From b1808932890a7f2f0d61dcfd015a644e4e5bcc16 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 21:15:40 +0100 Subject: gnu: r-dexseq: Update to 1.24.3. * gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.3. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c427a6d036..911a2ee762 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6017,14 +6017,14 @@ (define-public r-deseq2 (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 -- cgit v1.2.3 From 99e4b11d81292d6c2cdabe8018fd8da144f84d9c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 21:15:50 +0100 Subject: gnu: r-shortread: Update to 1.36.1. * gnu/packages/bioinformatics.scm (r-shortread): Update to 1.36.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 911a2ee762..0b9ac7b0bf 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6200,14 +6200,14 @@ (define-public r-gostats (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 -- cgit v1.2.3 From 22d96920d36ef87ba459dcf1db10641c5ba3ee25 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 21:16:00 +0100 Subject: gnu: r-edger: Update to 3.20.9. * gnu/packages/bioinformatics.scm (r-edger): Update to 3.20.9. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0b9ac7b0bf..0ce038ada7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6968,13 +6968,13 @@ (define-public r-genomeinfodb (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 -- cgit v1.2.3 From eb8971b7421ccca75d540f0d7b3b4ed09f283e89 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 21:16:12 +0100 Subject: gnu: r-limma: Update to 3.34.9. * gnu/packages/bioinformatics.scm (r-limma): Update to 3.34.9. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0ce038ada7..e76d91c062 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7034,13 +7034,13 @@ (define-public r-variantannotation (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") -- cgit v1.2.3 From 535014ce605ea10b1642b065a9cf08c565ae43d7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 21:16:23 +0100 Subject: gnu: r-genomicranges: Update to 1.30.3. * gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.30.3. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e76d91c062..97bbc6cf38 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7089,13 +7089,13 @@ (define-public r-xvector (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) -- cgit v1.2.3 From 61cbd49b305363e4965b3d14bf4b1935427138e2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 21:16:35 +0100 Subject: gnu: r-topgo: Update to 2.30.1. * gnu/packages/bioinformatics.scm (r-topgo): Update to 2.30.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 97bbc6cf38..8985156e52 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7519,13 +7519,13 @@ (define-public r-graph (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) -- cgit v1.2.3 From 6a0e13906b2832455ac6aacd02293a341c4e51fa Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 21:16:45 +0100 Subject: gnu: r-wgcna: Update to 1.63. * gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.63. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8985156e52..0b189378b4 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8365,14 +8365,14 @@ (define-public r-mutationalpatterns (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 -- cgit v1.2.3 From 9aaf2813e2601a89c4dd3584f49f170f18b6279a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 21:16:57 +0100 Subject: gnu: r-scran: Update to 1.6.8. * gnu/packages/bioinformatics.scm (r-scran): Update to 1.6.8. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0b189378b4..e5e9192993 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10588,14 +10588,14 @@ (define-public r-scater (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) -- cgit v1.2.3 From 3ede1550e8310a8a544c1fb0f7f372c60c00bbe0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 2 Mar 2018 23:44:16 +0100 Subject: gnu: cutadapt: Update to 1.16. * gnu/packages/bioinformatics.scm (cutadapt): Update to 1.16. [source]: Fetch via git. [arguments]: Remove. [native-inputs]: Replace python-nose with python-pytest. --- gnu/packages/bioinformatics.scm | 32 ++++++++------------------------ 1 file changed, 8 insertions(+), 24 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e5e9192993..e13f1b369f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1854,38 +1854,22 @@ (define-public crossmap (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 -- cgit v1.2.3 From bd975831c67af75c4603555195ac618765c06ccc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 23 Feb 2018 10:56:49 +0100 Subject: gnu: Add fastqc. * gnu/packages/bioinformatics.scm (fastqc): New variable. --- gnu/packages/bioinformatics.scm | 79 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 79 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e13f1b369f..065dc477d8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3195,6 +3195,85 @@ (define-public java-picard-1.113 ("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") -- cgit v1.2.3 From 5fef15e50679a4e18df4fafede913c26d0029126 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 19:41:37 +0100 Subject: gnu: Add java-biojava-core. * gnu/packages/bioinformatics.scm (java-biojava-core): New variable. --- gnu/packages/bioinformatics.scm | 56 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 56 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 065dc477d8..4a90f30128 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11949,3 +11949,59 @@ (define-public python-loompy graphs. This library makes it easy to work with @file{.loom} files for single-cell RNA-seq data.") (license license:bsd-3))) + +(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+))) -- cgit v1.2.3 From f09d16e5949b5d84529be9022034e217fbaad54d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 19:41:39 +0100 Subject: gnu: Add java-forester. * gnu/packages/bioinformatics.scm (java-forester): New variable. --- gnu/packages/bioinformatics.scm | 76 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 76 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4a90f30128..ef1e8606a9 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11950,6 +11950,82 @@ (define-public python-loompy 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-biojava-core (package (name "java-biojava-core") -- cgit v1.2.3 From 10645b9212d5eff74132edf60c90c3eb099a139f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 19:41:40 +0100 Subject: gnu: Add java-forester-1.005. * gnu/packages/bioinformatics.scm (java-forester-1.005): New variable. --- gnu/packages/bioinformatics.scm | 95 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 95 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ef1e8606a9..d64cda2340 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12026,6 +12026,101 @@ (define-public java-forester 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") -- cgit v1.2.3 From b28c803708d41c4a5323e31e01f7b6044fcc6dda Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 19:41:41 +0100 Subject: gnu: Add java-biojava-phylo. * gnu/packages/bioinformatics.scm (java-biojava-phylo): New variable. --- gnu/packages/bioinformatics.scm | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d64cda2340..fbb3264ef5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12176,3 +12176,39 @@ (define-public java-biojava-core 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."))) -- cgit v1.2.3 From 22c09c335beff3caa2b434165f09d88267269794 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 19:41:42 +0100 Subject: gnu: Add java-biojava-alignment. * gnu/packages/bioinformatics.scm (java-biojava-alignment): New variable. --- gnu/packages/bioinformatics.scm | 44 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fbb3264ef5..08d9be4bd7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12212,3 +12212,47 @@ (define-public java-biojava-phylo (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"))) -- cgit v1.2.3 From e44da58c16f8c0dd8d9fb80f38f3e86a08fa22f9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 19:41:43 +0100 Subject: gnu: Add java-biojava-core-4.0. * gnu/packages/bioinformatics.scm (java-biojava-core-4.0): New variable. --- gnu/packages/bioinformatics.scm | 14 ++++++++++++++ 1 file changed, 14 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 08d9be4bd7..2f5413b35e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12256,3 +12256,17 @@ (define-public java-biojava-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")))))) -- cgit v1.2.3 From 5528f9e8f09f4a63b40647d61ec100c4c5326b3b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 19:41:44 +0100 Subject: gnu: Add java-biojava-phylo-4.0. * gnu/packages/bioinformatics.scm (java-biojava-phylo-4.0): New variable. --- gnu/packages/bioinformatics.scm | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2f5413b35e..37647a9b9b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12270,3 +12270,39 @@ (define-public java-biojava-core-4.0 (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."))) -- cgit v1.2.3 From 9ac7db1830a1b324524aa7d383c5f1b5e348237f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 19:41:45 +0100 Subject: gnu: Add java-biojava-alignment-4.0. * gnu/packages/bioinformatics.scm (java-biojava-alignment-4.0): New variable. --- gnu/packages/bioinformatics.scm | 44 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 37647a9b9b..f44dc32aa7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12306,3 +12306,47 @@ (define-public java-biojava-phylo-4.0 (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"))) -- cgit v1.2.3 From 9a599c17b7dfca56ff8290902057ee6da933aed2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 19:41:46 +0100 Subject: gnu: Add java-htsjdk-latest. * gnu/packages/bioinformatics.scm (java-htsjdk-latest): New variable. --- gnu/packages/bioinformatics.scm | 43 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f44dc32aa7..505672624d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3003,6 +3003,49 @@ (define-public java-htsjdk 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 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 -- cgit v1.2.3 From 719fa958f395a44c87377eb61a6f81a7a57603fe Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 19:41:47 +0100 Subject: gnu: Add java-htsjdk-2.10.1. * gnu/packages/bioinformatics.scm (java-htsjdk-2.10.1): New variable. --- gnu/packages/bioinformatics.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 505672624d..09a64a8d4d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3046,6 +3046,33 @@ (define-public java-htsjdk-latest 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 -- cgit v1.2.3 From 72299db9feb6d9e1e0b5cc3262ec7c9cbf7fe729 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 19:41:48 +0100 Subject: gnu: Add java-picard-2.10.3. * gnu/packages/bioinformatics.scm (java-picard-2.10.3): New variable. --- gnu/packages/bioinformatics.scm | 84 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 84 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 09a64a8d4d..719f3e5f23 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3151,6 +3151,90 @@ (define-public java-picard 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) -- cgit v1.2.3 From 1adeef3194dd7c8da6e78b17fb33e71bb0c9e24f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 19:41:49 +0100 Subject: gnu: Add dropseq-tools. * gnu/packages/bioinformatics.scm (dropseq-tools): New variable. --- gnu/packages/bioinformatics.scm | 137 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 137 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 719f3e5f23..75468aa967 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12504,3 +12504,140 @@ (define-public java-biojava-alignment-4.0 @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))) -- cgit v1.2.3 From b1d4026dfb0a5f1fd12c6c0c03fe963c8fd49333 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 4 Mar 2018 11:45:40 +0200 Subject: gnu: r-dropbead: Declare a source file-name. * gnu/packages/bioinformatics.scm (r-dropbead)[source]: Declare a source file-name. --- gnu/packages/bioinformatics.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 75468aa967..6a9f13bdc6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10888,6 +10888,7 @@ (define-public r-dropbead (uri (git-reference (url "https://github.com/rajewsky-lab/dropbead.git") (commit commit))) + (file-name (git-file-name name version)) (sha256 (base32 "1b2lphsc236s1rdzlijxg8yl1jnqpwcvj4x938r89rqpj93jb780")))) -- cgit v1.2.3 From 51106724749a904b45738f9b4d1201ea4e11e760 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 4 Mar 2018 11:46:43 +0200 Subject: gnu: seek: Declare a source file-name. * gnu/packages/bioinformatics.scm (seek)[source]: Declare a source file-name. --- gnu/packages/bioinformatics.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6a9f13bdc6..139828111a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4846,6 +4846,7 @@ (define-public seek (uri (hg-reference (url "https://bitbucket.org/libsleipnir/sleipnir") (changeset changeset))) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "0qrvilwh18dpbhkf92qvxbmay0j75ra3jg2wrhz67gf538zzphsx")))) -- cgit v1.2.3 From d9a069c2d975e37ac2f01261d1c5b4b98f856228 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 4 Mar 2018 11:47:42 +0200 Subject: gnu: libdivsufsort: Declare a source file-name. * gnu/packages/bioinformatics.scm (libdivsufsort)[source]: Declare a source file-name. --- gnu/packages/bioinformatics.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 139828111a..fd00984dd5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11650,6 +11650,7 @@ (define-public libdivsufsort (uri (git-reference (url "https://github.com/y-256/libdivsufsort.git") (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 "0fgdz9fzihlvjjrxy01md1bv9vh12rkgkwbm90b1hj5xpbaqp7z2")))) -- cgit v1.2.3 From da49d137104229f35816bd09bf24c1756ac1613e Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 4 Mar 2018 11:48:40 +0200 Subject: gnu: piranha: Declare a source file-name. * gnu/packages/bioinformatics.scm (piranha)[source]: Declare a source file-name. --- gnu/packages/bioinformatics.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fd00984dd5..4756444d95 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8924,6 +8924,7 @@ (define-public piranha (uri (git-reference (url "https://github.com/smithlabcode/piranha.git") (commit commit))) + (file-name (git-file-name name version)) (sha256 (base32 "117dc0zf20c61jam69sk4abl57ah6yi6i7qra7d7y5zrbgk12q5n")))) -- cgit v1.2.3 From e325c890763e89b9baeeeb78110b3a50c822b25a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 6 Mar 2018 13:55:13 +0100 Subject: gnu: r-rhdf5: Make build reproducible. * gnu/packages/bioinformatics.scm (r-rhdf5)[arguments]: Remove timestamp and host system information from settings file. --- gnu/packages/bioinformatics.scm | 10 ++++++++++ 1 file changed, 10 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4756444d95..947f99aa71 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8760,6 +8760,16 @@ (define-public r-rhdf5 "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))) -- cgit v1.2.3 From 727d847980e61d8d0deaa4219ea730dc85e0a515 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 6 Mar 2018 15:50:08 +0100 Subject: gnu: htslib: Update to 1.7. * gnu/packages/bioinformatics.scm (htslib): Update to 1.7. [arguments]: Remove field. --- gnu/packages/bioinformatics.scm | 13 ++----------- 1 file changed, 2 insertions(+), 11 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 947f99aa71..c098562d2d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3431,7 +3431,7 @@ (define-public fastqc (define-public htslib (package (name "htslib") - (version "1.6") + (version "1.7") (source (origin (method url-fetch) (uri (string-append @@ -3439,17 +3439,8 @@ (define-public htslib 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) -- cgit v1.2.3 From c072cf57b927111d9a63b7349074052cb696280b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 6 Mar 2018 15:50:32 +0100 Subject: gnu: samtools: Update to 1.7. * gnu/packages/bioinformatics.scm (samtools): Update to 1.7. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c098562d2d..546b240f84 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4896,7 +4896,7 @@ (define-public seek (define-public samtools (package (name "samtools") - (version "1.5") + (version "1.7") (source (origin (method url-fetch) @@ -4905,7 +4905,7 @@ (define-public samtools version "/samtools-" version ".tar.bz2")) (sha256 (base32 - "1xidmv0jmfy7l0kb32hdnlshcxgzi1hmygvig0cqrq1fhckdlhl5")))) + "18acyqysbxpydlc44lqv2hpp57l06bs9a3yqmcvjk8va2xrrdc77")))) (build-system gnu-build-system) (arguments `(#:modules ((ice-9 ftw) -- cgit v1.2.3