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authorpjotrp2016-03-01 05:43:18 +0000
committerpjotrp2016-03-01 05:43:18 +0000
commit520fb0f8ef40589738123f0129ccc34e1c756c9e (patch)
treed48292f58cb83fde699958c858317815b1bd20fd /gn/packages/bioinformatics.scm
parent55915d466305bd00d15f605541ec926ca6fe0833 (diff)
parentf82b7c5b7ef5bdb9761e48761f683d62d3a05c48 (diff)
downloadguix-bioinformatics-520fb0f8ef40589738123f0129ccc34e1c756c9e.tar.gz
Merge branch 'master' into dennis
Diffstat (limited to 'gn/packages/bioinformatics.scm')
-rw-r--r--gn/packages/bioinformatics.scm197
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