diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 66 |
1 files changed, 4 insertions, 62 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 43a00f196c..987662fc89 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1836,64 +1836,6 @@ files between different genome assemblies. It supports most commonly used file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.") (license license:gpl2+))) -(define-public cufflinks - (package - (name "cufflinks") - (version "2.2.1") - (source (origin - (method url-fetch) - (uri (string-append "http://cole-trapnell-lab.github.io/" - "cufflinks/assets/downloads/cufflinks-" - version ".tar.gz")) - (sha256 - (base32 - "1bnm10p8m7zq4qiipjhjqb24csiqdm1pwc8c795z253r2xk6ncg8")))) - (build-system gnu-build-system) - (arguments - `(#:make-flags - (list - ;; The includes for "eigen" are located in a subdirectory. - (string-append "EIGEN_CPPFLAGS=" - "-I" (assoc-ref %build-inputs "eigen") - "/include/eigen3/") - ;; Cufflinks must be linked with various boost libraries. - (string-append "LDFLAGS=" - (string-join '("-lboost_system" - "-lboost_serialization" - "-lboost_thread")))) - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'fix-search-for-bam - (lambda _ - (substitute* '("ax_bam.m4" - "configure" - "src/hits.h") - (("<bam/sam\\.h>") "<samtools/sam.h>") - (("<bam/bam\\.h>") "<samtools/bam.h>") - (("<bam/version\\.hpp>") "<samtools/version.h>")) - #t))) - #:configure-flags - (list (string-append "--with-bam=" - (assoc-ref %build-inputs "samtools"))))) - (inputs - `(("eigen" ,eigen) - ("samtools" ,samtools-0.1) - ("htslib" ,htslib) - ("boost" ,boost) - ("python" ,python-2) - ("zlib" ,zlib))) - (home-page "http://cole-trapnell-lab.github.io/cufflinks/") - (synopsis "Transcriptome assembly and RNA-Seq expression analysis") - (description - "Cufflinks assembles RNA transcripts, estimates their abundances, -and tests for differential expression and regulation in RNA-Seq -samples. It accepts aligned RNA-Seq reads and assembles the -alignments into a parsimonious set of transcripts. Cufflinks then -estimates the relative abundances of these transcripts based on how -many reads support each one, taking into account biases in library -preparation protocols.") - (license license:boost1.0))) - (define-public cutadapt (package (name "cutadapt") @@ -2117,7 +2059,7 @@ identify enrichments with functional annotations of the genome.") (define-public diamond (package (name "diamond") - (version "0.9.10") + (version "0.9.11") (source (origin (method url-fetch) (uri (string-append @@ -2126,7 +2068,7 @@ identify enrichments with functional annotations of the genome.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "13qqzwg54n5dqh8pm5n3v8x6gqbczzakphwwjix63qv60hcd5bqd")))) + "1yqil5531p35xkqa44x75vvq8s7w8kqjqn1p5hf1nh0d91j9ihby")))) (build-system cmake-build-system) (arguments '(#:tests? #f ; no "check" target @@ -6199,7 +6141,7 @@ SELECT or UPDATE queries to an end-point.") (define-public vsearch (package (name "vsearch") - (version "2.5.0") + (version "2.5.2") (source (origin (method url-fetch) @@ -6209,7 +6151,7 @@ SELECT or UPDATE queries to an end-point.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1k8wf3qns4mqrsizywbkqcasqjw000m4drxsag3qd7390pwvf9kz")) + "1z10psrwhflchwzw1fvzwnsn59xglf94qrn7msj93fpnjgafvmks")) (patches (search-patches "vsearch-unbundle-cityhash.patch")) (snippet '(begin |