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-rw-r--r--gn/packages/bioinformatics.scm123
-rw-r--r--gn/packages/genenetwork.scm21
-rw-r--r--gn/packages/python.scm2
3 files changed, 115 insertions, 31 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 295a2b3..5bf7843 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -100,10 +100,11 @@ mappability data (files created by GEM). ")
(license license:gpl2+)))
(define-public freebayes
- (let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb"))
+ (let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb")
+ (revision "1"))
(package
(name "freebayes")
- (version (string-append "v1.0.2-" (string-take commit 7)))
+ (version (string-append "1.0.2-" revision "." (string-take commit 7)))
(source (origin
(method git-fetch)
(uri (git-reference
@@ -113,11 +114,18 @@ mappability data (files created by GEM). ")
(sha256
(base32 "1sbzwmcbn78ybymjnhwk7qc5r912azy5vqz2y7y81616yc3ba2a2"))))
(build-system gnu-build-system)
+ (inputs
+ `(("zlib" ,zlib)))
(native-inputs
- `(("cmake" ,cmake)
+ `(("bc" ,bc) ; Needed for running tests.
+ ("samtools" ,samtools) ; Needed for running tests.
+ ("parallel" ,parallel) ; Needed for running tests.
+ ("procps" ,procps) ; Needed for running tests.
+ ("bamtools" ,bamtools)
+ ("cmake" ,cmake)
("htslib" ,htslib)
- ("zlib" ,zlib)
("python" ,python-2)
+ ("r" ,r)
("perl" ,perl)
("bamtools-src"
,(origin
@@ -193,20 +201,34 @@ mappability data (files created by GEM). ")
(file-name "fastahack-src.tar.gz")
(sha256
(base32 "0j25lcl3jk1kls66zzxjfyq5ir6sfcvqrdwfcva61y3ajc9ssay2"))))
- ))
+ ;; These submodules are needed to run the tests.
+ ("bash-tap-src"
+ ,(origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/illusori/bash-tap/archive/"
+ "c38fbfa401600cc81ccda66bfc0da3ea56288d03" ".tar.gz"))
+ (file-name "bash-tap-src.tar.gz")
+ (sha256
+ (base32 "07ijb1p0aa65ajpg9nkghc183iha6lwiydkckay8pghapa01j6nz"))))
+ ("test-simple-bash-src"
+ ,(origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/ingydotnet/test-simple-bash/archive/"
+ "124673ff204b01c8e96b7fc9f9b32ee35d898acc" ".tar.gz"))
+ (file-name "test-simple-bash-src.tar.gz")
+ (sha256
+ (base32 "016xf3wbgqbav9dncvfdx5k0f10z5xwq8jdszajzmcvnhz5wis14"))))))
(arguments
- `(#:tests? #f
- #:phases
+ `(#:phases
(modify-phases %standard-phases
(delete 'configure)
- (delete 'check)
(add-after 'unpack 'unpack-submodule-sources
(lambda* (#:key inputs #:allow-other-keys)
(let ((unpack (lambda (source target)
(with-directory-excursion target
(zero? (system* "tar" "xvf"
- (assoc-ref inputs source)
- "--strip-components=1"))))))
+ (assoc-ref inputs source)
+ "--strip-components=1"))))))
(and
(unpack "bamtools-src" "bamtools")
(unpack "vcflib-src" "vcflib")
@@ -217,47 +239,46 @@ mappability data (files created by GEM). ")
(unpack "intervaltree-src" "vcflib/intervaltree")
(unpack "multichoose-src" "vcflib/multichoose")
(unpack "smithwaterman-src" "vcflib/smithwaterman")
- (unpack "tabixpp-src" "vcflib/tabixpp")))))
+ (unpack "tabixpp-src" "vcflib/tabixpp")
+ (unpack "test-simple-bash-src" "test/test-simple-bash")
+ (unpack "bash-tap-src" "test/bash-tap")))))
(add-after 'unpack-submodule-sources 'fix-makefile
(lambda* (#:key inputs #:allow-other-keys)
+ ;; We don't have the .git folder to get the version tag from.
+ ;; For this checkout of the code, it's v1.0.0.
(substitute* '("vcflib/Makefile")
(("^GIT_VERSION.*") "GIT_VERSION = v1.0.0"))))
- (replace
- 'build
+ (replace 'build
(lambda* (#:key inputs make-flags #:allow-other-keys)
(and
- ;; We must compile Bamtools before we can compile the main
- ;; project.
+ ;; Compile Bamtools before compiling the main project.
(with-directory-excursion "bamtools"
(system* "mkdir" "build")
(with-directory-excursion "build"
(and (zero? (system* "cmake" "../"))
(zero? (system* "make")))))
- ;; We must compile vcflib before we can compile the main
- ;; project.
+ ;; Compile vcflib before we compiling the main project.
(with-directory-excursion "vcflib"
(with-directory-excursion "tabixpp"
(zero? (system* "make")))
(zero? (system* "make" "CC=gcc"
(string-append "CFLAGS=\"" "-Itabixpp "
"-I" (assoc-ref inputs "htslib") "/include " "\"") "all")))
-
(with-directory-excursion "src"
(zero? (system* "make"))))))
- (replace
- 'install
+ (replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin")))
(install-file "bin/freebayes" bin)
(install-file "bin/bamleftalign" bin))))
- ;; (replace
- ;; 'check
- ;; (lambda* (#:key outputs #:allow-other-keys)
- ;; (with-directory-excursion "test"
- ;; (zero? (system* "make" "test")))))
- )))
+ ;; There are three tests that fail. All because of the -P
+ ;; (--perl-regexp) option in grep, which is not compiled into the
+ ;; version of grep in Guix.
+ (replace 'check
+ (lambda* (#:key inputs #:allow-other-keys)
+ (system* "make" "test"))))))
(home-page "https://github.com/ekg/freebayes")
- (synopsis "haplotype-based variant detector.")
+ (synopsis "Haplotype-based variant detector")
(description "FreeBayes is a Bayesian genetic variant detector designed to
find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms),
indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and
@@ -305,8 +326,8 @@ length of a short-read sequencing alignment.")
(propagated-inputs
`( ;; ("r-annotationdbi" ,r-annotationdbi)
; ("r-biocparallel" ,r-biocparallel)
- ("r-dynamictreecut" ,r-dynamictreecut)
("r-doparallel" ,r-doparallel)
+ ("r-dynamictreecut" ,r-dynamictreecut)
("r-fastcluster" ,r-fastcluster)
("r-foreach" ,r-foreach)
("r-go-db" ,r-go-db)
@@ -793,3 +814,49 @@ format, and a collection of command-line utilities for executing complex
manipulations on VCF files.")
(license license:expat))))
+(define-public pindel
+ (package
+ (name "pindel")
+ (version "0.2.5b8")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/genome/pindel/archive/v"
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "06bsf0psxwf7h5p3j97xkh9k5qrwhxh6xn942y1j1m2inyhgs8bz"))))
+ (build-system gnu-build-system)
+ (inputs
+ `(("samtools" ,samtools)
+ ("htslib" ,htslib)
+ ("zlib" ,zlib)))
+ (native-inputs
+ `(("cppcheck" ,cppcheck)
+ ("python" ,python-2)
+ ("perl" ,perl)))
+ (arguments
+ `(#:tests? #f
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure) ; There is no configure phase.
+ (replace 'build
+ (lambda* (#:key inputs #:allow-other-keys)
+ ;; The first run creates a Makefile.local file.
+ (system* "make" (string-append "SAMTOOLS=" (assoc-ref inputs "samtools")))
+ ;; The second run actually compiles the program.
+ (zero? (system* "make"))))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+ (install-file "src/pindel" bin)
+ (install-file "src/pindel2vcf" bin)
+ (install-file "src/pindel2vcf4tcga" bin)
+ (install-file "src/sam2pindel" bin)))))))
+ (home-page "https://github.com/genome/pindel")
+ (synopsis "Structural variants detector for next-gen sequencing data")
+ (description "Pindel can detect breakpoints of large deletions, medium sized
+insertions, inversions, tandem duplications and other structural variants at
+single-based resolution from next-gen sequence data. It uses a pattern growth
+approach to identify the breakpoints of these variants from paired-end short
+reads.")
+ (license license:gpl3+)))
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index fdcbb7f..3d62d55 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -154,10 +154,14 @@
(sha256
(base32
"1zs6jgrpwzxmfjz03whnaw8q6h8f53mycl440p058gfn8x7pd618"))))
+ (inputs `(
+ ("r-wgcna" ,r-wgcna)
+ ("r-qtl" ,r-qtl)))
(propagated-inputs `( ;; propagated for development purposes
("python" ,python-2) ;; probably superfluous
("r" ,r)
("r-wgcna" ,r-wgcna)
+ ("r-qtl" ,r-qtl)
("redis" ,redis)
("mysql" ,mysql)
("gemma" ,gemma-git)
@@ -181,6 +185,7 @@
("python2-passlib" ,python2-passlib)
("python2-piddle-gn" ,python2-piddle-gn)
("python2-redis" ,python2-redis)
+ ("python2-pil" ,python2-pil)
("python2-requests" ,python2-requests)
("python2-rpy2" ,python2-rpy2)
("python2-scipy" ,python2-scipy)
@@ -190,7 +195,6 @@
;; python-yolk is not needed
("plink" ,plink)
("qtlreaper" ,qtlreaper)
- ("r-qtl" ,r-qtl)
))
(build-system python-build-system)
(arguments
@@ -199,9 +203,20 @@
(modify-phases %standard-phases
(add-before 'install 'fix-paths
(lambda* (#:key inputs #:allow-other-keys)
- (let* ((datafiles (string-append (assoc-ref inputs "genenetwork2-files-small") "/share/genenetwork2" )))
+ (let* (
+ (datafiles (string-append (assoc-ref inputs "genenetwork2-files-small") "/share/genenetwork2" ))
+ (pylmmcmd (string-append (assoc-ref inputs "pylmm-gn2") "/bin/pylmm_redis"))
+ (plink2cmd (string-append (assoc-ref inputs "plink2") "/bin/plink2"))
+ (gemmacmd (string-append (assoc-ref inputs "gemma") "/bin/gemma"))
+ )
+
(substitute* '("etc/default_settings.py")
- (("^GENENETWORK_FILES =.*") (string-append "GENENETWORK_FILES = \"" datafiles "\"\n" )))))))
+ (("^GENENETWORK_FILES =.*") (string-append "GENENETWORK_FILES = \"" datafiles "\"\n" ))
+ (("^PYLMM_COMMAND =.*") (string-append "PYLMM_COMMAND = \"" pylmmcmd "\"\n" ))
+ (("^PLINK_COMMAND =.*") (string-append "PLINK_COMMAND = \"" plink2cmd "\"\n" ))
+ (("^GEMMA_COMMAND =.*") (string-append "GEMMA_COMMAND = \"" gemmacmd "\"\n" ))
+ )
+ ))))
#:tests? #f)) ; no 'setup.py test'
(home-page "http://genenetwork.org/")
(synopsis "Full genenetwork services")
diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index 6fff9a3..8157c0b 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -432,6 +432,8 @@ version ".tgz"))
(build-system python-build-system)
(native-inputs
`(("python2-setuptools" ,python2-setuptools)))
+ (propagated-inputs
+ `(("python2-pil" ,python2-pil)))
(arguments
`(
#:python ,python-2