diff options
Diffstat (limited to 'gn/packages/bioinformatics.scm')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 92 |
1 files changed, 23 insertions, 69 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index f62949d..e16c28e 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -37,7 +37,7 @@ #:use-module (gnu packages graphviz) #:use-module (gnu packages java) #:use-module (gnu packages linux) - #:use-module (gnu packages ldc) + #:use-module (gn packages ldc) #:use-module (gnu packages machine-learning) #:use-module (gnu packages maths) #:use-module (gnu packages mpi) @@ -772,41 +772,6 @@ to sample traits. Also includes a number of utility functions for data manipulation and visualization.") (license license:gpl2+)))) -(define-public qtlreaper - (package - (name "qtlreaper") - (version "1.1.1") - (source - (origin - (method url-fetch) - (uri (string-append - "mirror://sourceforge/qtlreaper/qtlreaper-" version ".tar.gz" - ;; "http://downloads.sourceforge.net/project/qtlreaper/qtlreaper/1.1.1/qtlreaper-1.1.1.tar.gz?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fqtlreaper%2Ffiles%2Flatest%2Fdownload&ts=1358975786&use_mirror=iweb")) - )) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "0rbf030940nbbbkggdq2dxiy3c0jv8l4y3vvyfxhqimgj0qv3l1x")))) - (build-system python-build-system) - ;; (native-inputs - ;; `(("python-setuptools" ,python-setuptools))) - (arguments - `(#:python ,python-2 - #:tests? #f)) ; no 'setup.py test' - (home-page "http://qtlreaper.sourceforge.net/") - (synopsis "Tool for scanning expression data for QTLs") - (description - "It is essentially the batch-oriented version of WebQTL. It -requires, as input, expression data from members of a set of -recombinant inbred lines and genotype information for the same -lines. It searches for an association between each expression trait -and all genotypes and evaluates that association by a permutation -test. For the permutation test, it performs only as many permutations -as are necessary to define the empirical P-value to a reasonable -precision. It also performs bootstrap resampling to estimate the -confidence region for the location of a putative QTL.") - (license license:gpl2+))) - (define-public plink2 (package (name "plink2") @@ -956,44 +921,38 @@ association studies (GWAS).") (license license:gpl3)))) (define-public sambamba - (let ((commit "c810c7ef14957f16288c205fd7b9d25c4ae7005d")) - ;;(let ((commit "2ca5a2dbac5ab90c3b4c588519edc3edcb71df84")) + (let ((commit "5a33d571339c966477c1f70ed08f64051f7b41c1")) (package (name "sambamba") - (version (string-append "0.5.9-1." (string-take commit 7))) + (version (string-append "0.6.5-" (string-take commit 7))) (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/roelj/sambamba.git") - ;;(url "https://github.com/pjotrp/sambamba.git") + (url "https://github.com/pjotrp/sambamba.git") (commit commit))) (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "0c4c13f021sl7mf5xc2v8dbwsz775n8dlsrrn7qa6qgbx05n54dv")))) - ;;"1f14wn9aaxwjkmla6pzq3s28741carbr2v0fd2v2mm1dcpwnrqz5")))) + "05nlhwjw17igcwiz4pq0r4f8flrqcy4065fhx4nhpc0g65p70mi5")))) (build-system gnu-build-system) + (outputs '("out" + "debug")) ;retain debug symbols - note that -O2 is used (native-inputs `(("ldc" ,ldc) - ;;("lz4" ,lz4) - ("rdmd" ,rdmd) + ("lz4" ,lz4) + ("coreutils" ,coreutils) ; for env ("zlib" ,zlib) ("perl" ,perl) ; Needed for htslib ("ruby" ,ruby) ; Needed for htslib - ("python" ,python) ; Needed for htslib + ("python" ,python-2) ; Needed for htslib ("gcc" ,gcc) - ("lz4-src" - ,(origin - (method url-fetch) - (uri "https://github.com/Cyan4973/lz4/archive/160661c7a4cbf805f4af74d2e3932a17a66e6ce7.tar.gz") - (sha256 - (base32 "131nnbsd5dh7c8sdqzc9kawh3mi0qi4qxznv7zhzfszlx4g2fd20")))) + ("which" ,which) ("htslib-src" ,(origin (method url-fetch) (uri "https://github.com/lomereiter/htslib/archive/2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5.tar.gz") ;;(uri "https://github.com/samtools/htslib/archive/1.3.tar.gz") - ;;(file-name "htslib-1.3.tar.gz") + (file-name "htslib-0.2.0-rc10-271-g2f3c3ea-dirty.tar.gz") (sha256 (base32 "0bl6w856afnbgdsw8bybsxpqsyf2ba3f12rqh47hhpxvv866g08w")))) ;;(base32 "1bqkif7yrqmiqak5yb74kgpb2lsdlg7y344qa1xkdg7k1l4m86i9")) @@ -1003,13 +962,12 @@ association studies (GWAS).") (method git-fetch) (uri (git-reference (url "https://github.com/biod/BioD.git") - (commit "7efdb8a2f7fdcd71c9ad9596be48d1262bb1bd5b"))) - (file-name "biod-src") + (commit "1248586b54af4bd4dfb28ebfebfc6bf012e7a587"))) + (file-name (string-append "biod-src-" (string-take commit 7) ".tar.gz")) (sha256 - (base32 "09icc2bjsg9y4hxjim4ql275izadf0kh1nnmapg8manyz6bc8svf")))))) + (base32 "1m8hi1n7x0ri4l6s9i0x6jg4z4v94xrfdzp7mbizdipfag0m17g3")))))) (arguments - `(#:tests? #f - #:make-flags (list "-f" "Makefile.guix") + `(#:tests? #f ; no tests available #:phases (modify-phases %standard-phases (delete 'configure) @@ -1022,16 +980,13 @@ association studies (GWAS).") (and (with-directory-excursion "htslib" (zero? (system* "tar" "xvf" (assoc-ref inputs "htslib-src") "--strip-components=1"))) - (with-directory-excursion "lz4" - (zero? (system* "tar" "xvf" (assoc-ref inputs "lz4-src") - "--strip-components=1"))) (zero? (system* "rm" "-r" "BioD")) (zero? (system* "ln" "--symbolic" "--no-target-directory" (assoc-ref inputs "biod-src") "BioD"))))) (replace 'build (lambda* (#:key inputs make-flags #:allow-other-keys) - (zero? (system* "make" "sambamba-ldmd2-64" "CC=gcc" "D_COMPILER=ldc2" + (zero? (system* "make" "-f" "Makefile.guix" "sambamba-ldmd2" (string-append "LDC_LIB_PATH=" (assoc-ref inputs "ldc") "/lib"))))) @@ -1041,16 +996,15 @@ association studies (GWAS).") (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) (install-file "build/sambamba" bin))))))) (home-page "https://github.com/lomereiter/sambamba") - (synopsis "A tool for working with SAM and BAM files written in D.") + (synopsis "Fast tool for working with SAM, BAM and CRAM files written in D.") (description - "Sambamba is a high performance modern robust and fast tool (and -library), written in the D programming language, for working with SAM -and BAM files. Current parallelised functionality is an important -subset of samtools functionality, including view, index, sort, -markdup, and depth.") + "Sambamba is a high performance modern robust and fast +tool (and library), written in the D programming language, for working +with SAM, BAM and CRAM files. Current parallelised functionality is +an important subset of samtools functionality, including view, index, +sort, markdup, and depth.") (license license:gpl2+)))) - (define-public vcflib (let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb")) (package |