diff options
| author | Ricardo Wurmus <rekado@elephly.net> | 2017-10-31 08:12:20 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2017-10-31 08:17:06 +0100 |
| commit | 7bf59f702179173055853fa940ae72292cd65a4e (patch) | |
| tree | 349f6eb123a313f9e1bad83e8afc8056165d6b85 | |
| parent | b275cd22d47a42098f465ca30aee24fdc6e23826 (diff) | |
gnu: Remove cufflinks.
Cufflinks includes essential non-free code.
Fixes <https://bugs.gnu.org/28946>.
* gnu/packages/bioinformatics.scm (cufflinks): Remove variable.
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 58 |
1 files changed, 0 insertions, 58 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index acf689d07a..53311346ca 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") |