#:use-module (gnu packages zip)
#:use-module (srfi srfi-1))
+(define-public r-ape
+ (package
+ (name "r-ape")
+ (version "4.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "ape" version))
+ (sha256
+ (base32
+ "0959fiiy11rzfzrzaknmgrx64bhszj02l0ycz79k5a6bmpfzanlk"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-lattice" ,r-lattice)
+ ("r-nlme" ,r-nlme)))
+ (home-page "http://ape-package.ird.fr/")
+ (synopsis "Analyses of phylogenetics and evolution")
+ (description
+ "This package provides functions for reading, writing, plotting, and
+manipulating phylogenetic trees, analyses of comparative data in a
+phylogenetic framework, ancestral character analyses, analyses of
+diversification and macroevolution, computing distances from DNA sequences,
+and several other tools.")
+ (license license:gpl2+)))
+
(define-public aragorn
(package
(name "aragorn")
(bin (string-append out "/bin"))
(man (string-append out "/share/man/man1")))
(mkdir-p bin)
- (copy-file "aragorn"
- (string-append bin "/aragorn"))
+ (install-file "aragorn" bin)
(mkdir-p man)
- (copy-file "aragorn.1"
- (string-append man "/aragorn.1")))
+ (install-file "aragorn.1" man))
#t)))))
(home-page "http://mbio-serv2.mbioekol.lu.se/ARAGORN")
(synopsis "Detect tRNA, mtRNA and tmRNA genes in nucleotide sequences")
(inputs
`(("bedtools" ,bedtools-2.18)
("samtools" ,samtools-0.1)
- ("r" ,r)
+ ("r-minimal" ,r-minimal)
("r-foreach" ,r-foreach)
("r-xnomial" ,r-xnomial)
("r-domc" ,r-domc)
(define-public python-pysam
(package
(name "python-pysam")
- (version "0.9.1.4")
+ (version "0.10.0")
(source (origin
(method url-fetch)
;; Test data is missing on PyPi.
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "0y41ssbg6nvn2jgcbnrvkzblpjcwszaiv1rgyd8dwzjkrbfsgsmc"))
+ "1mmvn91agr238kwz7226xq0i7k84lg2nxywn9712mzj7gvgqhfy8"))
(modules '((guix build utils)))
(snippet
;; Drop bundled htslib. TODO: Also remove samtools and bcftools.
'(delete-file-recursively "htslib"))))
(build-system python-build-system)
(arguments
- `(#:phases
+ `(#:modules ((ice-9 ftw)
+ (srfi srfi-26)
+ (guix build python-build-system)
+ (guix build utils))
+ #:phases
(modify-phases %standard-phases
(add-before 'build 'set-flags
(lambda* (#:key inputs #:allow-other-keys)
(setenv "LDFLAGS" "-lncurses")
(setenv "CFLAGS" "-D_CURSES_LIB=1")
#t))
- (delete 'check)
- (add-after 'install 'check
+ (replace 'check
(lambda* (#:key inputs outputs #:allow-other-keys)
+ ;; Add first subdirectory of "build" directory to PYTHONPATH.
(setenv "PYTHONPATH"
(string-append
(getenv "PYTHONPATH")
- ":" (assoc-ref outputs "out")
- "/lib/python"
- (string-take (string-take-right
- (assoc-ref inputs "python") 5) 3)
- "/site-packages"))
+ ":" (getcwd) "/build/"
+ (car (scandir "build"
+ (negate (cut string-prefix? "." <>))))))
;; Step out of source dir so python does not import from CWD.
- (chdir "tests")
- (setenv "HOME" "/tmp")
- (and (zero? (system* "make" "-C" "pysam_data"))
- (zero? (system* "make" "-C" "cbcf_data"))
- (zero? (system* "nosetests" "-v"))))))))
+ (with-directory-excursion "tests"
+ (setenv "HOME" "/tmp")
+ (and (zero? (system* "make" "-C" "pysam_data"))
+ (zero? (system* "make" "-C" "cbcf_data"))
+ (zero? (system* "nosetests" "-v"
+ "--processes"
+ (number->string (parallel-job-count)))))))))))
(propagated-inputs
`(("htslib" ,htslib))) ; Included from installed header files.
(inputs
(replace
'install
(lambda* (#:key outputs #:allow-other-keys)
- (let ((out (assoc-ref outputs "out")))
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin")))
(copy-recursively "src" (string-append out "/src"))
- (mkdir (string-append out "/bin"))
+ (mkdir bin)
;; Add "src" directory to module lookup path.
(substitute* "couger"
(("from argparse")
(string-append "import sys\nsys.path.append(\""
out "\")\nfrom argparse")))
- (copy-file "couger" (string-append out "/bin/couger")))
+ (install-file "couger" bin))
#t))
(add-after
'install 'wrap-program
("python2-scipy" ,python2-scipy)
("python2-matplotlib" ,python2-matplotlib)))
(propagated-inputs
- `(("r" ,r)
+ `(("r-minimal" ,r-minimal)
("libsvm" ,libsvm)
("randomjungle" ,randomjungle)))
(native-inputs
(define-public diamond
(package
(name "diamond")
- (version "0.8.36")
+ (version "0.8.37")
(source (origin
(method url-fetch)
(uri (string-append
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "092smzzjcg51n3x4h84k52ijpz9m40ri838j9k2i463ribc3c8rh"))))
+ "1zn7q8m41ayfnjvf9snrsnq00mm68alf9rhdadx5q1sk23lyvp2l"))))
(build-system cmake-build-system)
(arguments
'(#:tests? #f ; no "check" target
(base32
"0rah9ja4m0rl5mldd6vag9rwrivw1zrqxssfq8qx64m7961fp68k"))))
(build-system cmake-build-system)
- (arguments `(#:tests? #f)) ; there are no tests
+ (arguments
+ `(#:tests? #f ; there are no tests
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'add-missing-includes
+ (lambda _
+ (substitute* "src/executioninformation.hpp"
+ (("#define EXECUTIONINFORMATION_HPP" line)
+ (string-append line "\n#include <random>")))
+ (substitute* "src/plasma/fasta.hpp"
+ (("#define FASTA_HPP" line)
+ (string-append line "\n#include <random>")))
+ #t)))))
(inputs
`(("boost" ,boost)
("cairo" ,cairo)))
(let ((target (string-append (assoc-ref outputs "out")
"/bin")))
(mkdir-p target)
- (copy-file "edirect.pl"
- (string-append target "/edirect.pl"))
+ (install-file "edirect.pl" target)
#t)))
(add-after
'install 'wrap-program
(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"))
+ (install-file "scripts/convertToEBD.py" bin)
+ (install-file "bin/ExpressBetaDiversity" bin)
#t))))))
(inputs
`(("python" ,python-2)))
(let ((bin (string-append (assoc-ref outputs "out")
"/bin")))
(mkdir-p bin)
- (copy-file "FastTree"
- (string-append bin "/FastTree"))
- (copy-file "FastTreeMP"
- (string-append bin "/FastTreeMP"))
+ (install-file "FastTree" bin)
+ (install-file "FastTreeMP" bin)
#t))))))
(home-page "http://www.microbesonline.org/fasttree")
(synopsis "Infers approximately-maximum-likelihood phylogenetic trees")
(package
(name "hmmer")
(version "3.1b2")
- (source (origin
- (method url-fetch)
- (uri (string-append
- "http://eddylab.org/software/hmmer"
- (version-prefix version 1) "/"
- version "/hmmer-" version ".tar.gz"))
- (sha256
- (base32
- "0djmgc0pfli0jilfx8hql1axhwhqxqb8rxg2r5rg07aw73sfs5nx"))))
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append
+ "http://eddylab.org/software/hmmer"
+ (version-prefix version 1) "/"
+ version "/hmmer-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0djmgc0pfli0jilfx8hql1axhwhqxqb8rxg2r5rg07aw73sfs5nx"))
+ (patches (search-patches "hmmer-remove-cpu-specificity.patch"))))
(build-system gnu-build-system)
(native-inputs `(("perl" ,perl)))
(home-page "http://hmmer.org/")
`(("zlib" ,zlib)
("bzip2" ,bzip2)
("python-screed" ,python-screed)
- ("python-bz2file" ,python-bz2file)))
+ ("python-bz2file" ,python-bz2file)
+ ;; Tests fail when gcc-5 is used for compilation. Use gcc-4.9 at least
+ ;; until the next version of khmer (likely 2.1) is released.
+ ("gcc" ,gcc-4.9)))
(home-page "https://khmer.readthedocs.org/")
(synopsis "K-mer counting, filtering and graph traversal library")
(description "The khmer software is a set of command-line tools for
#:tests? #f)) ; no test target
(inputs
`(("python-numpy" ,python2-numpy)))
- (home-page "http://github.com/taoliu/MACS/")
+ (home-page "https://github.com/taoliu/MACS/")
(synopsis "Model based analysis for ChIP-Seq data")
(description
"MACS is an implementation of a ChIP-Seq analysis algorithm for
(define-public mafft
(package
(name "mafft")
- (version "7.305")
+ (version "7.310")
(source (origin
(method url-fetch)
(uri (string-append
(file-name (string-append name "-" version ".tgz"))
(sha256
(base32
- "0ziim7g58n3z8gppsa713f5fxprl60ldj3xck186z0n9dpp06i8r"))))
+ "0gbsaz6z2qa307kd7wfb06c3y4ikmv1hsdvlns11f6zq4w1z9pwc"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; no automated tests, though there are tests in the read me
("grep" ,grep)
("sed" ,sed)
("gawk" ,gawk)
- ("r" ,r)
+ ("r-minimal" ,r-minimal)
("r-ggplot2" ,r-ggplot2)
("coreutils" ,coreutils)))
(home-page "http://sanger-pathogens.github.io/Roary")
(define-public raxml
(package
(name "raxml")
- (version "8.2.9")
+ (version "8.2.10")
(source
(origin
(method url-fetch)
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "1pv8p2fy67y21a9y4cm7xpvxqjwz2v4201flfjshdq1p8j52rqf7"))))
+ "13s7aspfdcfr6asynwdg1x6vznys6pzap5f8wsffbnnwpkkg9ya8"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; There are no tests.
(mkdir-p bin)
(mkdir-p perl)
(for-each (lambda (file)
- (copy-file file
- (string-append bin (basename file))))
+ (install-file file bin))
(find-files "." "rsem-.*"))
- (copy-file "rsem_perl_utils.pm"
- (string-append perl "/rsem_perl_utils.pm")))
+ (install-file "rsem_perl_utils.pm" perl))
#t))
(add-after
'install 'wrap-program
(inputs
`(("boost" ,boost)
("ncurses" ,ncurses)
- ("r" ,r)
+ ("r-minimal" ,r-minimal)
("perl" ,perl)
("samtools" ,samtools-0.1)
("zlib" ,zlib)))
'install 'install-library
(lambda* (#:key outputs #:allow-other-keys)
(let ((lib (string-append (assoc-ref outputs "out") "/lib")))
- (install-file "libbam.a" lib)))
+ (install-file "libbam.a" lib)
+ #t))
(alist-cons-after
'install 'install-headers
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append
(assoc-ref outputs "out") "/bin")))
(mkdir-p bin)
- (copy-file "samtools"
- (string-append bin "/samtools")))))
+ (install-file "samtools" bin)
+ #t)))
(delete 'patch-tests)
(delete 'configure))))))))
(define-public ngs-sdk
(package
(name "ngs-sdk")
- (version "1.2.5")
+ (version "1.3.0")
(source
(origin
(method url-fetch)
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "04y1fsmdnb5y86m3gg6f5g9wcscr6r25n7m8mdlcxy0i2q6w6cia"))))
+ "1wiyf4c6nm2j87pv015cbi0qny5byf3pbvcw3likifz5dl56ag40"))))
(build-system gnu-build-system)
(arguments
`(#:parallel-build? #f ; not supported
(define-public ncbi-vdb
(package
(name "ncbi-vdb")
- (version "2.7.0")
+ (version "2.8.2")
(source
(origin
(method url-fetch)
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "0x1cg1x8vy0yjlkp0snc1533zcjhxqzqsaiwqk598n7vvw37n8lf"))))
+ "1acn4bv81mfl137qnbn9995mjjhwd36pm0b7qli1iw5skrxa9j8m"))))
(build-system gnu-build-system)
(arguments
`(#:parallel-build? #f ; not supported
#:tests? #f ; no "check" target
#:phases
- (alist-replace
- 'configure
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (let ((out (assoc-ref outputs "out")))
- ;; Override include path for libmagic
- (substitute* "setup/package.prl"
- (("name => 'magic', Include => '/usr/include'")
- (string-append "name=> 'magic', Include => '"
- (assoc-ref inputs "libmagic")
- "/include" "'")))
-
- ;; Install kdf5 library (needed by sra-tools)
- (substitute* "build/Makefile.install"
- (("LIBRARIES_TO_INSTALL =")
- "LIBRARIES_TO_INSTALL = kdf5.$(VERSION_LIBX) kdf5.$(VERSION_SHLX)"))
-
- (substitute* "build/Makefile.env"
- (("CFLAGS =" prefix)
- (string-append prefix "-msse2 ")))
-
- ;; The 'configure' script doesn't recognize things like
- ;; '--enable-fast-install'.
- (zero? (system*
- "./configure"
- (string-append "--build-prefix=" (getcwd) "/build")
- (string-append "--prefix=" (assoc-ref outputs "out"))
- (string-append "--debug")
- (string-append "--with-xml2-prefix="
- (assoc-ref inputs "libxml2"))
- (string-append "--with-ngs-sdk-prefix="
- (assoc-ref inputs "ngs-sdk"))
- (string-append "--with-ngs-java-prefix="
- (assoc-ref inputs "java-ngs"))
- (string-append "--with-hdf5-prefix="
- (assoc-ref inputs "hdf5"))))))
- (alist-cons-after
- 'install 'install-interfaces
- (lambda* (#:key outputs #:allow-other-keys)
- ;; Install interface libraries. On i686 the interface libraries
- ;; are installed to "linux/gcc/i386", so we need to use the Linux
- ;; architecture name ("i386") instead of the target system prefix
- ;; ("i686").
- (mkdir (string-append (assoc-ref outputs "out") "/ilib"))
- (copy-recursively (string-append "build/ncbi-vdb/linux/gcc/"
- ,(system->linux-architecture
- (or (%current-target-system)
- (%current-system)))
- "/rel/ilib")
- (string-append (assoc-ref outputs "out")
- "/ilib"))
- ;; Install interface headers
- (copy-recursively "interfaces"
- (string-append (assoc-ref outputs "out")
- "/include")))
- %standard-phases))))
+ (modify-phases %standard-phases
+ (replace 'configure
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out")))
+ ;; Override include path for libmagic
+ (substitute* "setup/package.prl"
+ (("name => 'magic', Include => '/usr/include'")
+ (string-append "name=> 'magic', Include => '"
+ (assoc-ref inputs "libmagic")
+ "/include" "'")))
+
+ ;; Install kdf5 library (needed by sra-tools)
+ (substitute* "build/Makefile.install"
+ (("LIBRARIES_TO_INSTALL =")
+ "LIBRARIES_TO_INSTALL = kdf5.$(VERSION_LIBX) kdf5.$(VERSION_SHLX)"))
+
+ (substitute* "build/Makefile.env"
+ (("CFLAGS =" prefix)
+ (string-append prefix "-msse2 ")))
+
+ ;; Override search path for ngs-java
+ (substitute* "setup/package.prl"
+ (("/usr/local/ngs/ngs-java")
+ (assoc-ref inputs "java-ngs")))
+
+ ;; The 'configure' script doesn't recognize things like
+ ;; '--enable-fast-install'.
+ (zero? (system*
+ "./configure"
+ (string-append "--build-prefix=" (getcwd) "/build")
+ (string-append "--prefix=" (assoc-ref outputs "out"))
+ (string-append "--debug")
+ (string-append "--with-xml2-prefix="
+ (assoc-ref inputs "libxml2"))
+ (string-append "--with-ngs-sdk-prefix="
+ (assoc-ref inputs "ngs-sdk"))
+ (string-append "--with-hdf5-prefix="
+ (assoc-ref inputs "hdf5")))))))
+ (add-after 'install 'install-interfaces
+ (lambda* (#:key outputs #:allow-other-keys)
+ ;; Install interface libraries. On i686 the interface libraries
+ ;; are installed to "linux/gcc/i386", so we need to use the Linux
+ ;; architecture name ("i386") instead of the target system prefix
+ ;; ("i686").
+ (mkdir (string-append (assoc-ref outputs "out") "/ilib"))
+ (copy-recursively (string-append "build/ncbi-vdb/linux/gcc/"
+ ,(system->linux-architecture
+ (or (%current-target-system)
+ (%current-system)))
+ "/rel/ilib")
+ (string-append (assoc-ref outputs "out")
+ "/ilib"))
+ ;; Install interface headers
+ (copy-recursively "interfaces"
+ (string-append (assoc-ref outputs "out")
+ "/include"))
+ #t))
+ ;; These files are needed by sra-tools.
+ (add-after 'install 'install-configuration-files
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((target (string-append (assoc-ref outputs "out") "/kfg")))
+ (mkdir target)
+ (install-file "libs/kfg/default.kfg" target)
+ (install-file "libs/kfg/certs.kfg" target))
+ #t)))))
(inputs
`(("libxml2" ,libxml2)
("ngs-sdk" ,ngs-sdk)
`(("python-nose" ,python-nose)))
(inputs
`(("python-bz2file" ,python-bz2file)))
- (home-page "http://github.com/dib-lab/screed/")
+ (home-page "https://github.com/dib-lab/screed/")
(synopsis "Short read sequence database utilities")
(description "Screed parses FASTA and FASTQ files and generates databases.
Values such as sequence name, sequence description, sequence quality and the
(define-public sra-tools
(package
(name "sra-tools")
- (version "2.7.0")
+ (version "2.8.2-1")
(source
(origin
(method url-fetch)
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "13paw7bq6y47d2pl0ac5gpgcqp1xsy1g7v1fwysm3hr8lb2dck17"))))
+ "1camsijmvv2s45mb4iyf44ghl4gkd4rl0viphpcgl3ccchy32a0g"))))
(build-system gnu-build-system)
(arguments
`(#:parallel-build? #f ; not supported
#:tests? #f ; no "check" target
#:make-flags
- (list (string-append "VDB_LIBDIR="
+ (list (string-append "DEFAULT_CRT="
+ (assoc-ref %build-inputs "ncbi-vdb")
+ "/kfg/certs.kfg")
+ (string-append "DEFAULT_KFG="
+ (assoc-ref %build-inputs "ncbi-vdb")
+ "/kfg/default.kfg")
+ (string-append "VDB_LIBDIR="
(assoc-ref %build-inputs "ncbi-vdb")
,(if (string-prefix? "x86_64"
(or (%current-target-system)
"/lib64"
"/lib32")))
#:phases
- (alist-replace
- 'configure
- (lambda* (#:key inputs outputs #:allow-other-keys)
- ;; The build system expects a directory containing the sources and
- ;; raw build output of ncbi-vdb, including files that are not
- ;; installed. Since we are building against an installed version of
- ;; ncbi-vdb, the following modifications are needed.
- (substitute* "setup/konfigure.perl"
- ;; Make the configure script look for the "ilib" directory of
- ;; "ncbi-vdb" without first checking for the existence of a
- ;; matching library in its "lib" directory.
- (("^ my \\$f = File::Spec->catdir\\(\\$libdir, \\$lib\\);")
- "my $f = File::Spec->catdir($ilibdir, $ilib);")
- ;; Look for interface libraries in ncbi-vdb's "ilib" directory.
- (("my \\$ilibdir = File::Spec->catdir\\(\\$builddir, 'ilib'\\);")
- "my $ilibdir = File::Spec->catdir($dir, 'ilib');"))
-
- ;; Dynamic linking
- (substitute* "tools/copycat/Makefile"
- (("smagic-static") "lmagic"))
-
- ;; The 'configure' script doesn't recognize things like
- ;; '--enable-fast-install'.
- (zero? (system*
- "./configure"
- (string-append "--build-prefix=" (getcwd) "/build")
- (string-append "--prefix=" (assoc-ref outputs "out"))
- (string-append "--debug")
- (string-append "--with-fuse-prefix="
- (assoc-ref inputs "fuse"))
- (string-append "--with-magic-prefix="
- (assoc-ref inputs "libmagic"))
- ;; TODO: building with libxml2 fails with linker errors
- ;; (string-append "--with-xml2-prefix="
- ;; (assoc-ref inputs "libxml2"))
- (string-append "--with-ncbi-vdb-sources="
- (assoc-ref inputs "ncbi-vdb"))
- (string-append "--with-ncbi-vdb-build="
- (assoc-ref inputs "ncbi-vdb"))
- (string-append "--with-ngs-sdk-prefix="
- (assoc-ref inputs "ngs-sdk"))
- (string-append "--with-hdf5-prefix="
- (assoc-ref inputs "hdf5")))))
- %standard-phases)))
+ (modify-phases %standard-phases
+ (replace 'configure
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ ;; The build system expects a directory containing the sources and
+ ;; raw build output of ncbi-vdb, including files that are not
+ ;; installed. Since we are building against an installed version of
+ ;; ncbi-vdb, the following modifications are needed.
+ (substitute* "setup/konfigure.perl"
+ ;; Make the configure script look for the "ilib" directory of
+ ;; "ncbi-vdb" without first checking for the existence of a
+ ;; matching library in its "lib" directory.
+ (("^ my \\$f = File::Spec->catdir\\(\\$libdir, \\$lib\\);")
+ "my $f = File::Spec->catdir($ilibdir, $ilib);")
+ ;; Look for interface libraries in ncbi-vdb's "ilib" directory.
+ (("my \\$ilibdir = File::Spec->catdir\\(\\$builddir, 'ilib'\\);")
+ "my $ilibdir = File::Spec->catdir($dir, 'ilib');"))
+
+ ;; Dynamic linking
+ (substitute* "tools/copycat/Makefile"
+ (("smagic-static") "lmagic"))
+
+ ;; The 'configure' script doesn't recognize things like
+ ;; '--enable-fast-install'.
+ (zero? (system*
+ "./configure"
+ (string-append "--build-prefix=" (getcwd) "/build")
+ (string-append "--prefix=" (assoc-ref outputs "out"))
+ (string-append "--debug")
+ (string-append "--with-fuse-prefix="
+ (assoc-ref inputs "fuse"))
+ (string-append "--with-magic-prefix="
+ (assoc-ref inputs "libmagic"))
+ ;; TODO: building with libxml2 fails with linker errors
+ ;; (string-append "--with-xml2-prefix="
+ ;; (assoc-ref inputs "libxml2"))
+ (string-append "--with-ncbi-vdb-sources="
+ (assoc-ref inputs "ncbi-vdb"))
+ (string-append "--with-ncbi-vdb-build="
+ (assoc-ref inputs "ncbi-vdb"))
+ (string-append "--with-ngs-sdk-prefix="
+ (assoc-ref inputs "ngs-sdk"))
+ (string-append "--with-hdf5-prefix="
+ (assoc-ref inputs "hdf5"))))))
+ ;; This version of sra-tools fails to build with glibc because of a
+ ;; naming conflict. glibc-2.25/include/bits/mathcalls.h already
+ ;; contains a definition of "canonicalize", so we rename it.
+ ;;
+ ;; See upstream bug report:
+ ;; https://github.com/ncbi/sra-tools/issues/67
+ (add-after 'unpack 'patch-away-glibc-conflict
+ (lambda _
+ (substitute* "tools/bam-loader/bam.c"
+ (("canonicalize\\(" line)
+ (string-append "sra_tools_" line)))
+ #t)))))
(native-inputs `(("perl" ,perl)))
(inputs
`(("ngs-sdk" ,ngs-sdk)
`(("python-biopython" ,python2-biopython-1.66)))
(native-inputs
`(("python-nose" ,python2-nose)))
- (home-page "http://github.com/fhcrc/seqmagick")
+ (home-page "https://github.com/fhcrc/seqmagick")
(synopsis "Tools for converting and modifying sequence files")
(description
"Bioinformaticians often have to convert sequence files between formats
(define-public star
(package
(name "star")
- (version "2.5.2b")
+ (version "2.5.3a")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/alexdobin/STAR/archive/"
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "1na6np880r1zaamiy00hy8bid5anpy0kgf63587v2yl080krk2zq"))
+ "013wirlz8lllgjyagl48l75n1isxyabqb3sj7qlsl0x1rmvqw99a"))
(modules '((guix build utils)))
(snippet
'(begin
(("#include \"(bam|sam|kstring).h\"" _ header)
(string-append "#include <samtools/" header ".h>")))
#t))
+ (add-after 'unpack 'remove-duplicate-typedef
+ (lambda _
+ ;; This typedef conflicts with the typedef in
+ ;; glibc-2.25/include/bits/types.h
+ (substitute* "gclib/GThreads.h"
+ (("typedef long long __intmax_t;") ""))
+ #t))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
(define-public r-vegan
(package
(name "r-vegan")
- (version "2.4-2")
+ (version "2.4-3")
(source
(origin
(method url-fetch)
(uri (cran-uri "vegan" version))
(sha256
(base32
- "12wf64izrpq9z3ix7mgm5421mq0xsm8dw5qblvcrz452nfhjf5w9"))))
+ "15zcxfix2d854897k1lr0sfmj2n00339nlsppcr3zrb238lb2mi5"))))
(build-system r-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'revert-test-deletion
- ;; The distributed sources do not include tests with the CRAN
- ;; package. Here we revert the commit
- ;; `591d0e8ba1deaaf82445474ec6619c0b43db4e63' which deletes these
- ;; tests. There are plans to not delete tests in future as
- ;; documented at https://github.com/vegandevs/vegan/issues/181.
- (lambda* (#:key inputs #:allow-other-keys)
- (zero?
- (system* "patch" "-R" "-p1" "-i"
- (assoc-ref inputs "r-vegan-delete-tests-patch"))))))))
(native-inputs
`(("gfortran" ,gfortran)
- ("r-knitr" ,r-knitr)
- ("r-vegan-delete-tests-patch"
- ,(origin
- (method url-fetch)
- (uri (string-append
- "https://github.com/vegandevs/vegan/commit/"
- "591d0e8ba1deaaf82445474ec6619c0b43db4e63.patch"))
- (sha256
- (base32
- "0b1bi7y4jjdl3ph721vm9apm51dr2z9piwvhy4355sf2b4kyyj5a"))))))
+ ("r-knitr" ,r-knitr)))
(propagated-inputs
`(("r-cluster" ,r-cluster)
("r-lattice" ,r-lattice)
+ ("r-mass" ,r-mass)
("r-mgcv" ,r-mgcv)
("r-permute" ,r-permute)))
(home-page "https://cran.r-project.org/web/packages/vegan")
(home-page
"http://bioconductor.org/packages/annotate")
(synopsis "Annotation for microarrays")
- (description "This package provides R enviroments for the annotation of
+ (description "This package provides R environments for the annotation of
microarrays.")
(license license:artistic2.0)))
`(("r-annotate" ,r-annotate)
("r-annotationdbi" ,r-annotationdbi)
("r-biobase" ,r-biobase)
- ("r-s4vectors" ,r-s4vectors)))
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-survival" ,r-survival)))
(home-page "http://bioconductor.org/packages/genefilter")
(synopsis "Filter genes from high-throughput experiments")
(description
"1walwkqryn1gnwz7zryr5764a0p6ia7ag4w6w9n8fskg8dkg0fqs"))))
(properties `((upstream-name . "DESeq2")))
(build-system r-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'link-against-armadillo
- (lambda _
- (substitute* "src/Makevars"
- (("PKG_LIBS =" prefix)
- (string-append prefix "-larmadillo"))))))))
(propagated-inputs
`(("r-biobase" ,r-biobase)
("r-biocgenerics" ,r-biocgenerics)
(define-public r-annotationforge
(package
(name "r-annotationforge")
- (version "1.16.0")
+ (version "1.16.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "AnnotationForge" version))
(sha256
(base32
- "02msyb9p3hywrryx00zpjkjl126mrv827i1ah1092s0cplm6xxvf"))))
+ "0l1g9hy88sh5g567svyfd8pnjvkyklkn6a3gjn8zalvh62qqjjq1"))))
(properties
`((upstream-name . "AnnotationForge")))
(build-system r-build-system)
(define-public r-shortread
(package
(name "r-shortread")
- (version "1.32.0")
+ (version "1.32.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ShortRead" version))
(sha256
(base32
- "0mjdlg92x5qw4x2djc4dv5lxwl7ai6ix56nnf86zr07jk8vc7yls"))))
+ "1m7lbfxs7xwcy9xs76zy5rky2mb96anvh457xfw60lh3kygwfpxc"))))
(properties `((upstream-name . "ShortRead")))
(build-system r-build-system)
(inputs
("r-genomicalignments" ,r-genomicalignments)
("r-genomicranges" ,r-genomicranges)
("r-iranges" ,r-iranges)
+ ("r-mass" ,r-mass)
("r-rtracklayer" ,r-rtracklayer)
("r-s4vectors" ,r-s4vectors)))
(home-page "https://github.com/Kraus-Lab/groHMM")
(define-public vsearch
(package
(name "vsearch")
- (version "2.4.0")
+ (version "2.4.3")
(source
(origin
(method url-fetch)
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "007q9a50hdw4vs2iajabvbw7qccml4r8cbqzyi5ipkkf42jk3vnr"))
+ "0hc110ycqpa54nr6x173qg7190hk08qp7yz7zzqxlsypqnpc5zzp"))
(patches (search-patches "vsearch-unbundle-cityhash.patch"))
(snippet
'(begin
"Very fast parallel big-data BLAST XML file parser which can be used as
command line utility. Use blastxmlparser to: Parse BLAST XML; filter output;
generate FASTA, JSON, YAML, RDF, JSON-LD, HTML, CSV, tabular output etc.")
- (home-page "http://github.com/pjotrp/blastxmlparser")
+ (home-page "https://github.com/pjotrp/blastxmlparser")
(license license:expat)))
(define-public bioruby
(define-public r-bioccheck
(package
(name "r-bioccheck")
- (version "1.10.0")
+ (version "1.10.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocCheck" version))
(sha256
(base32
- "1rfy37xg1nc2cmgbclvzsi7sgmdcdjiahsx9crgx3yaw7kxgiack"))))
+ "197kpiycyl3qawm6801fxyxj81d2g57a00qxaqprapsf1d140l52"))))
(properties
`((upstream-name . "BiocCheck")))
(build-system r-build-system)
(native-inputs
`(("which" ,which)))
(propagated-inputs
- `(("r-graph" ,r-graph)
- ("r-knitr" ,r-knitr)
+ `(("r-codetools" ,r-codetools)
+ ("r-graph" ,r-graph)
("r-httr" ,r-httr)
("r-optparse" ,r-optparse)
- ("r-devtools" ,r-devtools)
("r-biocinstaller" ,r-biocinstaller)
("r-biocviews" ,r-biocviews)))
(home-page "http://bioconductor.org/packages/BiocCheck")
(define-public r-s4vectors
(package
(name "r-s4vectors")
- (version "0.12.1")
+ (version "0.12.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "S4Vectors" version))
(sha256
(base32
- "0i36y3w36h3d8rmazxcrip4gvn54rd9av1wz4lygsprrjmylfhcc"))))
+ "0syx0qgipx97zsp3b8afhzamsr30835a2a99yb9wnq7b50g3v3p1"))))
(properties
`((upstream-name . "S4Vectors")))
(build-system r-build-system)
(define-public r-seqinr
(package
(name "r-seqinr")
- (version "3.3-3")
+ (version "3.3-6")
(source
(origin
(method url-fetch)
(uri (cran-uri "seqinr" version))
(sha256
(base32
- "0rk4yba8km26c0rh1f4h474zsb5n6kjmqsi55bnzr6p8pymp18hj"))))
+ "13d0qxm2244wgdl2dy2s8vnrnf5fx4n47if9gkb49dqx6c0sx8s2"))))
(build-system r-build-system)
(propagated-inputs
`(("r-ade4" ,r-ade4)
(define-public r-iranges
(package
(name "r-iranges")
- (version "2.8.1")
+ (version "2.8.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "IRanges" version))
(sha256
(base32
- "0cryqnpqb3p6l9jjw27hyqd550sxlljls3ka7b9rb38hkji7b5hw"))))
+ "0x8h74ik3xwdnwrkn89hq5ll0qa1lp9jgzlbmpa02dpws7snfwyr"))))
(properties
`((upstream-name . "IRanges")))
(build-system r-build-system)
(define-public r-genomeinfodb
(package
(name "r-genomeinfodb")
- (version "1.10.2")
+ (version "1.10.3")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomeInfoDb" version))
(sha256
(base32
- "0zh894qd1sgpjbn0wfvq6hs2dzn7y1pyicvzk2aa48y3zbidanv7"))))
+ "18g24cf6b3vi13w85ki2mam6i2gl4yxr1zchyga34xc3dkdngzrw"))))
(properties
`((upstream-name . "GenomeInfoDb")))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
("r-iranges" ,r-iranges)
+ ("r-rcurl" ,r-rcurl)
("r-s4vectors" ,r-s4vectors)))
(home-page "http://bioconductor.org/packages/GenomeInfoDb")
(synopsis "Utilities for manipulating chromosome identifiers")
(define-public r-variantannotation
(package
(name "r-variantannotation")
- (version "1.20.2")
+ (version "1.20.3")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "VariantAnnotation" version))
(sha256
(base32
- "165wda1d2jagd907pnra4m3sla66icyqxvd60xpv09jl5agd5mn9"))))
+ "10v8apgfw57nd4dxmdxdrijxpw135jpp2p8wrk3wjpb3hhfjp1qj"))))
(properties
`((upstream-name . "VariantAnnotation")))
(inputs
(define-public r-limma
(package
(name "r-limma")
- (version "3.30.7")
+ (version "3.30.13")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "limma" version))
(sha256
(base32
- "1xg9w4lmn9n4hwyflxiwi6g969lcy569cg4z1x47crwwg7z7qdka"))))
+ "1ji8kb19anwq2505zii2kzqlrnk75mk1mpz8vy4s1mckzs1cz4m0"))))
(build-system r-build-system)
(home-page "http://bioinf.wehi.edu.au/limma")
(synopsis "Package for linear models for microarray and RNA-seq data")
(define-public r-xvector
(package
(name "r-xvector")
- (version "0.14.0")
+ (version "0.14.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "XVector" version))
(sha256
(base32
- "09lbqxpqr80g0kw77mpz0p1a8cq706j33kz8194wp71il67cdzi7"))))
+ "1j14ip4c260kdp3zcmgfa2v8ky88csa0gfdg6a1xsb64s03hdbm6"))))
(properties
`((upstream-name . "XVector")))
(build-system r-build-system)
(define-public r-genomicranges
(package
(name "r-genomicranges")
- (version "1.26.2")
+ (version "1.26.4")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicRanges" version))
(sha256
(base32
- "0if5dswkp77lyqppd0z2iyvnwag9h1gsr03707s8npcx13mzpsia"))))
+ "1789ycqzv20d8p1axkxrhsz9v0ww6w1dk2mfvm85p8j53zd1f67c"))))
(properties
`((upstream-name . "GenomicRanges")))
(build-system r-build-system)
(define-public r-annotationdbi
(package
(name "r-annotationdbi")
- (version "1.36.0")
+ (version "1.36.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "AnnotationDbi" version))
(sha256
(base32
- "0ydrqw1k1j5p6w76bwc753cx545c055x88q87wzya93858synj6r"))))
+ "0574lmyisn3nv9aicz9x3iivx990da4q2j4i0f1jz0mpj9v3vc2w"))))
(properties
`((upstream-name . "AnnotationDbi")))
(build-system r-build-system)
(define-public r-biocparallel
(package
(name "r-biocparallel")
- (version "1.8.1")
+ (version "1.8.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocParallel" version))
(sha256
(base32
- "123i928rwi4h4sy4fpysv6pinw5nns0sm3myxi2ghqhm34ws8gyl"))))
+ "18zpa0vl375n9pvxsgbid1k96m17nqqgv1g1sfnlmm7kj34jxg6v"))))
(properties
`((upstream-name . "BiocParallel")))
(build-system r-build-system)
(define-public r-rsamtools
(package
(name "r-rsamtools")
- (version "1.26.1")
+ (version "1.26.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "Rsamtools" version))
(sha256
(base32
- "0pf4f6brf4bl5zgjrah0f38qslazrs49ayqgyh0xfqgrh63yx4ck"))))
+ "118nsajgghi4cy3h0wi7777kc70a5j1fdyxv5n1dy01glix2z4qk"))))
(properties
`((upstream-name . "Rsamtools")))
(build-system r-build-system)
("r-genomeinfodb" ,r-genomeinfodb)
("r-genomicranges" ,r-genomicranges)
("r-iranges" ,r-iranges)
+ ("r-matrix" ,r-matrix)
("r-s4vectors" ,r-s4vectors)))
(home-page "http://bioconductor.org/packages/SummarizedExperiment")
(synopsis "Container for representing genomic ranges by sample")
(define-public r-genomicalignments
(package
(name "r-genomicalignments")
- (version "1.10.0")
+ (version "1.10.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicAlignments" version))
(sha256
(base32
- "11vb0a0zd36i4yhg4mfijv787v0nihn6pkjj6q7rfy19gwy61xlc"))))
+ "1dilghbsyf64iz5c0kib2c7if72x7almd5w3ali09a2b2ff2mcjk"))))
(properties
`((upstream-name . "GenomicAlignments")))
(build-system r-build-system)
(define-public r-rtracklayer
(package
(name "r-rtracklayer")
- (version "1.34.1")
+ (version "1.34.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "rtracklayer" version))
(sha256
(base32
- "0x59k2fd0iaqi93gy6bm58p2j2z90z1b7a6w5b4c098y98n096rc"))))
+ "1j3cyvg1wg1d9l0lkcjk3jn7pb96zi17nd1qsa5lglsimja19mpl"))))
(build-system r-build-system)
(arguments
`(#:phases
(define-public r-genomicfeatures
(package
(name "r-genomicfeatures")
- (version "1.26.2")
+ (version "1.26.4")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicFeatures" version))
(sha256
(base32
- "1ybi6r3bax07wlv2qcd34y5qjdvcqcfayfvlrjc39ifrkk65wv4f"))))
+ "1y16lqach0v3ym5zhdhj4r2imfi0kpa0djlb51hj85yf7xkzwdlb"))))
(properties
`((upstream-name . "GenomicFeatures")))
(build-system r-build-system)
("r-biobase" ,r-biobase)
("r-biocgenerics" ,r-biocgenerics)
("r-go-db" ,r-go-db)
- ("r-matrixstats" ,r-matrixstats)
("r-graph" ,r-graph)
+ ("r-lattice" ,r-lattice)
+ ("r-matrixstats" ,r-matrixstats)
("r-sparsem" ,r-sparsem)))
(home-page "http://bioconductor.org/packages/topGO")
(synopsis "Enrichment analysis for gene ontology")
`("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))))
#t)))))
(inputs
- `(("r" ,r)
+ `(("r-minimal" ,r-minimal)
("r-rcas" ,r-rcas)
- ("guile-next" ,guile-next)
+ ("guile-next" ,guile-2.2)
("guile-json" ,guile2.2-json)
("guile-redis" ,guile2.2-redis)))
(native-inputs
"1wc1fjm6dzlsqqagm43y57w8jh8nsh0r0m8z1p6ximcb5gxqh7hn"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-genefilter" ,r-genefilter)))
+ `(("r-genefilter" ,r-genefilter)
+ ("r-mgcv" ,r-mgcv)))
(home-page "http://bioconductor.org/packages/sva")
(synopsis "Surrogate variable analysis")
(description
(define-public r-seqminer
(package
(name "r-seqminer")
- (version "5.3")
+ (version "5.7")
(source
(origin
(method url-fetch)
(uri (cran-uri "seqminer" version))
(sha256
(base32
- "0y0gc5lws3hdxasjb84m532ics6imb7qg9sl1zy62h503jh4j9gw"))))
+ "0p75wyl70cvp36mwg5y74nv573j1gdqi15ac2a7xf61jmsq7ycpy"))))
(build-system r-build-system)
(inputs
`(("zlib" ,zlib)))
(propagated-inputs
`(("r-seqminer" ,r-seqminer)
("r-mvtnorm" ,r-mvtnorm)
+ ("r-mass" ,r-mass)
("r-compquadform" ,r-compquadform)
("r-getopt" ,r-getopt)))
(home-page "http://genome.sph.umich.edu/wiki/RareMETALS2")
(define-public r-maldiquant
(package
(name "r-maldiquant")
- (version "1.16")
+ (version "1.16.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "MALDIquant" version))
(sha256
(base32
- "067xbmy10mpsvmv77g62chd7wwhdhcfn5hmp5fisbnz2h5rq0q60"))))
+ "0z5srzsfgsgi4bssr4chls4ry6d18y2g9143znqmraylppwrrqzr"))))
(properties `((upstream-name . "MALDIquant")))
(build-system r-build-system)
(home-page "http://cran.r-project.org/web/packages/MALDIquant")
`(("r-affy" ,r-affy)
("r-biobase" ,r-biobase)
("r-ggplot2" ,r-ggplot2)
+ ("r-lattice" ,r-lattice)
("r-limma" ,r-limma)))
(home-page "http://bioconductor.org/packages/release/bioc/html/vsn.html")
(synopsis "Variance stabilization and calibration for microarray data")
(propagated-inputs
`(("r-biobase" ,r-biobase)
("r-biocgenerics" ,r-biocgenerics)
+ ("r-mass" ,r-mass)
("r-rcpp" ,r-rcpp)))
(home-page "https://github.com/hredestig/pcamethods")
(synopsis "Collection of PCA methods")
and irregular enzymatic cleavages, mass measurement accuracy, etc.")
(license license:artistic2.0)))
+(define-public r-seurat
+ ;; Source releases are only made for new x.0 versions. All newer versions
+ ;; are only released as pre-built binaries. At the time of this writing the
+ ;; latest binary release is 1.4.0.12, which is equivalent to this commit.
+ (let ((commit "fccb77d1452c35ee47e47ebf8e87bddb59f3b08d")
+ (revision "1"))
+ (package
+ (name "r-seurat")
+ (version (string-append "1.4.0.12-" revision "." (string-take commit 7)))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/satijalab/seurat")
+ (commit commit)))
+ (file-name (string-append name "-" version "-checkout"))
+ (sha256
+ (base32
+ "101wq3aqrdmbfi3lqmq4iivk9iwbf10d4z216ss25hf7n9091cyl"))
+ ;; Delete pre-built jar.
+ (snippet
+ '(begin (delete-file "inst/java/ModularityOptimizer.jar")
+ #t))))
+ (build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'build-jar
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((classesdir "tmp-classes"))
+ (setenv "JAVA_HOME" (assoc-ref inputs "jdk"))
+ (mkdir classesdir)
+ (and (zero? (apply system* `("javac" "-d" ,classesdir
+ ,@(find-files "java" "\\.java$"))))
+ (zero? (system* "jar"
+ "-cf" "inst/java/ModularityOptimizer.jar"
+ "-C" classesdir ".")))))))))
+ (native-inputs
+ `(("jdk" ,icedtea "jdk")))
+ (propagated-inputs
+ `(("r-ape" ,r-ape)
+ ("r-caret" ,r-caret)
+ ("r-cowplot" ,r-cowplot)
+ ("r-dplyr" ,r-dplyr)
+ ("r-fastica" ,r-fastica)
+ ("r-fnn" ,r-fnn)
+ ("r-fpc" ,r-fpc)
+ ("r-gdata" ,r-gdata)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-gplots" ,r-gplots)
+ ("r-gridextra" ,r-gridextra)
+ ("r-igraph" ,r-igraph)
+ ("r-irlba" ,r-irlba)
+ ("r-lars" ,r-lars)
+ ("r-mixtools" ,r-mixtools)
+ ("r-pbapply" ,r-pbapply)
+ ("r-plyr" ,r-plyr)
+ ("r-ranger" ,r-ranger)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rcppeigen" ,r-rcppeigen)
+ ("r-rcppprogress" ,r-rcppprogress)
+ ("r-reshape2" ,r-reshape2)
+ ("r-rocr" ,r-rocr)
+ ("r-rtsne" ,r-rtsne)
+ ("r-stringr" ,r-stringr)
+ ("r-tclust" ,r-tclust)
+ ("r-tsne" ,r-tsne)
+ ("r-vgam" ,r-vgam)))
+ (home-page "http://www.satijalab.org/seurat")
+ (synopsis "Seurat is an R toolkit for single cell genomics")
+ (description
+ "This package is an R package designed for QC, analysis, and
+exploration of single cell RNA-seq data. It easily enables widely-used
+analytical techniques, including the identification of highly variable genes,
+dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering
+algorithms; density clustering, hierarchical clustering, k-means, and the
+discovery of differentially expressed genes and markers.")
+ (license license:gpl3))))
+
(define htslib-for-sambamba
(let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5"))
(package
HCoop / jackhill / guix / guix.git / blobdiff