diff options
Diffstat (limited to 'gn/packages/bioinformatics.scm')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 197 |
1 files changed, 88 insertions, 109 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 3363ea2..b503e22 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -48,43 +48,79 @@ #:use-module (gn packages statistics) #:use-module (srfi srfi-1)) + +(define-public r-biocpreprocesscore + (package + (name "r-biocpreprocesscore") + (version "1.32.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "preprocessCore" version)) + (sha256 + (base32 + "07isghjkqm91rg37l1fzpjrbq36b7w4pbsi95wwh6a8qq7r69z1n")))) + (properties + `((upstream-name . "BiocpreprocessCore") + (r-repository . bioconductor))) + (build-system r-build-system) + (home-page "http://bioconductor.org/packages/preprocessCore") + (synopsis "Preprocess functions for Bioconductor") + (description + "A library of core preprocessing routines.") + (license license:lgpl2.0+))) + + (define-public r-wgcna + (let ((commit "425bc170cc0873ddbd414675ac40f6d4d724c7cb")) (package (name "r-wgcna") - (version "1.48") - (source - (origin - (method url-fetch) - (uri (cran-uri "WGCNA" version)) - (sha256 - (base32 - "18yl2v3s279saq318vd5hlwnqfm89rxmjjji778d2d26vviaf6bn")))) + (version (string-append "1.49-" commit)) + (source (origin + (method git-fetch) + (uri (git-reference + ;; (url "https://github.com/genenetwork/WGCNA.git") + (url "https://github.com/pjotrp/WGCNA.git") + (commit commit))) + (file-name (string-append name "-" commit)) + (sha256 + (base32 + "1zqnsb8s3065rq1y2y3l79zi8wmdwjkcjls96ypycrb7pmdil58j")))) (properties `((upstream-name . "WGCNA"))) (build-system r-build-system) - ;; (propagated-inputs - ;; `( ;; ("r-annotationdbi" ,r-annotationdbi) - ;; ("r-doparallel" ,r-doparallel) - ;; ("r-dynamictreecut" ,r-dynamictreecut) - ;; ("r-fastcluster" ,r-fastcluster) - ;; ("r-foreach" ,r-foreach) - ;; ("r-go.db" ,r-go.db) - ;; ("r-grdevices" ,r-grdevices) - ;; ("r-hmisc" ,r-hmisc) - ;; ("r-impute" ,r-impute) - ;; ("r-matrixstats" ,r-matrixstats) - ;; ("r-parallel" ,r-parallel) - ;; ("r-preprocesscore" ,r-preprocesscore) - ;; ("r-splines" ,r-splines) - ;; ("r-stats" ,r-stats) - ;; ("r-survival" ,r-survival) - ;; ("r-utils" ,r-utils))) + (propagated-inputs + `( ;; ("r-annotationdbi" ,r-annotationdbi) + ; ("r-biocparallel" ,r-biocparallel) + ("r-dynamictreecut" ,r-dynamictreecut) + ("r-doparallel" ,r-doparallel) + ("r-fastcluster" ,r-fastcluster) + ("r-foreach" ,r-foreach) + ("r-go-db" ,r-go-db) + ; ("r-grdevices" ,r-grdevices) + ("r-hmisc" ,r-hmisc) + ("r-impute" ,r-impute) + ("r-matrixstats" ,r-matrixstats) + ; ("r-parallel" ,r-parallel) + ("r-biocpreprocesscore" ,r-biocpreprocesscore) + ; ("r-splines" ,r-splines) + ; ("r-stats" ,r-stats) + ; ("r-survival" ,r-survival) + ; ("r-utils" ,r-utils) + )) + (arguments + `( + #:tests? #f)) ; no 'setup.py test' (home-page "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/") (synopsis - "Weighted Correlation Network Analysis") + "Weighted gene correlation network analysis (wgcna)") (description - "Functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data. Includes functions for rudimentary data cleaning, construction of correlation networks, module identification, summarization, and relating of variables and modules to sample traits. Also includes a number of utility functions for data manipulation and visualization.") - (license license:gpl2+))) + "Functions necessary to perform Weighted Correlation Network +Analysis on high-dimensional data. Includes functions for rudimentary +data cleaning, construction of correlation networks, module +identification, summarization, and relating of variables and modules +to sample traits. Also includes a number of utility functions for +data manipulation and visualization.") + (license license:gpl2+)))) (define-public qtlreaper (package @@ -119,7 +155,7 @@ 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))) + (license license:gpl2+))) (define-public plink2 (package @@ -268,48 +304,6 @@ mixed model and some of its close relatives for genome-wide association studies (GWAS).") (license license:gpl3)))) -(define-public rdmd - (let ((commit "4dba6877c")) - (package - (name "rdmd") - (version "20160217") - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/D-Programming-Language/tools.git") - (commit commit))) - (file-name (string-append name "-" commit)) - (sha256 - (base32 - "1pcx5lyqzrip86f4vv60x292rpvnwsq2hvl1znm9x9rn68f34m45")))) - (build-system gnu-build-system) - (arguments - '(#:phases - (modify-phases %standard-phases - (delete 'configure) - (delete 'check) ; There is no Makefile, so there's no 'make check'. - (replace - 'build - (lambda _ - (zero? (system* "ldc2" "rdmd.d")))) - (replace - 'install - (lambda* (#:key outputs #:allow-other-keys) - (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) - (mkdir-p bin) - (copy-file "rdmd" (string-append bin "/rdmd")))))))) - (native-inputs - `(("ldc" ,ldc))) - (home-page "https://github.com/D-Programming-Language/tools/") - (synopsis "Tool for the D language which is used for compiling") - (description - "rdmd is a companion to the dmd compiler that simplifies the typical -edit-compile-link-run or edit-make-run cycle to a rapid edit-run cycle. Like -make and other tools, rdmd uses the relative dates of the files involved to -minimize the amount of work necessary. Unlike make, rdmd tracks dependencies -and freshness without requiring additional information from the user.") - (license license:boost1.0)))) - (define-public sambamba (let ((commit "2ca5a2dbac5ab90c3b4c588519edc3edcb71df84")) (package @@ -325,39 +319,23 @@ and freshness without requiring additional information from the user.") (base32 "1f14wn9aaxwjkmla6pzq3s28741carbr2v0fd2v2mm1dcpwnrqz5")))) (build-system gnu-build-system) - ;; (inputs - ;; `(("ldc" ,ldc) - ;; ;; These are currently included in "ldc". - ;; ;;("druntime-ldc" ,druntime-ldc) - ;; ;;("phobos2-ldc" ,phobos2-ldc) - ;; ("lz4" ,lz4))) (native-inputs `(("ldc" ,ldc) - ;;("druntime-ldc" ,druntime-ldc) - ;;("phobos2-ldc" ,phobos2-ldc) ("lz4" ,lz4) ("rdmd" ,rdmd) ("zlib" ,zlib) - ("perl" ,perl) ; Needed for htslib - ("ruby" ,ruby) ; Needed for htslib - ("python" ,python) ; Needed for htslib + ("perl" ,perl) ; Needed for htslib tests? + ("ruby" ,ruby) ; Needed for htslib tests? + ("python" ,python) ; Needed for htslib tests? ("gcc" ,gcc) - ("lz4-src" - ,(origin - (method url-fetch) - (uri (string-append - "https://github.com/Cyan4973/lz4/archive/r131.tar.gz")) - (file-name "lz4-r131.tar.gz") - (sha256 - (base32 "1vfg305zvj50hwscad24wan9jar6nqj14gdk2hqyr7bb9mhh0kcx")))) ("htslib-src" ,(origin (method url-fetch) - (uri (string-append - "https://github.com/lomereiter/htslib/archive/0.2.0-rc10.tar.gz")) - (file-name "htslib-0.2.0-rc10.tar.gz") + (uri "https://github.com/samtools/htslib/archive/1.3.tar.gz") + (file-name "htslib-1.3.tar.gz") (sha256 - (base32 "1k6dlf6m8yayhcp7b4yisgw1xqdy1xg2xyrllss6ld0wg00hfcbs")))) + (base32 "1bqkif7yrqmiqak5yb74kgpb2lsdlg7y344qa1xkdg7k1l4m86i9")) + (patches (list (search-patch "htslib-add-cram_to_bam.patch"))))) ("biod-src" ,(origin (method git-fetch) @@ -369,33 +347,34 @@ and freshness without requiring additional information from the user.") (base32 "09icc2bjsg9y4hxjim4ql275izadf0kh1nnmapg8manyz6bc8svf")))))) (arguments `(#:tests? #f - ;;#:make-flags + #:make-flags (list "-f" "Makefile.guix") #:phases (modify-phases %standard-phases (delete 'configure) (delete 'check) (add-after 'unpack 'unpack-htslib-sources (lambda* (#:key inputs #:allow-other-keys) - ;; Unfortunately, the current build compiles htslib statically - ;; into the executable. Instead of patching the build files - ;; for Guix, this should be resolved on Sambamba upstream. For - ;; now, just extract the source code to the desired directory. + ;; The current build compiles htslib statically into the + ;; executable. On top of that, we need to patch the latest + ;; version of htslib to have it working with Sambamba. (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"))) - (and (zero? (system* "rm" "-r" "BioD")) - (zero? (system* "ln" "--symbolic" "--no-target-directory" - (assoc-ref inputs "biod-src") "BioD")))))) - ;; Building a production-quality executable is done with a - ;; non-default make target. Adding it with #:make-flags breaks - ;; building tests. Therefore, the default make got replaced by this. + (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" "-f" "Makefile.guix" "CC=gcc" "D_COMPILER=ldc2"))))))) + (zero? (system* "make" "-f" "Makefile.guix" + (string-append "LDC_LIB_PATH=" + (assoc-ref inputs "ldc") + "/lib"))))) + (replace + 'install + (lambda* (#:key outputs #:allow-other-keys) + (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.") (description |