diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 94 |
1 files changed, 87 insertions, 7 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ab9dc185a3..91bb94c549 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11735,19 +11735,39 @@ using nucleotide or amino-acid sequence data.") (define-public kallisto (package (name "kallisto") - (version "0.43.1") + (version "0.44.0") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/pachterlab/" - "kallisto/archive/v" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/pachterlab/kallisto.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "03j3iqhvq7ya3c91gidly3k3jvgm97vjq4scihrlxh315j696r11")))) + "0nj382jiywqnpgvyhichajpkkh5r0bapn43f4dx40zdaq5v4m40m")))) (build-system cmake-build-system) - (arguments `(#:tests? #f)) ; no "check" target + (arguments + `(#:tests? #f ; no "check" target + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'do-not-use-bundled-htslib + (lambda _ + (substitute* "CMakeLists.txt" + (("^ExternalProject_Add" m) + (string-append "if (NEVER)\n" m)) + (("^\\)") + (string-append ")\nendif(NEVER)")) + (("include_directories\\(\\$\\{htslib_PREFIX.*" m) + (string-append "# " m))) + (substitute* "src/CMakeLists.txt" + (("target_link_libraries\\(kallisto kallisto_core pthread \ +\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/../ext/htslib/libhts.a\\)") + "target_link_libraries(kallisto kallisto_core pthread hts)") + (("include_directories\\(\\.\\./ext/htslib\\)") "")) + #t))))) (inputs `(("hdf5" ,hdf5) + ("htslib" ,htslib) ("zlib" ,zlib))) (home-page "http://pachterlab.github.io/kallisto/") (synopsis "Near-optimal RNA-Seq quantification") @@ -14057,3 +14077,63 @@ absolute GSEA.") (description "Ngless is a domain-specific language for @dfn{next-generation sequencing} (NGS) data processing.") (license license:expat))) + +(define-public filtlong + ;; The recommended way to install is to clone the git repository + ;; https://github.com/rrwick/Filtlong#installation + ;; and the lastest release is more than nine months old + (let ((commit "d1bb46dfe8bc7efe6257b5ce222c04bfe8aedaab") + (revision "1")) + (package + (name "filtlong") + (version (git-version "0.2.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rrwick/Filtlong.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1xr92r820x8qlkcr3b57iw223yq8vjgyi42jr79w2xgw47qzr575")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; no check target + #:phases + (modify-phases %standard-phases + (delete 'configure) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (scripts (string-append out "/share/filtlong/scripts"))) + (install-file "bin/filtlong" bin) + (install-file "scripts/histogram.py" scripts) + (install-file "scripts/read_info_histograms.sh" scripts)) + #t)) + (add-after 'install 'wrap-program + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (path (getenv "PYTHONPATH"))) + (wrap-program (string-append out + "/share/filtlong/scripts/histogram.py") + `("PYTHONPATH" ":" prefix (,path)))) + #t)) + (add-before 'check 'patch-tests + (lambda _ + (substitute* "scripts/read_info_histograms.sh" + (("awk") (which "gawk"))) + #t))))) + (inputs + `(("gawk" ,gawk) ;for read_info_histograms.sh + ("python" ,python-2) ;required for histogram.py + ("zlib" ,zlib))) + (home-page "https://github.com/rrwick/Filtlong/") + (synopsis "Tool for quality filtering of Nanopore and PacBio data") + (description + "The Filtlong package is a tool for filtering long reads by quality. +It can take a set of long reads and produce a smaller, better subset. It uses +both read length (longer is better) and read identity (higher is better) when +choosing which reads pass the filter.") + (license (list license:gpl3 ;filtlong + license:asl2.0))))) ;histogram.py |