diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 866 |
1 files changed, 813 insertions, 53 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c427a6d036..546b240f84 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1854,38 +1854,22 @@ file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.") (define-public cutadapt (package (name "cutadapt") - (version "1.14") + (version "1.16") (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/marcelm/cutadapt/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/marcelm/cutadapt.git") + (commit (string-append "v" version)))) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "16gbpiwy4m48vq2h5wqar3i8vr6vcj9gcl2qvqim19x6ya9dp8kd")))) + "09pr02067jiks19nc0aby4xp70hhgvb554i2y1c04rv1m401w7q8")))) (build-system python-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - ;; The tests must be run after installation. - (delete 'check) - (add-after 'install 'check - (lambda* (#:key inputs outputs #:allow-other-keys) - (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")) - (zero? (system* "nosetests" "-P" "tests"))))))) (inputs `(("python-xopen" ,python-xopen))) (native-inputs `(("python-cython" ,python-cython) - ("python-nose" ,python-nose))) + ("python-pytest" ,python-pytest))) (home-page "https://cutadapt.readthedocs.io/en/stable/") (synopsis "Remove adapter sequences from nucleotide sequencing reads") (description @@ -3019,6 +3003,76 @@ sequencing (HTS) data. There are also an number of useful utilities for manipulating HTS data.") (license license:expat))) +(define-public java-htsjdk-latest + (package + (name "java-htsjdk") + (version "2.14.3") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/samtools/htsjdk.git") + (commit version))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "1lmya1fdjy03mz6zmdmd86j9v9vfhqb3952mqq075navx1i6g4bc")))) + (build-system ant-build-system) + (arguments + `(#:tests? #f ; test require Scala + #:jdk ,icedtea-8 + #:jar-name "htsjdk.jar" + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'remove-useless-build.xml + (lambda _ (delete-file "build.xml") #t)) + ;; The tests require the scalatest package. + (add-after 'unpack 'remove-tests + (lambda _ (delete-file-recursively "src/test") #t))))) + (inputs + `(("java-ngs" ,java-ngs) + ("java-snappy-1" ,java-snappy-1) + ("java-commons-compress" ,java-commons-compress) + ("java-commons-logging-minimal" ,java-commons-logging-minimal) + ("java-commons-jexl-2" ,java-commons-jexl-2) + ("java-xz" ,java-xz))) + (native-inputs + `(("java-junit" ,java-junit))) + (home-page "http://samtools.github.io/htsjdk/") + (synopsis "Java API for high-throughput sequencing data (HTS) formats") + (description + "HTSJDK is an implementation of a unified Java library for accessing +common file formats, such as SAM and VCF, used for high-throughput +sequencing (HTS) data. There are also an number of useful utilities for +manipulating HTS data.") + (license license:expat))) + +;; This is needed for picard 2.10.3 +(define-public java-htsjdk-2.10.1 + (package (inherit java-htsjdk-latest) + (name "java-htsjdk") + (version "2.10.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/samtools/htsjdk.git") + (commit version))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "1kxh7slm2pm3x9p6jxa1wqsq9a31dhiiflhxnxqcisan4k3rwia2")))) + (build-system ant-build-system) + (arguments + `(#:tests? #f ; tests require Scala + #:jdk ,icedtea-8 + #:jar-name "htsjdk.jar" + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'remove-useless-build.xml + (lambda _ (delete-file "build.xml") #t)) + ;; The tests require the scalatest package. + (add-after 'unpack 'remove-tests + (lambda _ (delete-file-recursively "src/test") #t))))))) + ;; This version matches java-htsjdk 2.3.0. Later versions also require a more ;; recent version of java-htsjdk, which depends on gradle. (define-public java-picard @@ -3097,6 +3151,90 @@ commonly used for high-throughput sequencing data such as SAM, BAM, CRAM and VCF.") (license license:expat))) +;; This is needed for dropseq-tools +(define-public java-picard-2.10.3 + (package + (name "java-picard") + (version "2.10.3") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/broadinstitute/picard.git") + (commit version))) + (file-name (string-append "java-picard-" version "-checkout")) + (sha256 + (base32 + "1ajlx31l6i1k3y2rhnmgq07sz99g2czqfqgkr9mihmdjp3gwjhvi")))) + (build-system ant-build-system) + (arguments + `(#:jar-name "picard.jar" + ;; Tests require jacoco:coverage. + #:tests? #f + #:jdk ,icedtea-8 + #:main-class "picard.cmdline.PicardCommandLine" + #:modules ((guix build ant-build-system) + (guix build utils) + (guix build java-utils) + (sxml simple) + (sxml transform) + (sxml xpath)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'remove-useless-build.xml + (lambda _ (delete-file "build.xml") #t)) + ;; This is necessary to ensure that htsjdk is found when using + ;; picard.jar as an executable. + (add-before 'build 'edit-classpath-in-manifest + (lambda* (#:key inputs #:allow-other-keys) + (chmod "build.xml" #o664) + (call-with-output-file "build.xml.new" + (lambda (port) + (sxml->xml + (pre-post-order + (with-input-from-file "build.xml" + (lambda _ (xml->sxml #:trim-whitespace? #t))) + `((target . ,(lambda (tag . kids) + (let ((name ((sxpath '(name *text*)) + (car kids))) + ;; FIXME: We're breaking the line + ;; early with a dummy path to + ;; ensure that the store reference + ;; isn't broken apart and can still + ;; be found by the reference + ;; scanner. + (msg (format #f + "\ +Class-Path: /~a \ + ~a/share/java/htsjdk.jar${line.separator}" + ;; maximum line length is 70 + (string-tabulate (const #\b) 57) + (assoc-ref inputs "java-htsjdk")))) + (if (member "manifest" name) + `(,tag ,@kids + (echo + (@ (message ,msg) + (file "${manifest.file}") + (append "true")))) + `(,tag ,@kids))))) + (*default* . ,(lambda (tag . kids) `(,tag ,@kids))) + (*text* . ,(lambda (_ txt) txt)))) + port))) + (rename-file "build.xml.new" "build.xml") + #t))))) + (propagated-inputs + `(("java-htsjdk" ,java-htsjdk-2.10.1))) + (native-inputs + `(("java-testng" ,java-testng) + ("java-guava" ,java-guava))) + (home-page "http://broadinstitute.github.io/picard/") + (synopsis "Tools for manipulating high-throughput sequencing data and formats") + (description "Picard is a set of Java command line tools for manipulating +high-throughput sequencing (HTS) data and formats. Picard is implemented +using the HTSJDK Java library to support accessing file formats that are +commonly used for high-throughput sequencing data such as SAM, BAM, CRAM and +VCF.") + (license license:expat))) + ;; This is the last version of Picard to provide net.sf.samtools (define-public java-picard-1.113 (package (inherit java-picard) @@ -3211,10 +3349,89 @@ VCF.") ("jdk" ,icedtea-8 "jdk") ("jdk-src" ,(car (assoc-ref (package-native-inputs icedtea-8) "jdk-drop"))))))) +(define-public fastqc + (package + (name "fastqc") + (version "0.11.5") + (source + (origin + (method url-fetch) + (uri (string-append "http://www.bioinformatics.babraham.ac.uk/" + "projects/fastqc/fastqc_v" + version "_source.zip")) + (sha256 + (base32 + "18rrlkhcrxvvvlapch4dpj6xc6mpayzys8qfppybi8jrpgx5cc5f")))) + (build-system ant-build-system) + (arguments + `(#:tests? #f ; there are no tests + #:build-target "build" + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-dependencies + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "build.xml" + (("jbzip2-0.9.jar") + (string-append (assoc-ref inputs "java-jbzip2") + "/share/java/jbzip2.jar")) + (("sam-1.103.jar") + (string-append (assoc-ref inputs "java-picard-1.113") + "/share/java/sam-1.112.jar")) + (("cisd-jhdf5.jar") + (string-append (assoc-ref inputs "java-cisd-jhdf5") + "/share/java/sis-jhdf5.jar"))) + #t)) + ;; There is no installation target + (replace 'install + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (share (string-append out "/share/fastqc/")) + (exe (string-append share "/fastqc"))) + (for-each mkdir-p (list bin share)) + (copy-recursively "bin" share) + (substitute* exe + (("my \\$java_bin = 'java';") + (string-append "my $java_bin = '" + (assoc-ref inputs "java") + "/bin/java';"))) + (chmod exe #o555) + (symlink exe (string-append bin "/fastqc")) + #t)))))) + (inputs + `(("java" ,icedtea) + ("perl" ,perl) ; needed for the wrapper script + ("java-cisd-jhdf5" ,java-cisd-jhdf5) + ("java-picard-1.113" ,java-picard-1.113) + ("java-jbzip2" ,java-jbzip2))) + (native-inputs + `(("unzip" ,unzip))) + (home-page "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/") + (synopsis "Quality control tool for high throughput sequence data") + (description + "FastQC aims to provide a simple way to do some quality control +checks on raw sequence data coming from high throughput sequencing +pipelines. It provides a modular set of analyses which you can use to +give a quick impression of whether your data has any problems of which +you should be aware before doing any further analysis. + +The main functions of FastQC are: + +@itemize +@item Import of data from BAM, SAM or FastQ files (any variant); +@item Providing a quick overview to tell you in which areas there may + be problems; +@item Summary graphs and tables to quickly assess your data; +@item Export of results to an HTML based permanent report; +@item Offline operation to allow automated generation of reports + without running the interactive application. +@end itemize\n") + (license license:gpl3+))) + (define-public htslib (package (name "htslib") - (version "1.6") + (version "1.7") (source (origin (method url-fetch) (uri (string-append @@ -3222,17 +3439,8 @@ VCF.") version "/htslib-" version ".tar.bz2")) (sha256 (base32 - "1jsca3hg4rbr6iqq6imkj4lsvgl8g9768bcmny3hlff2w25vx24m")))) + "1il6i2p84b0y9c93dhvzzki1ifw9bvapm2mvpr0xvb2nq8jlwgdy")))) (build-system gnu-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after - 'unpack 'patch-tests - (lambda _ - (substitute* "test/test.pl" - (("/bin/bash") (which "bash"))) - #t))))) (inputs `(("openssl" ,openssl) ("curl" ,curl) @@ -4629,6 +4837,7 @@ distribution, coverage uniformity, strand specificity, etc.") (uri (hg-reference (url "https://bitbucket.org/libsleipnir/sleipnir") (changeset changeset))) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "0qrvilwh18dpbhkf92qvxbmay0j75ra3jg2wrhz67gf538zzphsx")))) @@ -4687,7 +4896,7 @@ to the user's query of interest.") (define-public samtools (package (name "samtools") - (version "1.5") + (version "1.7") (source (origin (method url-fetch) @@ -4696,7 +4905,7 @@ to the user's query of interest.") version "/samtools-" version ".tar.bz2")) (sha256 (base32 - "1xidmv0jmfy7l0kb32hdnlshcxgzi1hmygvig0cqrq1fhckdlhl5")))) + "18acyqysbxpydlc44lqv2hpp57l06bs9a3yqmcvjk8va2xrrdc77")))) (build-system gnu-build-system) (arguments `(#:modules ((ice-9 ftw) @@ -6017,14 +6226,14 @@ distribution.") (define-public r-dexseq (package (name "r-dexseq") - (version "1.24.2") + (version "1.24.3") (source (origin (method url-fetch) (uri (bioconductor-uri "DEXSeq" version)) (sha256 (base32 - "18nh8ynxirfwkmc4sawdxgl7w1sl9ny5zpv8zbhv9vi5vgb8pxmj")))) + "0xip73hlbr3zry9d7ly9vvvsbb3xjcmfa09lr9fdy528dwjrf084")))) (properties `((upstream-name . "DEXSeq"))) (build-system r-build-system) (propagated-inputs @@ -6200,14 +6409,14 @@ testing and other simple calculations.") (define-public r-shortread (package (name "r-shortread") - (version "1.36.0") + (version "1.36.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ShortRead" version)) (sha256 (base32 - "06mknlsmd4hnaxzdjapgvp2kgdnf9w103y500dsac5jgsz4vwzcz")))) + "1cyv47632m9ljkxfsvnvmd19sb607ys5kz8fwh6v39dnw16g0a6m")))) (properties `((upstream-name . "ShortRead"))) (build-system r-build-system) (inputs @@ -6968,13 +7177,13 @@ names in their natural, rather than lexicographic, order.") (define-public r-edger (package (name "r-edger") - (version "3.20.8") + (version "3.20.9") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "0g7bj6w61blw3m22hw9rc01n554k9qkjizh7njr3j4shmhads58d")))) + "0y52snwbz37xzdd7gihdkqczbndlfzmmypv6hri3ymjyfmlx6qaw")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs @@ -7034,13 +7243,13 @@ coding changes and predict coding outcomes.") (define-public r-limma (package (name "r-limma") - (version "3.34.8") + (version "3.34.9") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "0bmxsgz2yll83sd3wbxsrsfd35468igb0d8lldym0d0lqfz906bw")))) + "1y2fm61g5i0fn0j3l31xvwh9zww9bpkc4nwzb1d0yv1cag20jkdc")))) (build-system r-build-system) (home-page "http://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") @@ -7089,13 +7298,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") (define-public r-genomicranges (package (name "r-genomicranges") - (version "1.30.2") + (version "1.30.3") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicRanges" version)) (sha256 (base32 - "0c3r155603vb4zjs3adqa72770bh8karc11y8gl62l1m24jrkbnj")))) + "07cszc9ri94nzk4dffwnsj247ih6pchnrzrvnb0q4dkk33gwy8n1")))) (properties `((upstream-name . "GenomicRanges"))) (build-system r-build-system) @@ -7519,13 +7728,13 @@ information about the latest version of the Gene Ontologies.") (define-public r-topgo (package (name "r-topgo") - (version "2.30.0") + (version "2.30.1") (source (origin (method url-fetch) (uri (bioconductor-uri "topGO" version)) (sha256 (base32 - "1hqffz5qp7glxdvjp37005g8qk5nam3f9wpf6d1wjnzpar04f3dz")))) + "1cgz4knxr328xfqlhl6ypxl6x86rfrlqz748kn94ainxjzz55i6x")))) (properties `((upstream-name . "topGO"))) (build-system r-build-system) @@ -8365,14 +8574,14 @@ in SNV base substitution data.") (define-public r-wgcna (package (name "r-wgcna") - (version "1.62") + (version "1.63") (source (origin (method url-fetch) (uri (cran-uri "WGCNA" version)) (sha256 (base32 - "0c52rp09gqphz6g5x9jzkdcsyvfrknq0dkq9saslgy8q8ap974vx")))) + "1225dqm68bynkmklnsxdqdd3zqrpzbvqwyly8ibxmk75z33xz309")))) (properties `((upstream-name . "WGCNA"))) (build-system r-build-system) (propagated-inputs @@ -8542,6 +8751,16 @@ of gene-level counts.") "src/hdf5source/hdf5small.tgz" "-C" "src/" ) (substitute* "src/hdf5/configure" (("/bin/mv") "mv")) + ;; Remove timestamp and host system information to make + ;; the build reproducible. + (substitute* "src/hdf5/src/libhdf5.settings.in" + (("Configured on: @CONFIG_DATE@") + "Configured on: Guix") + (("Uname information:.*") + "Uname information: Linux\n") + ;; Remove unnecessary store reference. + (("C Compiler:.*") + "C Compiler: GCC\n")) #t))))) (propagated-inputs `(("r-zlibbioc" ,r-zlibbioc))) @@ -8706,6 +8925,7 @@ intervals (e.g. genes, sequence alignments).") (uri (git-reference (url "https://github.com/smithlabcode/piranha.git") (commit commit))) + (file-name (git-file-name name version)) (sha256 (base32 "117dc0zf20c61jam69sk4abl57ah6yi6i7qra7d7y5zrbgk12q5n")))) @@ -10588,14 +10808,14 @@ quality control.") (define-public r-scran (package (name "r-scran") - (version "1.6.7") + (version "1.6.8") (source (origin (method url-fetch) (uri (bioconductor-uri "scran" version)) (sha256 (base32 - "0zfm5i8xrnzb3894xygqd6zkbwaa2x3z74wbxw39fcjhyhxv2hmb")))) + "07wniyrh2fhhkz28v0bfgpvpi1hkkn2cvhacrvvvck142j79944x")))) (build-system r-build-system) (propagated-inputs `(("r-beachmat" ,r-beachmat) @@ -10671,6 +10891,7 @@ memory usage and processing time is minimized.") (uri (git-reference (url "https://github.com/rajewsky-lab/dropbead.git") (commit commit))) + (file-name (git-file-name name version)) (sha256 (base32 "1b2lphsc236s1rdzlijxg8yl1jnqpwcvj4x938r89rqpj93jb780")))) @@ -11431,6 +11652,7 @@ dependency like SeqAn.") (uri (git-reference (url "https://github.com/y-256/libdivsufsort.git") (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 "0fgdz9fzihlvjjrxy01md1bv9vh12rkgkwbm90b1hj5xpbaqp7z2")))) @@ -11886,3 +12108,541 @@ variable number of row and column annotations. Loom also supports sparse graphs. This library makes it easy to work with @file{.loom} files for single-cell RNA-seq data.") (license license:bsd-3))) + +;; We cannot use the latest commit because it requires Java 9. +(define-public java-forester + (let ((commit "86b07efe302d5094b42deed9260f719a4c4ac2e6") + (revision "1")) + (package + (name "java-forester") + (version (string-append "0-" revision "." (string-take commit 7))) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/cmzmasek/forester.git") + (commit commit))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "0vxavc1yrf84yrnf20dq26hi0lglidk8d382xrxsy4qmlbjd276z")) + (modules '((guix build utils))) + (snippet + '(begin + ;; Delete bundled jars and pre-built classes + (delete-file-recursively "forester/java/resources") + (delete-file-recursively "forester/java/classes") + (for-each delete-file (find-files "forester/java/" "\\.jar$")) + ;; Delete bundled applications + (delete-file-recursively "forester_applications") + #t)))) + (build-system ant-build-system) + (arguments + `(#:tests? #f ; there are none + #:jdk ,icedtea-8 + #:modules ((guix build ant-build-system) + (guix build utils) + (guix build java-utils) + (sxml simple) + (sxml transform)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'chdir + (lambda _ (chdir "forester/java") #t)) + (add-after 'chdir 'fix-dependencies + (lambda _ + (chmod "build.xml" #o664) + (call-with-output-file "build.xml.new" + (lambda (port) + (sxml->xml + (pre-post-order + (with-input-from-file "build.xml" + (lambda _ (xml->sxml #:trim-whitespace? #t))) + `(;; Remove all unjar tags to avoid repacking classes. + (unjar . ,(lambda _ '())) + (*default* . ,(lambda (tag . kids) `(,tag ,@kids))) + (*text* . ,(lambda (_ txt) txt)))) + port))) + (rename-file "build.xml.new" "build.xml") + #t)) + ;; FIXME: itext is difficult to package as it depends on a few + ;; unpackaged libraries. + (add-after 'chdir 'remove-dependency-on-unpackaged-itext + (lambda _ + (delete-file "src/org/forester/archaeopteryx/PdfExporter.java") + (substitute* "src/org/forester/archaeopteryx/MainFrame.java" + (("pdf_written_to = PdfExporter.*") + "throw new IOException(\"PDF export is not available.\");")) + #t)) + ;; There is no install target + (replace 'install (install-jars "."))))) + (propagated-inputs + `(("java-commons-codec" ,java-commons-codec) + ("java-openchart2" ,java-openchart2))) + (home-page "https://sites.google.com/site/cmzmasek/home/software/forester") + (synopsis "Phylogenomics libraries for Java") + (description "Forester is a collection of Java libraries for +phylogenomics and evolutionary biology research. It includes support for +reading, writing, and exporting phylogenetic trees.") + (license license:lgpl2.1+)))) + +(define-public java-forester-1.005 + (package + (name "java-forester") + (version "1.005") + (source (origin + (method url-fetch) + (uri (string-append "http://search.maven.org/remotecontent?" + "filepath=org/biojava/thirdparty/forester/" + version "/forester-" version "-sources.jar")) + (file-name (string-append name "-" version ".jar")) + (sha256 + (base32 + "04r8qv4rk3p71z4ajrvp11py1z46qrx0047j3zzs79s6lnsm3lcv")))) + (build-system ant-build-system) + (arguments + `(#:tests? #f ; there are none + #:jdk ,icedtea-8 + #:modules ((guix build ant-build-system) + (guix build utils) + (guix build java-utils) + (sxml simple) + (sxml transform)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-dependencies + (lambda* (#:key inputs #:allow-other-keys) + (call-with-output-file "build.xml" + (lambda (port) + (sxml->xml + (pre-post-order + (with-input-from-file "src/build.xml" + (lambda _ (xml->sxml #:trim-whitespace? #t))) + `(;; Remove all unjar tags to avoid repacking classes. + (unjar . ,(lambda _ '())) + (*default* . ,(lambda (tag . kids) `(,tag ,@kids))) + (*text* . ,(lambda (_ txt) txt)))) + port))) + (copy-file (assoc-ref inputs "synth_look_and_feel_1.xml") + "synth_look_and_feel_1.xml") + (copy-file (assoc-ref inputs "phyloxml.xsd") + "phyloxml.xsd") + (substitute* "build.xml" + (("../resources/synth_laf/synth_look_and_feel_1.xml") + "synth_look_and_feel_1.xml") + (("../resources/phyloxml_schema/1.10/phyloxml.xsd") + "phyloxml.xsd")) + #t)) + ;; FIXME: itext is difficult to package as it depends on a few + ;; unpackaged libraries. + (add-after 'unpack 'remove-dependency-on-unpackaged-itext + (lambda _ + (delete-file "src/org/forester/archaeopteryx/PdfExporter.java") + (substitute* '("src/org/forester/archaeopteryx/MainFrame.java" + "src/org/forester/archaeopteryx/MainFrameApplication.java") + (("pdf_written_to = PdfExporter.*") + "throw new IOException(\"PDF export is not available.\"); /*") + ((".getPrintSizeX\\(\\), getOptions\\(\\).getPrintSizeY\\(\\) \\);") "*/") + (("getCurrentTreePanel\\(\\).getHeight\\(\\) \\);") "*/")) + #t)) + (add-after 'unpack 'delete-pre-built-classes + (lambda _ (delete-file-recursively "src/classes") #t)) + ;; There is no install target + (replace 'install (install-jars "."))))) + (propagated-inputs + `(("java-commons-codec" ,java-commons-codec) + ("java-openchart2" ,java-openchart2))) + ;; The source archive does not contain the resources. + (native-inputs + `(("phyloxml.xsd" + ,(origin + (method url-fetch) + (uri (string-append "https://raw.githubusercontent.com/cmzmasek/forester/" + "b61cc2dcede0bede317db362472333115756b8c6/" + "forester/resources/phyloxml_schema/1.10/phyloxml.xsd")) + (file-name (string-append name "-phyloxml-" version ".xsd")) + (sha256 + (base32 + "1zxc4m8sn4n389nqdnpxa8d0k17qnr3pm2y5y6g6vh4k0zm52npv")))) + ("synth_look_and_feel_1.xml" + ,(origin + (method url-fetch) + (uri (string-append "https://raw.githubusercontent.com/cmzmasek/forester/" + "29e04321615da6b35c1e15c60e52caf3f21d8e6a/" + "forester/java/classes/resources/synth_look_and_feel_1.xml")) + (file-name (string-append name "-synth-look-and-feel-" version ".xml")) + (sha256 + (base32 + "1gv5602gv4k7y7713y75a4jvj7i9s7nildsbdl7n9q10sc2ikg8h")))))) + (home-page "https://sites.google.com/site/cmzmasek/home/software/forester") + (synopsis "Phylogenomics libraries for Java") + (description "Forester is a collection of Java libraries for +phylogenomics and evolutionary biology research. It includes support for +reading, writing, and exporting phylogenetic trees.") + (license license:lgpl2.1+))) + +(define-public java-biojava-core + (package + (name "java-biojava-core") + (version "4.2.11") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/biojava/biojava") + (commit (string-append "biojava-" version)))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "1bvryh2bpsvash8ln79cmc9sqm8qw72hz4xzwqxcrjm8ssxszhqk")))) + (build-system ant-build-system) + (arguments + `(#:jdk ,icedtea-8 + #:jar-name "biojava-core.jar" + #:source-dir "biojava-core/src/main/java/" + #:test-dir "biojava-core/src/test" + ;; These tests seem to require internet access. + #:test-exclude (list "**/SearchIOTest.java" + "**/BlastXMLParserTest.java" + "**/GenbankCookbookTest.java" + "**/GenbankProxySequenceReaderTest.java") + #:phases + (modify-phases %standard-phases + (add-before 'build 'copy-resources + (lambda _ + (copy-recursively "biojava-core/src/main/resources" + "build/classes") + #t)) + (add-before 'check 'copy-test-resources + (lambda _ + (copy-recursively "biojava-core/src/test/resources" + "build/test-classes") + #t))))) + (propagated-inputs + `(("java-log4j-api" ,java-log4j-api) + ("java-log4j-core" ,java-log4j-core) + ("java-slf4j-api" ,java-slf4j-api) + ("java-slf4j-simple" ,java-slf4j-simple))) + (native-inputs + `(("java-junit" ,java-junit) + ("java-hamcrest-core" ,java-hamcrest-core))) + (home-page "http://biojava.org") + (synopsis "Core libraries of Java framework for processing biological data") + (description "BioJava is a project dedicated to providing a Java framework +for processing biological data. It provides analytical and statistical +routines, parsers for common file formats, reference implementations of +popular algorithms, and allows the manipulation of sequences and 3D +structures. The goal of the biojava project is to facilitate rapid +application development for bioinformatics. + +This package provides the core libraries.") + (license license:lgpl2.1+))) + +(define-public java-biojava-phylo + (package (inherit java-biojava-core) + (name "java-biojava-phylo") + (build-system ant-build-system) + (arguments + `(#:jdk ,icedtea-8 + #:jar-name "biojava-phylo.jar" + #:source-dir "biojava-phylo/src/main/java/" + #:test-dir "biojava-phylo/src/test" + #:phases + (modify-phases %standard-phases + (add-before 'build 'copy-resources + (lambda _ + (copy-recursively "biojava-phylo/src/main/resources" + "build/classes") + #t)) + (add-before 'check 'copy-test-resources + (lambda _ + (copy-recursively "biojava-phylo/src/test/resources" + "build/test-classes") + #t))))) + (propagated-inputs + `(("java-log4j-api" ,java-log4j-api) + ("java-log4j-core" ,java-log4j-core) + ("java-slf4j-api" ,java-slf4j-api) + ("java-slf4j-simple" ,java-slf4j-simple) + ("java-biojava-core" ,java-biojava-core) + ("java-forester" ,java-forester))) + (native-inputs + `(("java-junit" ,java-junit) + ("java-hamcrest-core" ,java-hamcrest-core))) + (home-page "http://biojava.org") + (synopsis "Biojava interface to the forester phylogenomics library") + (description "The phylo module provides a biojava interface layer to the +forester phylogenomics library for constructing phylogenetic trees."))) + +(define-public java-biojava-alignment + (package (inherit java-biojava-core) + (name "java-biojava-alignment") + (build-system ant-build-system) + (arguments + `(#:jdk ,icedtea-8 + #:jar-name "biojava-alignment.jar" + #:source-dir "biojava-alignment/src/main/java/" + #:test-dir "biojava-alignment/src/test" + #:phases + (modify-phases %standard-phases + (add-before 'build 'copy-resources + (lambda _ + (copy-recursively "biojava-alignment/src/main/resources" + "build/classes") + #t)) + (add-before 'check 'copy-test-resources + (lambda _ + (copy-recursively "biojava-alignment/src/test/resources" + "build/test-classes") + #t))))) + (propagated-inputs + `(("java-log4j-api" ,java-log4j-api) + ("java-log4j-core" ,java-log4j-core) + ("java-slf4j-api" ,java-slf4j-api) + ("java-slf4j-simple" ,java-slf4j-simple) + ("java-biojava-core" ,java-biojava-core) + ("java-biojava-phylo" ,java-biojava-phylo) + ("java-forester" ,java-forester))) + (native-inputs + `(("java-junit" ,java-junit) + ("java-hamcrest-core" ,java-hamcrest-core))) + (home-page "http://biojava.org") + (synopsis "Biojava API for genetic sequence alignment") + (description "The alignment module of BioJava provides an API that +contains + +@itemize +@item implementations of dynamic programming algorithms for sequence + alignment; +@item reading and writing of popular alignment file formats; +@item a single-, or multi- threaded multiple sequence alignment algorithm. +@end itemize\n"))) + +(define-public java-biojava-core-4.0 + (package (inherit java-biojava-core) + (name "java-biojava-core") + (version "4.0.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/biojava/biojava") + (commit (string-append "biojava-" version)))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "13675f6y9aqi7bi2lk3s1z7a22ynccjiqwa8izh7p97xi9wsfmd8")))))) + +(define-public java-biojava-phylo-4.0 + (package (inherit java-biojava-core-4.0) + (name "java-biojava-phylo") + (build-system ant-build-system) + (arguments + `(#:jdk ,icedtea-8 + #:jar-name "biojava-phylo.jar" + #:source-dir "biojava-phylo/src/main/java/" + #:test-dir "biojava-phylo/src/test" + #:phases + (modify-phases %standard-phases + (add-before 'build 'copy-resources + (lambda _ + (copy-recursively "biojava-phylo/src/main/resources" + "build/classes") + #t)) + (add-before 'check 'copy-test-resources + (lambda _ + (copy-recursively "biojava-phylo/src/test/resources" + "build/test-classes") + #t))))) + (propagated-inputs + `(("java-log4j-api" ,java-log4j-api) + ("java-log4j-core" ,java-log4j-core) + ("java-slf4j-api" ,java-slf4j-api) + ("java-slf4j-simple" ,java-slf4j-simple) + ("java-biojava-core" ,java-biojava-core-4.0) + ("java-forester" ,java-forester-1.005))) + (native-inputs + `(("java-junit" ,java-junit) + ("java-hamcrest-core" ,java-hamcrest-core))) + (home-page "http://biojava.org") + (synopsis "Biojava interface to the forester phylogenomics library") + (description "The phylo module provides a biojava interface layer to the +forester phylogenomics library for constructing phylogenetic trees."))) + +(define-public java-biojava-alignment-4.0 + (package (inherit java-biojava-core-4.0) + (name "java-biojava-alignment") + (build-system ant-build-system) + (arguments + `(#:jdk ,icedtea-8 + #:jar-name "biojava-alignment.jar" + #:source-dir "biojava-alignment/src/main/java/" + #:test-dir "biojava-alignment/src/test" + #:phases + (modify-phases %standard-phases + (add-before 'build 'copy-resources + (lambda _ + (copy-recursively "biojava-alignment/src/main/resources" + "build/classes") + #t)) + (add-before 'check 'copy-test-resources + (lambda _ + (copy-recursively "biojava-alignment/src/test/resources" + "build/test-classes") + #t))))) + (propagated-inputs + `(("java-log4j-api" ,java-log4j-api) + ("java-log4j-core" ,java-log4j-core) + ("java-slf4j-api" ,java-slf4j-api) + ("java-slf4j-simple" ,java-slf4j-simple) + ("java-biojava-core" ,java-biojava-core-4.0) + ("java-biojava-phylo" ,java-biojava-phylo-4.0) + ("java-forester" ,java-forester-1.005))) + (native-inputs + `(("java-junit" ,java-junit) + ("java-hamcrest-core" ,java-hamcrest-core))) + (home-page "http://biojava.org") + (synopsis "Biojava API for genetic sequence alignment") + (description "The alignment module of BioJava provides an API that +contains + +@itemize +@item implementations of dynamic programming algorithms for sequence + alignment; +@item reading and writing of popular alignment file formats; +@item a single-, or multi- threaded multiple sequence alignment algorithm. +@end itemize\n"))) + +(define-public dropseq-tools + (package + (name "dropseq-tools") + (version "1.13") + (source + (origin + (method url-fetch) + (uri "http://mccarrolllab.com/download/1276/") + (file-name (string-append "dropseq-tools-" version ".zip")) + (sha256 + (base32 + "0yrffckxqk5l8b5xb6z4laq157zd9mdypr2p4b4vq2bhjzi1sj0s")) + ;; Delete bundled libraries + (modules '((guix build utils))) + (snippet + '(begin + (for-each delete-file (find-files "jar/lib" "\\.jar$")) + (delete-file-recursively "3rdParty"))))) + (build-system ant-build-system) + (arguments + `(#:tests? #f ; test data are not included + #:test-target "test" + #:build-target "all" + #:source-dir "public/src/" + #:jdk ,icedtea-8 + #:make-flags + (list (string-append "-Dpicard.executable.dir=" + (assoc-ref %build-inputs "java-picard") + "/share/java/")) + #:modules ((ice-9 match) + (srfi srfi-1) + (guix build utils) + (guix build java-utils) + (guix build ant-build-system)) + #:phases + (modify-phases %standard-phases + ;; All dependencies must be linked to "lib", because that's where + ;; they will be searched for when the Class-Path property of the + ;; manifest is computed. + (add-after 'unpack 'record-references + (lambda* (#:key inputs #:allow-other-keys) + (mkdir-p "jar/lib") + (let ((dirs (filter-map (match-lambda + ((name . dir) + (if (and (string-prefix? "java-" name) + (not (string=? name "java-testng"))) + dir #f))) + inputs))) + (for-each (lambda (jar) + (symlink jar (string-append "jar/lib/" (basename jar)))) + (append-map (lambda (dir) (find-files dir "\\.jar$")) + dirs))) + #t)) + ;; There is no installation target + (replace 'install + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (share (string-append out "/share/java/")) + (lib (string-append share "/lib/")) + (scripts (list "BAMTagHistogram" + "BAMTagofTagCounts" + "BaseDistributionAtReadPosition" + "CollapseBarcodesInPlace" + "CollapseTagWithContext" + "ConvertToRefFlat" + "CreateIntervalsFiles" + "DetectBeadSynthesisErrors" + "DigitalExpression" + "Drop-seq_alignment.sh" + "FilterBAM" + "FilterBAMByTag" + "GatherGeneGCLength" + "GatherMolecularBarcodeDistributionByGene" + "GatherReadQualityMetrics" + "PolyATrimmer" + "ReduceGTF" + "SelectCellsByNumTranscripts" + "SingleCellRnaSeqMetricsCollector" + "TagBamWithReadSequenceExtended" + "TagReadWithGeneExon" + "TagReadWithInterval" + "TrimStartingSequence" + "ValidateReference"))) + (for-each mkdir-p (list bin share lib)) + (install-file "dist/dropseq.jar" share) + (for-each (lambda (script) + (chmod script #o555) + (install-file script bin)) + scripts) + (substitute* (map (lambda (script) + (string-append bin "/" script)) + scripts) + (("^java") (which "java")) + (("jar_deploy_dir=.*") + (string-append "jar_deploy_dir=" share "\n")))) + #t)) + ;; FIXME: We do this after stripping jars because we don't want it to + ;; copy all these jars and strip them. We only want to install + ;; links. Arguably, this is a problem with the ant-build-system. + (add-after 'strip-jar-timestamps 'install-links + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (share (string-append out "/share/java/")) + (lib (string-append share "/lib/"))) + (for-each (lambda (jar) + (symlink (readlink jar) + (string-append lib (basename jar)))) + (find-files "jar/lib" "\\.jar$"))) + #t))))) + (inputs + `(("jdk" ,icedtea-8) + ("java-picard" ,java-picard-2.10.3) + ("java-log4j-1.2-api" ,java-log4j-1.2-api) + ("java-commons-math3" ,java-commons-math3) + ("java-commons-jexl2" ,java-commons-jexl-2) + ("java-commons-collections4" ,java-commons-collections4) + ("java-commons-lang2" ,java-commons-lang) + ("java-commons-io" ,java-commons-io) + ("java-snappy-1.0.3-rc3" ,java-snappy-1) + ("java-guava" ,java-guava) + ("java-la4j" ,java-la4j) + ("java-biojava-core" ,java-biojava-core-4.0) + ("java-biojava-alignment" ,java-biojava-alignment-4.0) + ("java-jdistlib" ,java-jdistlib) + ("java-simple-xml" ,java-simple-xml) + ("java-snakeyaml" ,java-snakeyaml))) + (native-inputs + `(("unzip" ,unzip) + ("java-testng" ,java-testng))) + (home-page "http://mccarrolllab.com/dropseq/") + (synopsis "Tools for Drop-seq analyses") + (description "Drop-seq is a technology to enable biologists to +analyze RNA expression genome-wide in thousands of individual cells at +once. This package provides tools to perform Drop-seq analyses.") + (license license:expat))) |