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| -rw-r--r-- | gnu/packages/bioinformatics.scm | 76 |
1 files changed, 76 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 00a74a6837..9eaf40adbd 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14357,6 +14357,82 @@ approximate the gradient at each iteration of gradient descent. This package is a Cython wrapper for FIt-SNE.") (license license:bsd-4))) +(define-public bbmap + (package + (name "bbmap") + (version "35.82") + (source (origin + (method url-fetch) + (uri (string-append + "mirror://sourceforge/bbmap/BBMap_" version ".tar.gz")) + (sha256 + (base32 + "1q4rfhxcb6z3gm8zg2davjz98w22lkf4hm9ikxz9kdl93pil3wkd")))) + (build-system ant-build-system) + (arguments + `(#:build-target "dist" + #:tests? #f ; there are none + #:make-flags + (list (string-append "-Dmpijar=" + (assoc-ref %build-inputs "java-openmpi") + "/lib/mpi.jar")) + #:modules ((guix build ant-build-system) + (guix build utils) + (guix build java-utils)) + #:phases + (modify-phases %standard-phases + (add-after 'build 'build-jni-library + (lambda _ + (with-directory-excursion "jni" + (invoke "make" "-f" "makefile.linux")))) + ;; There is no install target + (replace 'install (install-jars "dist")) + (add-after 'install 'install-scripts-and-documentation + (lambda* (#:key outputs #:allow-other-keys) + (substitute* "calcmem.sh" + (("\\| awk ") (string-append "| " (which "awk") " "))) + (let* ((scripts (find-files "." "\\.sh$")) + (out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (doc (string-append out "/share/doc/bbmap")) + (jni (string-append out "/lib/jni"))) + (substitute* scripts + (("\\$DIR\"\"docs") doc) + (("^CP=.*") + (string-append "CP=" out "/share/java/BBTools.jar\n")) + (("^NATIVELIBDIR.*") + (string-append "NATIVELIBDIR=" jni "\n")) + (("CMD=\"java") + (string-append "CMD=\"" (which "java")))) + (for-each (lambda (script) (install-file script bin)) scripts) + + ;; Install JNI library + (install-file "jni/libbbtoolsjni.so" jni) + + ;; Install documentation + (install-file "docs/readme.txt" doc) + (copy-recursively "docs/guides" doc)) + #t))) + #:jdk ,openjdk11)) + (inputs + `(("gawk" ,gawk) + ("java-eclipse-jdt-core" ,java-eclipse-jdt-core) + ("java-eclipse-jdt-compiler-apt" ,java-eclipse-jdt-compiler-apt) + ("java-openmpi" ,java-openmpi))) + (home-page "http://sourceforge.net/projects/bbmap/") + (synopsis "Aligner and other tools for short sequencing reads") + (description + "This package provides bioinformatic tools to align, deduplicate, +reformat, filter and normalize DNA and RNA-seq data. It includes the +following tools: BBMap, a short read aligner for DNA and RNA-seq data; BBNorm, +a kmer-based error-correction and normalization tool; Dedupe, a tool to +simplify assemblies by removing duplicate or contained subsequences that share +a target percent identity; Reformat, to convert reads between +fasta/fastq/scarf/fasta+qual/sam, interleaved/paired, and ASCII-33/64, at over +500 MB/s; and BBDuk, a tool to filter, trim, or mask reads with kmer matches +to an artifact/contaminant file.") + (license license:bsd-3))) + (define-public velvet (package (name "velvet") |