(string-append " strcpy(train_dir, \"" share "/train/\");"))))
#t))
(replace 'build
- (lambda _ (and (zero? (system* "make" "clean"))
- (zero? (system* "make" "fgs")))))
+ (lambda _
+ (invoke "make" "clean")
+ (invoke "make" "fgs")
+ #t))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (string-append (assoc-ref outputs "out")))
(let* ((out (string-append (assoc-ref outputs "out")))
(bin (string-append out "/bin/"))
(frag (string-append bin "run_FragGeneScan.pl")))
- (and (zero? (system* frag ; Test complete genome.
- "-genome=./example/NC_000913.fna"
- "-out=./test2"
- "-complete=1"
- "-train=complete"))
- (file-exists? "test2.faa")
- (file-exists? "test2.ffn")
- (file-exists? "test2.gff")
- (file-exists? "test2.out")
- (zero? (system* ; Test incomplete sequences.
- frag
- "-genome=./example/NC_000913-fgs.ffn"
- "-out=out"
- "-complete=0"
- "-train=454_30")))))))))
+ ;; Test complete genome.
+ (invoke frag
+ "-genome=./example/NC_000913.fna"
+ "-out=./test2"
+ "-complete=1"
+ "-train=complete")
+ (unless (and (file-exists? "test2.faa")
+ (file-exists? "test2.ffn")
+ (file-exists? "test2.gff")
+ (file-exists? "test2.out"))
+ (error "Expected files do not exist."))
+ ;; Test incomplete sequences.
+ (invoke frag
+ "-genome=./example/NC_000913-fgs.ffn"
+ "-out=out"
+ "-complete=0"
+ "-train=454_30")
+ #t))))))
(inputs
`(("perl" ,perl)
("python" ,python-2))) ;not compatible with python 3.
(lambda* (#:key inputs #:allow-other-keys)
(mkdir-p "lib/jni")
(mkdir-p "jdk-src")
- (and (zero? (system* "tar" "--strip-components=1" "-C" "jdk-src"
- "-xf" (assoc-ref inputs "jdk-src")))
- (zero? (system* "javah" "-jni"
- "-classpath" "classes"
- "-d" "lib/"
- "net.sf.samtools.util.zip.IntelDeflater"))
- (with-directory-excursion "src/c/inteldeflater"
- (zero? (system* "gcc" "-I../../../lib" "-I."
- (string-append "-I" (assoc-ref inputs "jdk")
- "/include/linux")
- "-I../../../jdk-src/src/share/native/common/"
- "-I../../../jdk-src/src/solaris/native/common/"
- "-c" "-O3" "-fPIC" "IntelDeflater.c"))
- (zero? (system* "gcc" "-shared"
- "-o" "../../../lib/jni/libIntelDeflater.so"
- "IntelDeflater.o" "-lz" "-lstdc++"))))))
+ (invoke "tar" "--strip-components=1" "-C" "jdk-src"
+ "-xf" (assoc-ref inputs "jdk-src"))
+ (invoke "javah" "-jni"
+ "-classpath" "classes"
+ "-d" "lib/"
+ "net.sf.samtools.util.zip.IntelDeflater")
+ (with-directory-excursion "src/c/inteldeflater"
+ (invoke "gcc" "-I../../../lib" "-I."
+ (string-append "-I" (assoc-ref inputs "jdk")
+ "/include/linux")
+ "-I../../../jdk-src/src/share/native/common/"
+ "-I../../../jdk-src/src/solaris/native/common/"
+ "-c" "-O3" "-fPIC" "IntelDeflater.c")
+ (invoke "gcc" "-shared"
+ "-o" "../../../lib/jni/libIntelDeflater.so"
+ "IntelDeflater.o" "-lz" "-lstdc++"))
+ #t))
;; We can only build everything else after building the JNI library.
(add-after 'build-jni 'build-rest
(lambda* (#:key make-flags #:allow-other-keys)
- (zero? (apply system* `("ant" "all" ,@make-flags)))))
+ (apply invoke `("ant" "all" ,@make-flags))
+ #t))
(add-before 'build 'set-JAVA6_HOME
(lambda _
(setenv "JAVA6_HOME" (getenv "JAVA_HOME"))
"src/mash/CommandScreen.cpp")
(("^#include \"kseq\\.h\"")
"#include \"htslib/kseq.h\""))
- #t))
- (add-after 'fix-includes 'autoconf
- (lambda _ (zero? (system* "autoconf")))))))
+ #t)))))
(native-inputs
`(("autoconf" ,autoconf)
;; Capnproto and htslib are statically embedded in the final
(delete 'configure)
(replace 'check
;; There are no tests, so just test if it runs.
- (lambda _ (zero? (system* "./muscle" "-version"))))
+ (lambda _ (invoke "./muscle" "-version") #t))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(bin (string-append out "/bin")))
- (install-file "muscle" bin)))))))
+ (install-file "muscle" bin)
+ #t))))))
(home-page "http://www.drive5.com/muscle")
(synopsis "Multiple sequence alignment program")
(description
(base32
"1hkw21rq1mwf7xp0rmbb2gqc0i6p11108m69i7mr7xcjl268pxnb"))))
(build-system gnu-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'autoconf
- (lambda _ (zero? (system* "autoreconf" "-vif")))))))
(inputs
;; XXX: TODO: Enable Lua and Guile bindings.
;; https://github.com/tjunier/newick_utils/issues/13
(add-after 'unpack 'enter-scripts-dir
(lambda _ (chdir "scripts")))
(replace 'check
- (lambda _
- (zero? (system* "python" "-m" "unittest" "discover" "-v"))))
+ (lambda _ (invoke "python" "-m" "unittest" "discover" "-v") #t))
(add-after 'install 'wrap-executables
(lambda* (#:key inputs outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(getenv "PATH")))
(setenv "PERL5LIB" (string-append (getcwd) "/lib" ":"
(getenv "PERL5LIB")))
- (zero? (length (filter (lambda (file)
- (display file)(display "\n")
- (not (zero? (system* "perl" file))))
- (find-files "t" ".*\\.t$"))))))
+ (for-each (lambda (file)
+ (display file)(display "\n")
+ (invoke "perl" file))
+ (find-files "t" ".*\\.t$"))
+ #t))
(replace 'install
;; There is no 'install' target in the Makefile.
(lambda* (#:key outputs #:allow-other-keys)
(modify-phases %standard-phases
(replace 'bootstrap
(lambda _
- (invoke "bash" "gen_auto")))
+ (substitute* "gen_tools_am"
+ (("/usr/bin/env.*") (which "perl")))
+ (invoke "bash" "gen_auto")
+ #t))
(add-after 'build 'build-additional-tools
(lambda* (#:key make-flags #:allow-other-keys)
- (every (lambda (dir)
- (with-directory-excursion (string-append "tools/" dir)
- (zero? (apply system* "make" make-flags))))
- dirs)))
+ (for-each (lambda (dir)
+ (with-directory-excursion (string-append "tools/" dir)
+ (apply invoke "make" make-flags)))
+ dirs)
+ #t))
(add-after 'install 'install-additional-tools
(lambda* (#:key make-flags #:allow-other-keys)
- (fold (lambda (dir result)
- (with-directory-excursion (string-append "tools/" dir)
- (and result
- (zero? (apply system*
- `("make" ,@make-flags "install"))))))
- #t dirs)))))))
+ (for-each (lambda (dir)
+ (with-directory-excursion (string-append "tools/" dir)
+ (apply invoke `("make" ,@make-flags "install"))))
+ dirs)
+ #t))))))
(inputs
`(("gsl" ,gsl)
("boost" ,boost)
(define-public ngs-sdk
(package
(name "ngs-sdk")
- (version "1.3.0")
+ (version "2.9.3")
(source (origin
(method git-fetch)
(uri (git-reference
(file-name (git-file-name name version))
(sha256
(base32
- "1l8p81azb9p6nsdfai0hvyai33z6nsgy7hj30arh9b5kb6m443dx"))))
+ "17c0v1nah3g3d2ib5bbi0vhma1ghd6vb9xycavqsh64lhp840rk3"))))
(build-system gnu-build-system)
(arguments
`(#:parallel-build? #f ; not supported
;; The 'configure' script doesn't recognize things like
;; '--enable-fast-install'.
- (zero? (system* "./configure"
- (string-append "--build-prefix=" (getcwd) "/build")
- (string-append "--prefix=" out))))))
+ (invoke "./configure"
+ (string-append "--build-prefix=" (getcwd) "/build")
+ (string-append "--prefix=" out))
+ #t)))
(add-after 'unpack 'enter-dir
(lambda _ (chdir "ngs-sdk") #t)))))
(native-inputs `(("perl" ,perl)))
(define-public ncbi-vdb
(package
(name "ncbi-vdb")
- (version "2.8.2")
+ (version "2.9.3")
(source (origin
(method git-fetch)
(uri (git-reference
(file-name (git-file-name name version))
(sha256
(base32
- "1ssy5wlqdm86pmbv9mfdjx518lbsk32wfv2qgr7m1z77kaicw7zq"))))
+ "1l4ny67nxwv1lagk9wwjbrgm7ln7adci6dnpc7k1yaln6shj0qpm"))))
(build-system gnu-build-system)
(arguments
`(#:parallel-build? #f ; not supported
(version "1.90b4")
(source
(origin
- (method url-fetch)
- (uri (string-append "https://github.com/chrchang/plink-ng/archive/v"
- version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/chrchang/plink-ng.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
(sha256
- (base32 "09ixrds009aczjswxr2alcb774mksq5g0v78dgjjn1h4dky0kf9a"))))
+ (base32 "02npdwgkpfkdnhw819rhj5kw02a5k5m90b14zq9zzya4hyg929c0"))))
(build-system gnu-build-system)
(arguments
'(#:tests? #f ;no "check" target
(define-public sra-tools
(package
(name "sra-tools")
- (version "2.8.2-1")
+ (version "2.9.3")
(source
(origin
(method git-fetch)
(file-name (git-file-name name version))
(sha256
(base32
- "12ln0pk8yajhmmj9xsfwa1qgv5m05ji40jsg17wdcls62zz6fwrk"))))
+ "0663gcdxkziwsmlznjxysb00621rllpbz6jwsfifq7z3dj3lwm8b"))))
(build-system gnu-build-system)
(arguments
`(#:parallel-build? #f ; not supported
;; The 'configure' script doesn't recognize things like
;; '--enable-fast-install'.
- (zero? (system*
- "./configure"
+ (invoke "./configure"
(string-append "--build-prefix=" (getcwd) "/build")
(string-append "--prefix=" (assoc-ref outputs "out"))
(string-append "--debug")
(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)))
+ (assoc-ref inputs "hdf5")))
#t)))))
(native-inputs `(("perl" ,perl)))
(inputs
#:phases
(modify-phases %standard-phases
(replace 'check
- (lambda _
- (zero? (system* "python" "-m" "unittest" "discover" "-v")))))))
+ (lambda _ (invoke "python" "-m" "unittest" "discover" "-v") #t)))))
(propagated-inputs
`(("python-sqlalchemy" ,python2-sqlalchemy)
("python-decorator" ,python2-decorator)
(define-public vsearch
(package
(name "vsearch")
- (version "2.8.0")
+ (version "2.9.1")
(source
(origin
(method git-fetch)
(file-name (git-file-name name version))
(sha256
(base32
- "0lrw6n75gmqkxl053yi2pwwvnzwf1r79ypzxgv6m0kw6df5fwv6r"))
+ "0vhrpjfdf75ba04b24xknp41790cvcgwl0vgpy7qbzj5xh2521ss"))
(patches (search-patches "vsearch-unbundle-cityhash.patch"))
(snippet
'(begin
(delete-file "src/city.cc")
#t))))
(build-system gnu-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'autogen
- (lambda _ (zero? (system* "autoreconf" "-vif")))))))
(inputs
`(("zlib" ,zlib)
("bzip2" ,bzip2)
(define-public r-biocviews
(package
(name "r-biocviews")
- (version "1.50.1")
+ (version "1.50.5")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "biocViews" version))
(sha256
(base32
- "0hjm3r58i0r9qhyar9pk250cx7sfijg0lnvi12a9s6brmmbip1a3"))))
+ "0rc1n89n04ylvy9gvsgvizcs77bh70jg1nkjjsjs7rqbr3zzdysz"))))
(properties
`((upstream-name . "biocViews")))
(build-system r-build-system)
(define-public r-s4vectors
(package
(name "r-s4vectors")
- (version "0.20.0")
+ (version "0.20.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "S4Vectors" version))
(sha256
(base32
- "0qgiykjhnsvvpcp3zwmrnpx3bv3msvj0szchyvb1yb0fxw716xc5"))))
+ "18whrw67nxn82xshckl2pjy7d14sa3c27h3n9naqyqwz88lr6dzg"))))
(properties
`((upstream-name . "S4Vectors")))
(build-system r-build-system)
(define-public r-genomeinfodbdata
(package
(name "r-genomeinfodbdata")
- (version "1.1.0")
+ (version "1.2.0")
(source (origin
(method url-fetch)
;; We cannot use bioconductor-uri here because this tarball is
version ".tar.gz"))
(sha256
(base32
- "0k1hsjx6n2i1sf14hyrgdhxqxm5mxk0bgnivhiax944whcicmzbf"))))
+ "0di6nlqpsyqf693k2na65ayqldih563x3zfrczpqc5q2hl5kg35c"))))
(properties
`((upstream-name . "GenomeInfoDbData")))
(build-system r-build-system)
(define-public r-genomeinfodb
(package
(name "r-genomeinfodb")
- (version "1.18.0")
+ (version "1.18.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomeInfoDb" version))
(sha256
(base32
- "1xqpgngd8by0yn627v9kz26a03v5a1lhcfwlnx2i0ivplk9bd40s"))))
+ "049pyzr8iszv3g7wdqf3pz7vg7bzd450c20ln6fgw4g5xnkkr10s"))))
(properties
`((upstream-name . "GenomeInfoDb")))
(build-system r-build-system)
(define-public r-biostrings
(package
(name "r-biostrings")
- (version "2.50.0")
+ (version "2.50.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "Biostrings" version))
(sha256
(base32
- "0zw0dj67fnpbz4iqnam5fxs92c1c8w8d7mzl0rkq4ksx0xl8vgg7"))))
+ "1qyv1ps7vy6gy78pm2rcikg0bgf1mv7falahjp3pkwqq1272hrl8"))))
(properties
`((upstream-name . "Biostrings")))
(build-system r-build-system)
(define-public r-go-db
(package
(name "r-go-db")
- (version "3.6.0")
+ (version "3.7.0")
(source (origin
(method url-fetch)
(uri (string-append "https://www.bioconductor.org/packages/"
version ".tar.gz"))
(sha256
(base32
- "0fi2qywr9apg5lwfqfq9qq6bgrnv4rdhxx25656qn4bsy62i838j"))))
+ "0i3wcf5h3n0dawzc1hy0kv74f06j80c47n4p3g3fmrcxlhi3jpa5"))))
(properties
`((upstream-name . "GO.db")))
(build-system r-build-system)
(define-public r-genomationdata
(package
(name "r-genomationdata")
- (version "1.10.0")
+ (version "1.14.0")
(source (origin
(method url-fetch)
;; We cannot use bioconductor-uri here because this tarball is
"genomationData_" version ".tar.gz"))
(sha256
(base32
- "0h7g5x3kyb50qlblz5hc85lfm6n6f5nb68i146way3ggs04sqvla"))))
+ "10xyb8akjrhmak2i0mnv1agny2ipy364q9nlibyplpzc7vdb6bw7"))))
(build-system r-build-system)
;; As this package provides little more than large data files, it doesn't
;; make sense to build substitutes.
(define-public r-org-hs-eg-db
(package
(name "r-org-hs-eg-db")
- (version "3.5.0")
+ (version "3.7.0")
(source (origin
(method url-fetch)
;; We cannot use bioconductor-uri here because this tarball is
"org.Hs.eg.db_" version ".tar.gz"))
(sha256
(base32
- "1v6wa5613cjq59xd7x1qz8lr9nb2abm9abl2cci1khrnrlpla927"))))
+ "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim"))))
(properties
`((upstream-name . "org.Hs.eg.db")))
(build-system r-build-system)
(define-public r-org-ce-eg-db
(package
(name "r-org-ce-eg-db")
- (version "3.5.0")
+ (version "3.7.0")
(source (origin
(method url-fetch)
;; We cannot use bioconductor-uri here because this tarball is
"org.Ce.eg.db_" version ".tar.gz"))
(sha256
(base32
- "02ggchixlmzywhsbr0h2ms4dravv7m5964cjxqcjxqs16vjwlbk9"))))
+ "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz"))))
(properties
`((upstream-name . "org.Ce.eg.db")))
(build-system r-build-system)
(define-public r-org-dm-eg-db
(package
(name "r-org-dm-eg-db")
- (version "3.5.0")
+ (version "3.7.0")
(source (origin
(method url-fetch)
;; We cannot use bioconductor-uri here because this tarball is
"org.Dm.eg.db_" version ".tar.gz"))
(sha256
(base32
- "033qak1d3wwz17va0bh8z8p8arx0aw2va6gm1qfwsvdkj9cd9d7d"))))
+ "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3"))))
(properties
`((upstream-name . "org.Dm.eg.db")))
(build-system r-build-system)
(define-public r-org-mm-eg-db
(package
(name "r-org-mm-eg-db")
- (version "3.5.0")
+ (version "3.7.0")
(source (origin
(method url-fetch)
;; We cannot use bioconductor-uri here because this tarball is
"org.Mm.eg.db_" version ".tar.gz"))
(sha256
(base32
- "11q21p3ki4bn4hb3aix0g775l45l66jmas6m94nfhqqnpjhv4d6g"))))
+ "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx"))))
(properties
`((upstream-name . "org.Mm.eg.db")))
(build-system r-build-system)
(define-public r-txdb-mmusculus-ucsc-mm10-knowngene
(package
(name "r-txdb-mmusculus-ucsc-mm10-knowngene")
- (version "3.4.0")
+ (version "3.4.4")
(source (origin
(method url-fetch)
;; We cannot use bioconductor-uri here because this tarball is
version ".tar.gz"))
(sha256
(base32
- "08gava9wsvpcqz51k2sni3pj03n5155v32d9riqbf305nbirqbkb"))))
+ "01lgxc1fx5nhlpbwjd5zqghkkbmh6axd98ikx4b0spv0jdg6gf39"))))
(properties
`((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
(build-system r-build-system)
(("\\$\\(bindir\\)/embossupdate") ""))
#t))
(add-after 'disable-update-check 'autogen
- (lambda _ (zero? (system* "autoreconf" "-vif")))))))
+ (lambda _ (invoke "autoreconf" "-vif") #t)))))
(inputs
`(("perl" ,perl)
("libpng" ,libpng)
(define-public r-msnbase
(package
(name "r-msnbase")
- (version "2.8.0")
+ (version "2.8.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MSnbase" version))
(sha256
(base32
- "0nnlydpklmv9kwlk3gkjgabx7l6y4gav3imq98w8wskb1fhm50c0"))))
+ "0y658anh06vnvbkfs7r8q40gqgyqr2r8kj7jlpnp33fy1lvp1nv7"))))
(properties `((upstream-name . "MSnbase")))
(build-system r-build-system)
(propagated-inputs
(define-public r-ensembldb
(package
(name "r-ensembldb")
- (version "2.6.0")
+ (version "2.6.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ensembldb" version))
(sha256
(base32
- "12jqz9h6w4mxyfr43w5qbwmacn512aw0mnl0zvhsg5i7p4qj45ks"))))
+ "0hdz1f34v7sas2v4225icwl3wd4sf17ykpd5dkbx1hc7wcy4w3np"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
(define-public sambamba
(package
(name "sambamba")
- (version "0.6.7-10-g223fa20")
+ (version "0.6.8")
(source
(origin
(method git-fetch)
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32
- "1zb9hrxglxqh13ava9wwri30cvf85hjnbn8ccnr8l60a3k5avczn"))))
+ "0k0cz3qcv98p6cq09zlbgnjsggxcqbcmzxg5zikgcgbr2nfq4lry"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; there is no test target
(add-after 'unpack 'fix-ldc-version
(lambda _
(substitute* "gen_ldc_version_info.py"
- (("/usr/bin/env.*") (which "python")))
+ (("/usr/bin/env.*") (which "python3")))
(substitute* "Makefile"
- (("\\$\\(shell which ldmd2\\)") (which "ldmd2")))
+ ;; We use ldc2 instead of ldmd2 to compile sambamba.
+ (("\\$\\(shell which ldmd2\\)") (which "ldc2")))
#t))
(add-after 'unpack 'place-biod-and-undead
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "Makefile"
(("htslib/libhts.a lz4/lib/liblz4.a")
"-L-lhts -L-llz4")
- ((" htslib-static lz4-static") ""))
+ ((" lz4-static htslib-static") ""))
#t))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(bin (string-append out "/bin")))
(mkdir-p bin)
- (install-file "build/sambamba" bin)
+ (install-file "bin/sambamba" bin)
#t))))))
(native-inputs
`(("ldc" ,ldc)
("rdmd" ,rdmd)
- ("python" ,python2-minimal)
+ ("python" ,python-minimal)
("biod"
- ,(let ((commit "c778e4f2d8bacea7499283ce39f5577b232732c6"))
+ ,(let ((commit "4f1a7d2fb7ef3dfe962aa357d672f354ebfbe42e"))
(origin
(method git-fetch)
(uri (git-reference
"-checkout"))
(sha256
(base32
- "1z90562hg47i63gx042wb3ak2vqjg5z7hwgn9bp2pdxfg3nxrw37")))))
+ "1k5pdjv1qvi0a3rwd1sfq6zbj37l86i7bf710m4c0y6737lxj426")))))
("undead"
- ,(let ((commit "92803d25c88657e945511f0976a0c79d8da46e89"))
+ ,(let ((commit "9be93876982b5f14fcca60832563b3cd767dd84d"))
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/dlang/undeaD.git")
+ (url "https://github.com/biod/undeaD.git")
(commit commit)))
(file-name (string-append "undead-"
(string-take commit 9)
"-checkout"))
(sha256
(base32
- "0vq6n81vzqvgphjw54lz2isc1j8lcxwjdbrhqz1h5gwrvw9w5138")))))))
+ "1xfarj0nqlmi5jd1vmcmm7pabzaf9hxyvk6hp0d6jslb5k9r8r3d")))))))
(inputs
`(("lz4" ,lz4)
("htslib" ,htslib-for-sambamba)))
(include "external/install/include/rapmap/")
(rapmap (assoc-ref inputs "rapmap")))
(mkdir-p "/tmp/rapmap")
- (system* "tar" "xf"
- (assoc-ref inputs "rapmap")
- "-C" "/tmp/rapmap"
- "--strip-components=1")
+ (invoke "tar" "xf"
+ (assoc-ref inputs "rapmap")
+ "-C" "/tmp/rapmap"
+ "--strip-components=1")
(mkdir-p src)
(mkdir-p include)
(for-each (lambda (file)
absolute GSEA.")
(license license:gpl2)))
+(define-public jamm
+ (package
+ (name "jamm")
+ (version "1.0.7.5")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/mahmoudibrahim/JAMM.git")
+ (commit (string-append "JAMMv" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0ls889jcma1ch9h21jjhnkadgszgqj41842hhcjh6cg88f85qf3i"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; there are none
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (replace 'build
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (substitute* "JAMM.sh"
+ (("^sPath=.*")
+ (string-append "")))
+ #t))
+ (replace 'install
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (libexec (string-append out "/libexec/jamm"))
+ (bin (string-append out "/bin")))
+ (substitute* '("JAMM.sh"
+ "SignalGenerator.sh")
+ (("^sPath=.*")
+ (string-append "sPath=\"" libexec "\"\n")))
+ (for-each (lambda (file)
+ (install-file file libexec))
+ (list "bincalculator.r"
+ "peakfinder.r"
+ "peakhelper.r"
+ "signalmaker.r"
+ "xcorr.r"
+ "xcorrhelper.r"
+ ;; Perl scripts
+ "peakfilter.pl"
+ "readshifter.pl"))
+
+ (for-each
+ (lambda (script)
+ (chmod script #o555)
+ (install-file script bin)
+ (wrap-program (string-append bin "/" script)
+ `("PATH" ":" prefix
+ (,(string-append (assoc-ref inputs "coreutils") "/bin")
+ ,(string-append (assoc-ref inputs "gawk") "/bin")
+ ,(string-append (assoc-ref inputs "perl") "/bin")
+ ,(string-append (assoc-ref inputs "r-minimal") "/bin")))
+ `("PERL5LIB" ":" prefix (,(getenv "PERL5LIB")))
+ `("R_LIBS_SITE" ":" prefix (,(getenv "R_LIBS_SITE")))))
+ (list "JAMM.sh" "SignalGenerator.sh")))
+ #t)))))
+ (inputs
+ `(("bash" ,bash)
+ ("coreutils" ,coreutils)
+ ("gawk" ,gawk)
+ ("perl" ,perl)
+ ("r-minimal" ,r-minimal)
+ ;;("r-parallel" ,r-parallel)
+ ("r-signal" ,r-signal)
+ ("r-mclust" ,r-mclust)))
+ (home-page "https://github.com/mahmoudibrahim/JAMM")
+ (synopsis "Peak finder for NGS datasets")
+ (description
+ "JAMM is a peak finder for next generation sequencing datasets (ChIP-Seq,
+ATAC-Seq, DNase-Seq, etc.) that can integrate replicates and assign peak
+boundaries accurately. JAMM is applicable to both broad and narrow
+datasets.")
+ (license license:gpl3+)))
+
(define-public ngless
(package
(name "ngless")
choosing which reads pass the filter.")
(license (list license:gpl3 ;filtlong
license:asl2.0))))) ;histogram.py
+
+(define-public nanopolish
+ ;; The recommended way to install is to clone the git repository
+ ;; <https://github.com/jts/nanopolish#installing-a-particular-release>.
+ ;; Also, the differences between release and current version seem to be
+ ;; significant.
+ (let ((commit "50e8b5cc62f9b46f5445f5c5e8c5ab7263ea6d9d")
+ (revision "1"))
+ (package
+ (name "nanopolish")
+ (version (git-version "0.10.2" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/jts/nanopolish.git")
+ (commit commit)
+ (recursive? #t)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "09j5gz57yr9i34a27vbl72i4g8syv2zzgmsfyjq02yshmnrvkjs6"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:make-flags
+ `("HDF5=noinstall" "EIGEN=noinstall" "HTS=noinstall" "CC=gcc")
+ #:tests? #f ; no check target
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'find-eigen
+ (lambda* (#:key inputs #:allow-other-keys)
+ (setenv "CPATH"
+ (string-append (assoc-ref inputs "eigen")
+ "/include/eigen3"))
+ #t))
+ (delete 'configure)
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin"))
+ (scripts (string-append out "/share/nanopolish/scripts")))
+
+ (install-file "nanopolish" bin)
+ (for-each (lambda (file) (install-file file scripts))
+ (find-files "scripts" ".*"))
+ #t)))
+ (add-after 'install 'wrap-programs
+ (lambda* (#:key outputs #:allow-other-keys)
+ (for-each (lambda (file)
+ (wrap-program file `("PYTHONPATH" ":" prefix (,path))))
+ (find-files "/share/nanopolish/scripts" "\\.py"))
+ (for-each (lambda (file)
+ (wrap-program file `("PERL5LIB" ":" prefix (,path))))
+ (find-files "/share/nanopolish/scripts" "\\.pl"))
+ #t)))))
+ (inputs
+ `(("eigen" ,eigen)
+ ("hdf5" ,hdf5)
+ ("htslib" ,htslib)
+ ("perl" ,perl)
+ ("python" ,python)
+ ("python-biopython" ,python-biopython)
+ ("python-numpy" ,python-numpy)
+ ("python-pysam" ,python-pysam)
+ ("python-scikit-learn" , python-scikit-learn)
+ ("python-scipy" ,python-scipy)
+ ("zlib" ,zlib)))
+ (home-page "https://github.com/jts/nanopolish")
+ (synopsis "Signal-level analysis of Oxford Nanopore sequencing data")
+ (description
+ "This package analyses the Oxford Nanopore sequencing data at signal-level.
+Nanopolish can calculate an improved consensus sequence for a draft genome
+assembly, detect base modifications, call SNPs (Single nucleotide
+polymorphisms) and indels with respect to a reference genome and more.")
+ (license license:expat))))
HCoop / jackhill / guix / guix.git / blobdiff