpslf9f400fgj"))))
(build-system gnu-build-system)
(arguments
`(#:parallel-build? #f ; not supported
'configure
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
- ;; Only replace the version suffix, not the version number in the
- ;; directory name; fixed in commit 4dbba5c6a809 (no release yet).
- (substitute* "setup/konfigure.perl"
- (((string-append "\\$\\(subst "
- "(\\$\\(VERSION[^\\)]*\\)),"
- "(\\$\\([^\\)]+\\)),"
- "(\\$\\([^\\)]+\\)|\\$\\@)"
- "\\)")
- _ pattern replacement target)
- (string-append "$(patsubst "
- "%" pattern ","
- "%" replacement ","
- target ")")))
-
;; Override include path for libmagic
(substitute* "setup/package.prl"
(("name => 'magic', Include => '/usr/include'")
HCoop / jackhill / guix / guix.git / blobdiff