diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 512 |
1 files changed, 252 insertions, 260 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1fac960eff..8820ba0d8e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -753,15 +753,15 @@ e.g. microbiome samples, genomes, metagenomes.") (package (inherit base) (arguments - `(#:phases - (modify-phases %standard-phases - ;; Do not require the unmaintained pyqi library. - (add-after 'unpack 'remove-pyqi - (lambda _ - (substitute* "setup.py" - (("install_requires.append\\(\"pyqi\"\\)") "pass")) - #t))) - ,@(package-arguments base)))))) + (substitute-keyword-arguments (package-arguments base) + ((#:phases phases) + `(modify-phases ,phases + ;; Do not require the unmaintained pyqi library. + (add-after 'unpack 'remove-pyqi + (lambda _ + (substitute* "setup.py" + (("install_requires.append\\(\"pyqi\"\\)") "pass")) + #t))))))))) (define-public bioperl-minimal (let* ((inputs `(("perl-module-build" ,perl-module-build) @@ -2716,8 +2716,10 @@ Illumina, Roche 454, and the SOLiD platform.") (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"))) @@ -2734,21 +2736,24 @@ Illumina, Roche 454, and the SOLiD platform.") (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. @@ -3471,26 +3476,28 @@ VCF.") (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")) @@ -3977,16 +3984,16 @@ sequences).") (define-public mash (package (name "mash") - (version "2.0") + (version "2.1") (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/marbl/mash/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/marbl/mash.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "00fx14vpmgsijwxd1xql3if934l82v8ckqgjjyyhnr36qb9qrskv")) + "049hwcc059p2fd9vwndn63laifvvsi0wmv84i6y1fr79k15dxwy6")) (modules '((guix build utils))) (snippet '(begin @@ -4011,9 +4018,7 @@ sequences).") "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 @@ -4040,13 +4045,14 @@ form of assemblies or reads.") (version "2.12.1") (source (origin - (method url-fetch) - (uri (string-append "https://bitbucket.org/berkeleylab/metabat/get/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://bitbucket.org/berkeleylab/metabat.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "1hmvdalz3zj5sqqklg0l4npjdv37cv2hsdi1al9iby2ndxjs1b73")) + "0hyg2smw1nz69mfvjpk45xyyychmda92c80a0cv7baji84ri4iyn")) (patches (search-patches "metabat-fix-compilation.patch")))) (build-system scons-build-system) (arguments @@ -4109,16 +4115,16 @@ probabilistic distances of genome abundance and tetranucleotide frequency.") (define-public minced (package (name "minced") - (version "0.2.0") + (version "0.3.2") (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/ctSkennerton/minced/archive/" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/ctSkennerton/minced.git") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "0wxmlsapxfpxfd3ps9636h7i2xy6la8i42mwh0j2lsky63h63jp1")))) + "1f5h9him0gd355cnx7p6pnxpknhckd4g0v62mg8zyhfbx9as25fv")))) (build-system gnu-build-system) (arguments `(#:test-target "test" @@ -4230,12 +4236,13 @@ that a read originated from a particular isoform.") (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 @@ -4260,11 +4267,6 @@ program for nucleotide and protein sequences.") (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 @@ -4309,19 +4311,20 @@ interrupted by stop codons. OrfM finds and prints these ORFs.") (license license:lgpl3+))) (define-public pplacer - (let ((commit "g807f6f3")) + (let ((commit "807f6f3")) (package (name "pplacer") ;; The commit should be updated with each version change. (version "1.1.alpha19") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/matsen/pplacer/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/matsen/pplacer.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 - (base32 "0z1lnd2s8sh6kpzg106wzbh2szw7h0hvq8syd5a6wv4rmyyz6x0f")))) + (base32 "11ppbbbx20p2g9wj3ff64dhnarb12q79v7qh4rk0gj6lkbz4n7cn")))) (build-system ocaml-build-system) (arguments `(#:ocaml ,ocaml-4.01 @@ -4338,11 +4341,12 @@ interrupted by stop codons. OrfM finds and prints these ORFs.") (local-dir "cddlib_guix")) (mkdir local-dir) (with-directory-excursion local-dir - (system* "tar" "xvf" cddlib-src)) + (invoke "tar" "xvf" cddlib-src)) (let ((cddlib-src-folder (string-append local-dir "/" (list-ref (scandir local-dir) 2) "/lib-src"))) + (for-each make-file-writable (find-files "cdd_src" ".*")) (for-each (lambda (file) (copy-file file @@ -4406,8 +4410,7 @@ downstream analysis.") (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")) @@ -4667,13 +4670,14 @@ large-scale data and can be applied to hundreds of species at once.") (version "2.0.7") (source (origin - (method url-fetch) - (uri (string-append "https://bitbucket.org/regulatorygenomicsupf/" - "pyicoteo/get/v" version ".tar.bz2")) - (file-name (string-append name "-" version ".tar.bz2")) + (method git-fetch) + (uri (git-reference + (url "https://bitbucket.org/regulatorygenomicsupf/pyicoteo.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "0d6087f29xp8wxwlj111c3sylli98n0l8ry58c51ixzq0zfm50wa")))) + "0hz5g8d25lbjy1wpscr490l0lmyvaix893hhax4fxnh1h9w34w8p")))) (build-system python-build-system) (arguments `(#:python ,python-2 ; does not work with Python 3 @@ -4757,10 +4761,11 @@ partial genes, and identifies translation initiation sites.") (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) @@ -4849,18 +4854,17 @@ extremely diverse sets of genomes.") (define-public raxml (package (name "raxml") - (version "8.2.10") + (version "8.2.12") (source (origin - (method url-fetch) - (uri - (string-append - "https://github.com/stamatak/standard-RAxML/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/stamatak/standard-RAxML.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "13s7aspfdcfr6asynwdg1x6vznys6pzap5f8wsffbnnwpkkg9ya8")))) + "1jqjzhch0rips0vp04prvb8vmc20c5pdmsqn8knadcf91yy859fh")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; There are no tests. @@ -5053,21 +5057,24 @@ distribution, coverage uniformity, strand specificity, etc.") (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) @@ -5233,17 +5240,16 @@ Roche 454, Ion Torrent and Pacific BioSciences SMRT.") (define-public ngs-sdk (package (name "ngs-sdk") - (version "1.3.0") - (source - (origin - (method url-fetch) - (uri - (string-append "https://github.com/ncbi/ngs/archive/" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "1wiyf4c6nm2j87pv015cbi0qny5byf3pbvcw3likifz5dl56ag40")))) + (version "2.9.3") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ncbi/ngs.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "17c0v1nah3g3d2ib5bbi0vhma1ghd6vb9xycavqsh64lhp840rk3")))) (build-system gnu-build-system) (arguments `(#:parallel-build? #f ; not supported @@ -5259,9 +5265,10 @@ Roche 454, Ion Torrent and Pacific BioSciences SMRT.") ;; 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))) @@ -5299,23 +5306,24 @@ simultaneously.") (define-public ncbi-vdb (package (name "ncbi-vdb") - (version "2.8.2") - (source - (origin - (method url-fetch) - (uri - (string-append "https://github.com/ncbi/ncbi-vdb/archive/" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "1acn4bv81mfl137qnbn9995mjjhwd36pm0b7qli1iw5skrxa9j8m")))) + (version "2.9.3") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ncbi/ncbi-vdb.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1l4ny67nxwv1lagk9wwjbrgm7ln7adci6dnpc7k1yaln6shj0qpm")))) (build-system gnu-build-system) (arguments `(#:parallel-build? #f ; not supported #:tests? #f ; no "check" target #:phases (modify-phases %standard-phases + (add-after 'unpack 'make-files-writable + (lambda _ (for-each make-file-writable (find-files "." ".*")) #t)) (add-before 'configure 'set-perl-search-path (lambda _ ;; Work around "dotless @INC" build failure. @@ -5349,8 +5357,7 @@ simultaneously.") ;; 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") @@ -5359,7 +5366,8 @@ simultaneously.") (string-append "--with-ngs-sdk-prefix=" (assoc-ref inputs "ngs-sdk")) (string-append "--with-hdf5-prefix=" - (assoc-ref inputs "hdf5"))))))) + (assoc-ref inputs "hdf5"))) + #t))) (add-after 'install 'install-interfaces (lambda* (#:key outputs #:allow-other-keys) ;; Install interface libraries. On i686 the interface libraries @@ -5464,12 +5472,13 @@ subsequent visualization, annotation and storage of results.") (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 @@ -5551,14 +5560,14 @@ structures, classes for genomic regions, mapped sequencing reads, etc.") (define-public preseq (package (name "preseq") - (version "2.0") + (version "2.0.3") (source (origin (method url-fetch) - (uri (string-append "https://github.com/smithlabcode/" - "preseq/archive/v" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (uri (string-append "https://github.com/smithlabcode/preseq/" + "releases/download/v" version + "/preseq_v" version ".tar.bz2")) (sha256 - (base32 "08r684l50pnxjpvmhzjgqq56yv9rfw90k8vx0nsrnrzk8mf9hsdq")) + (base32 "149x9xmk1wy1gff85325yfzqc0qk4sgp1w6gbyj9cnji4x1dszbl")) (modules '((guix build utils))) (snippet '(begin ;; Remove bundled samtools. @@ -5648,17 +5657,17 @@ sequence itself can be retrieved from these databases.") (define-public sra-tools (package (name "sra-tools") - (version "2.8.2-1") + (version "2.9.3") (source (origin - (method url-fetch) - (uri - (string-append "https://github.com/ncbi/sra-tools/archive/" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/ncbi/sra-tools.git") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "1camsijmvv2s45mb4iyf44ghl4gkd4rl0viphpcgl3ccchy32a0g")))) + "0663gcdxkziwsmlznjxysb00621rllpbz6jwsfifq7z3dj3lwm8b")))) (build-system gnu-build-system) (arguments `(#:parallel-build? #f ; not supported @@ -5708,8 +5717,7 @@ sequence itself can be retrieved from these databases.") ;; 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") @@ -5727,18 +5735,7 @@ sequence itself can be retrieved from these databases.") (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 @@ -5865,24 +5862,16 @@ is one that takes arguments.") (define-public seqtk (package (name "seqtk") - (version "1.2") + (version "1.3") (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/lh3/seqtk/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/lh3/seqtk.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "0ywdyzpmfiz2wp6ampbzqg4y8bj450nfgqarpamg045b8mk32lxx")) - (modules '((guix build utils))) - (snippet - '(begin - ;; Remove extraneous header files, as is done in the seqtk - ;; master branch. - (for-each (lambda (file) (delete-file file)) - (list "ksort.h" "kstring.h" "kvec.h")) - #t)))) + "1bfzlqa84b5s1qi22blmmw2s8xdyp9h9ydcq22pfjhh5gab3yz6l")))) (build-system gnu-build-system) (arguments `(#:phases @@ -5890,11 +5879,12 @@ is one that takes arguments.") (delete 'configure) (replace 'check ;; There are no tests, so we just run a sanity check. - (lambda _ (zero? (system* "./seqtk" "seq")))) + (lambda _ (invoke "./seqtk" "seq") #t)) (replace 'install (lambda* (#:key outputs #:allow-other-keys) (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) - (install-file "seqtk" bin))))))) + (install-file "seqtk" bin) + #t)))))) (inputs `(("zlib" ,zlib))) (home-page "https://github.com/lh3/seqtk") @@ -5910,20 +5900,20 @@ optionally compressed by gzip.") (name "snap-aligner") (version "1.0beta.18") (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/amplab/snap/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/amplab/snap.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "1vnsjwv007k1fl1q7d681kbwn6bc66cgw6h16hym6gvyy71qv2ly")))) + "01w3qq4wm07z73vky0cfwlmrbf50n3w722cxrlzxfi99mnb808d8")))) (build-system gnu-build-system) (arguments '(#:phases (modify-phases %standard-phases (delete 'configure) - (replace 'check (lambda _ (zero? (system* "./unit_tests")))) + (replace 'check (lambda _ (invoke "./unit_tests") #t)) (replace 'install (lambda* (#:key outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) @@ -5952,14 +5942,14 @@ of these reads to align data quickly through a hash-based indexing scheme.") (version "2.1b") (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/biocore/sortmerna/archive/" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/biocore/sortmerna.git") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "1ghaghvd82af9j5adavxh77g7hm247d1r69m3fbi6f1jdivj5ldk")))) + "0j3mbz4n25738yijmjbr5r4fyvkgm8v5vn3sshyfvmyqf5q9byqf")))) (build-system gnu-build-system) (outputs '("out" ;for binaries "db")) ;for sequence databases @@ -6205,8 +6195,7 @@ Cuffdiff or Ballgown programs.") #: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) @@ -6839,17 +6828,17 @@ SELECT or UPDATE queries to an end-point.") (define-public vsearch (package (name "vsearch") - (version "2.8.0") + (version "2.9.1") (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/torognes/vsearch/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/torognes/vsearch.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "15pbirgzhvflj4pi5n82vybbzjy9mlb0lv5l3qhrmdkfzpbyahw3")) + "0vhrpjfdf75ba04b24xknp41790cvcgwl0vgpy7qbzj5xh2521ss")) (patches (search-patches "vsearch-unbundle-cityhash.patch")) (snippet '(begin @@ -6860,11 +6849,6 @@ SELECT or UPDATE queries to an end-point.") (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) @@ -8874,13 +8858,14 @@ Sequences.") (version "1.1.4") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/ManuSetty/SeqGL/" - "archive/" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/ManuSetty/SeqGL.git") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "0pnk1p3sci5yipyc8xnb6jbmydpl80fld927xgnbcv104hy8h8yh")))) + "1r6ywvhxl3ffv48lgj7sbd582mcc6dha3ksgc2qjlvjrnkbj3799")))) (build-system r-build-system) (propagated-inputs `(("r-biostrings" ,r-biostrings) @@ -9042,7 +9027,7 @@ AM_CONDITIONAL(AMPNG, true)")) (("\\$\\(bindir\\)/embossupdate") "")) #t)) (add-after 'disable-update-check 'autogen - (lambda _ (zero? (system* "autoreconf" "-vif"))))))) + (lambda _ (invoke "autoreconf" "-vif") #t))))) (inputs `(("perl" ,perl) ("libpng" ,libpng) @@ -9215,12 +9200,14 @@ group or two ChIP groups run under different conditions.") (name "filevercmp") (version (string-append "0-1." (string-take commit 7))) (source (origin - (method url-fetch) - (uri (string-append "https://github.com/ekg/filevercmp/archive/" - commit ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 "0yp5jswf5j2pqc6517x277s4s6h1ss99v57kxw9gy0jkfl3yh450")))) + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/filevercmp.git") + (commit commit))) + (file-name (git-file-name name commit)) + (sha256 + (base32 + "1j9vxsy0y050v59h0q1d6501fcw1kjvj0d18l1xk2zyg0jzj247c")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; There are no tests to run. @@ -9230,7 +9217,8 @@ group or two ChIP groups run under different conditions.") (replace 'install (lambda* (#:key outputs #:allow-other-keys) (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) - (install-file "filevercmp" bin))))))) + (install-file "filevercmp" bin) + #t)))))) (home-page "https://github.com/ekg/filevercmp") (synopsis "This program compares version strings") (description "This program compares version strings. It intends to be a @@ -11259,16 +11247,16 @@ sort, markdup, and depth.") (define-public ritornello (package (name "ritornello") - (version "1.0.0") + (version "2.0.1") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/KlugerLab/" - "Ritornello/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/KlugerLab/Ritornello.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "02nik86gq9ljjriv6pamwlmqnfky3ads1fpklx6mc3hx6k40pg38")))) + "1xahvq215qld7x1w8vpa5zbrsj6p9crb9shqa2x89sb0aaxa02jk")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; there are no tests @@ -11277,7 +11265,7 @@ sort, markdup, and depth.") (add-after 'unpack 'patch-samtools-references (lambda* (#:key inputs #:allow-other-keys) (substitute* '("src/SamStream.h" - "src/BufferedGenomeReader.h") + "src/FLD.cpp") (("<sam.h>") "<samtools/sam.h>")) #t)) (delete 'configure) @@ -11503,15 +11491,16 @@ applications for tackling some common problems in a user-friendly way.") (define-public tadbit (package (name "tadbit") - (version "0.2") + (version "0.2.0") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/3DGenomes/TADbit/" - "archive/v" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/3DGenomes/TADbit.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "1cnfqrl4685zar4nnw94j94nhvl2h29jm448nadqi1h05z6fdk4f")))) + "07g3aj648prmsvxp9caz5yl41k0y0647vxh0f5p3w8376mfiljd0")))) (build-system python-build-system) (arguments `(;; Tests are included and must be run after installation, but @@ -11566,13 +11555,14 @@ models. TADbit is complemented by TADkit for visualizing 3D models.") (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")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/ENCODE-DCC/kentUtils.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "134aja3k1cj32kbk1nnw0q9gxjb2krr15q6sga8qldzvc0585rmm")) + "0n1wbyjpzii2b9qhyp9r1q76j623cggpg3y8fmw78ld3z4y7ivha")) (modules '((guix build utils) (srfi srfi-26) (ice-9 ftw))) @@ -11623,6 +11613,8 @@ models. TADbit is complemented by TADkit for visualizing 3D models.") #:tests? #f #:phases (modify-phases %standard-phases + (add-after 'unpack 'fix-permissions + (lambda _ (make-file-writable "src/inc/localEnvironment.mk") #t)) (add-after 'unpack 'fix-paths (lambda _ (substitute* "Makefile" @@ -11918,14 +11910,14 @@ accurate as existing quantification tools.") (name "libgff") (version "1.0") (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/Kingsford-Group/" - "libgff/archive/v" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/Kingsford-Group/libgff.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "0vc4nxyhlm6g9vvmx5l4lfs5pnvixsv1hiiy4kddf2y3p6jna8ls")))) + "0n6vfjnq7a2mianipscbshrvbncss8z4zkgkbjw754p9043nfkps")))) (build-system cmake-build-system) (arguments `(#:tests? #f)) ; no tests included (home-page "https://github.com/Kingsford-Group/libgff") @@ -11970,14 +11962,14 @@ bytes of memory space, where n is the length of the string.") (name "sailfish") (version "0.10.1") (source (origin - (method url-fetch) - (uri - (string-append "https://github.com/kingsfordgroup/" - "sailfish/archive/v" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/kingsfordgroup/sailfish.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "1inn60dxiwsz8g9w7kvfhjxj4bwfb0r12dyhpzzhfbig712dkmm0")) + "1amcc5hqvsl42hg4x19bi9vy47cl874s0lw1fmi0hwsdk9i8c03v")) (modules '((guix build utils))) (snippet '(begin @@ -12025,10 +12017,10 @@ bytes of memory space, where n is the length of the string.") (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) |