diff options
Diffstat (limited to 'gn/packages/bioinformatics.scm')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 388 |
1 files changed, 373 insertions, 15 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index b503e22..295a2b3 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -20,6 +20,7 @@ #:use-module (gnu packages boost) #:use-module (gnu packages compression) #:use-module (gnu packages databases) + #:use-module (gnu packages cmake) #:use-module (gnu packages cpio) #:use-module (gnu packages file) #:use-module (gnu packages gcc) @@ -48,6 +49,221 @@ #:use-module (gn packages statistics) #:use-module (srfi srfi-1)) +(define-public freec + (package + (name "control-freec") + (version "8.7") + (source (origin + (method url-fetch) + (uri "http://bioinfo-out.curie.fr/projects/freec/src/FREEC_Linux64.tar.gz") + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "12sl7gxbklhvv0687qjhml1z4lwpcn159zcyxvawvclsrzqjmv0h")))) + (build-system gnu-build-system) + ;; The source code's filename indicates only a 64-bit Linux build. + ;; We need to investigate whether this is true. + (supported-systems '("x86_64-linux")) + (arguments + `(#:phases + (modify-phases %standard-phases + ;; There's no configure phase because there are no external + ;; dependencies. + (delete 'configure) + ;; There are no tests. + (delete 'check) + (replace + 'unpack + (lambda* (#:key source #:allow-other-keys) + (and + (zero? (system* "mkdir" "source")) + (with-directory-excursion "source" + (zero? (system* "tar" "xvf" source)))))) + (replace + 'build + (lambda* (#:key inputs #:allow-other-keys) + (with-directory-excursion "source" + (zero? (system* "make"))))) + (replace + 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) + (install-file "source/freec" bin))))))) + (home-page "http://bioinfo-out.curie.fr/projects/freec/") + (synopsis "Tool for detection of copy-number changes and allelic imbalances +(including LOH) using deep-sequencing data") + (description "Control-FREEC automatically computes, normalizes, segments +copy number and beta allele frequency (BAF) profiles, then calls copy number +alterations and LOH. The control (matched normal) sample is optional for whole +genome sequencing data but mandatory for whole exome or targeted sequencing +data. For whole genome sequencing data analysis, the program can also use +mappability data (files created by GEM). ") + (license license:gpl2+))) + +(define-public freebayes + (let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb")) + (package + (name "freebayes") + (version (string-append "v1.0.2-" (string-take commit 7))) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/freebayes.git") + (commit commit))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 "1sbzwmcbn78ybymjnhwk7qc5r912azy5vqz2y7y81616yc3ba2a2")))) + (build-system gnu-build-system) + (native-inputs + `(("cmake" ,cmake) + ("htslib" ,htslib) + ("zlib" ,zlib) + ("python" ,python-2) + ("perl" ,perl) + ("bamtools-src" + ,(origin + (method url-fetch) + (uri (string-append "https://github.com/ekg/bamtools/archive/" + "e77a43f5097ea7eee432ee765049c6b246d49baa" ".tar.gz")) + (file-name "bamtools-src.tar.gz") + (sha256 + (base32 "0rqymka21g6lfjfgxzr40pxz4c4fcl77jpy1np1li70pnc7h2cs1")))) + ("vcflib-src" + ,(origin + (method url-fetch) + (uri (string-append "https://github.com/vcflib/vcflib/archive/" + "5ac091365fdc716cc47cc5410bb97ee5dc2a2c92" ".tar.gz")) + (file-name "vcflib-5ac0913.tar.gz") + (sha256 + (base32 "0ywshwpif059z5h0g7zzrdfzzdj2gr8xvwlwcsdxrms3p9iy35h8")))) + ;; These are submodules for the vcflib version used in freebayes + ("tabixpp-src" + ,(origin + (method url-fetch) + (uri (string-append "https://github.com/ekg/tabixpp/archive/" + "bbc63a49acc52212199f92e9e3b8fba0a593e3f7" ".tar.gz")) + (file-name "tabixpp-src.tar.gz") + (sha256 + (base32 "1s06wmpgj4my4pik5kp2lc42hzzazbp5ism2y4i2ajp2y1c68g77")))) + ("intervaltree-src" + ,(origin + (method url-fetch) + (uri (string-append + "https://github.com/ekg/intervaltree/archive/" + "dbb4c513d1ad3baac516fc1484c995daf9b42838" ".tar.gz")) + (file-name "intervaltree-src.tar.gz") + (sha256 + (base32 "19prwpn2wxsrijp5svfqvfcxl5nj7zdhm3jycd5kqhl9nifpmcks")))) + ("smithwaterman-src" + ,(origin + (method url-fetch) + (uri (string-append "https://github.com/ekg/smithwaterman/archive/" + "203218b47d45ac56ef234716f1bd4c741b289be1" ".tar.gz")) + (file-name "smithwaterman-src.tar.gz") + (sha256 + (base32 "1lkxy4xkjn96l70jdbsrlm687jhisgw4il0xr2dm33qwcclzzm3b")))) + ("multichoose-src" + ,(origin + (method url-fetch) + (uri (string-append "https://github.com/ekg/multichoose/archive/" + "73d35daa18bf35729b9ba758041a9247a72484a5" ".tar.gz")) + (file-name "multichoose-src.tar.gz") + (sha256 + (base32 "07aizwdabmlnjaq4p3v0vsasgz1xzxid8xcxcw3paq8kh9c1099i")))) + ("fsom-src" + ,(origin + (method url-fetch) + (uri (string-append "https://github.com/ekg/fsom/archive/" + "a6ef318fbd347c53189384aef7f670c0e6ce89a3" ".tar.gz")) + (file-name "fsom-src.tar.gz") + (sha256 + (base32 "0q6b57ppxfvsm5cqmmbfmjpn5qvx2zi5pamvp3yh8gpmmz8cfbl3")))) + ("filevercmp-src" + ,(origin + (method url-fetch) + (uri (string-append "https://github.com/ekg/filevercmp/archive/" + "1a9b779b93d0b244040274794d402106907b71b7" ".tar.gz")) + (file-name "filevercmp-src.tar.gz") + (sha256 + (base32 "0yp5jswf5j2pqc6517x277s4s6h1ss99v57kxw9gy0jkfl3yh450")))) + ("fastahack-src" + ,(origin + (method url-fetch) + (uri (string-append "https://github.com/ekg/fastahack/archive/" + "c68cebb4f2e5d5d2b70cf08fbdf1944e9ab2c2dd" ".tar.gz")) + (file-name "fastahack-src.tar.gz") + (sha256 + (base32 "0j25lcl3jk1kls66zzxjfyq5ir6sfcvqrdwfcva61y3ajc9ssay2")))) + )) + (arguments + `(#:tests? #f + #: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")))))) + (and + (unpack "bamtools-src" "bamtools") + (unpack "vcflib-src" "vcflib") + (unpack "intervaltree-src" "intervaltree") + (unpack "fastahack-src" "vcflib/fastahack") + (unpack "filevercmp-src" "vcflib/filevercmp") + (unpack "fsom-src" "vcflib/fsom") + (unpack "intervaltree-src" "vcflib/intervaltree") + (unpack "multichoose-src" "vcflib/multichoose") + (unpack "smithwaterman-src" "vcflib/smithwaterman") + (unpack "tabixpp-src" "vcflib/tabixpp"))))) + (add-after 'unpack-submodule-sources 'fix-makefile + (lambda* (#:key inputs #:allow-other-keys) + (substitute* '("vcflib/Makefile") + (("^GIT_VERSION.*") "GIT_VERSION = v1.0.0")))) + (replace + 'build + (lambda* (#:key inputs make-flags #:allow-other-keys) + (and + ;; We must compile Bamtools before we can compile 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. + (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 + (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"))))) + ))) + (home-page "https://github.com/ekg/freebayes") + (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 +complex events (composite insertion and substitution events) smaller than the +length of a short-read sequencing alignment.") + (license license:expat)))) (define-public r-biocpreprocesscore (package @@ -69,7 +285,6 @@ "A library of core preprocessing routines.") (license license:lgpl2.0+))) - (define-public r-wgcna (let ((commit "425bc170cc0873ddbd414675ac40f6d4d724c7cb")) (package @@ -305,37 +520,48 @@ association studies (GWAS).") (license license:gpl3)))) (define-public sambamba - (let ((commit "2ca5a2dbac5ab90c3b4c588519edc3edcb71df84")) + (let ((commit "c810c7ef14957f16288c205fd7b9d25c4ae7005d")) + ;;(let ((commit "2ca5a2dbac5ab90c3b4c588519edc3edcb71df84")) (package (name "sambamba") (version (string-append "0.5.9-1." (string-take commit 7))) (source (origin (method git-fetch) - (uri (git-reference - (url "https://github.com/pjotrp/sambamba.git") + (uri (git-reference + (url "https://github.com/roelj/sambamba.git") + ;;(url "https://github.com/pjotrp/sambamba.git") (commit commit))) (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "1f14wn9aaxwjkmla6pzq3s28741carbr2v0fd2v2mm1dcpwnrqz5")))) + "0c4c13f021sl7mf5xc2v8dbwsz775n8dlsrrn7qa6qgbx05n54dv")))) + ;;"1f14wn9aaxwjkmla6pzq3s28741carbr2v0fd2v2mm1dcpwnrqz5")))) (build-system gnu-build-system) (native-inputs `(("ldc" ,ldc) - ("lz4" ,lz4) + ;;("lz4" ,lz4) ("rdmd" ,rdmd) ("zlib" ,zlib) - ("perl" ,perl) ; Needed for htslib tests? - ("ruby" ,ruby) ; Needed for htslib tests? - ("python" ,python) ; Needed for htslib tests? + ("perl" ,perl) ; Needed for htslib + ("ruby" ,ruby) ; Needed for htslib + ("python" ,python) ; Needed for htslib ("gcc" ,gcc) + ("lz4-src" + ,(origin + (method url-fetch) + (uri "https://github.com/Cyan4973/lz4/archive/160661c7a4cbf805f4af74d2e3932a17a66e6ce7.tar.gz") + (sha256 + (base32 "131nnbsd5dh7c8sdqzc9kawh3mi0qi4qxznv7zhzfszlx4g2fd20")))) ("htslib-src" ,(origin (method url-fetch) - (uri "https://github.com/samtools/htslib/archive/1.3.tar.gz") - (file-name "htslib-1.3.tar.gz") + (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") (sha256 - (base32 "1bqkif7yrqmiqak5yb74kgpb2lsdlg7y344qa1xkdg7k1l4m86i9")) - (patches (list (search-patch "htslib-add-cram_to_bam.patch"))))) + (base32 "0bl6w856afnbgdsw8bybsxpqsyf2ba3f12rqh47hhpxvv866g08w")))) + ;;(base32 "1bqkif7yrqmiqak5yb74kgpb2lsdlg7y344qa1xkdg7k1l4m86i9")) + ;;(patches (list (search-patch "htslib-add-cram_to_bam.patch"))))) ("biod-src" ,(origin (method git-fetch) @@ -360,14 +586,17 @@ 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" "-f" "Makefile.guix" - (string-append "LDC_LIB_PATH=" + (zero? (system* "make" "sambamba-ldmd2-64" "CC=gcc" "D_COMPILER=ldc2" + (string-append "LDC_LIB_PATH=" (assoc-ref inputs "ldc") "/lib"))))) (replace @@ -435,3 +664,132 @@ supported.") (description "FastQC aims to provide a QC report which can spot problems which originate either in the sequencer or in the starting library material. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files.") (license license:gpl3+))) + +(define-public vcflib + (let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb")) + (package + (name "vcflib") + (version (string-append "v1.0.2-" (string-take commit 7))) + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/vcflib/vcflib/archive/" + "5ac091365fdc716cc47cc5410bb97ee5dc2a2c92" ".tar.gz")) + (file-name "vcflib-5ac0913.tar.gz") + (sha256 + (base32 "0ywshwpif059z5h0g7zzrdfzzdj2gr8xvwlwcsdxrms3p9iy35h8")))) + (build-system gnu-build-system) + (native-inputs + `(("htslib" ,htslib) + ("zlib" ,zlib) + ("python" ,python-2) + ("perl" ,perl) + ("tabixpp-src" + ,(origin + (method url-fetch) + (uri (string-append "https://github.com/ekg/tabixpp/archive/" + "bbc63a49acc52212199f92e9e3b8fba0a593e3f7" ".tar.gz")) + (file-name "tabixpp-src.tar.gz") + (sha256 + (base32 "1s06wmpgj4my4pik5kp2lc42hzzazbp5ism2y4i2ajp2y1c68g77")))) + ("intervaltree-src" + ,(origin + (method url-fetch) + (uri (string-append + "https://github.com/ekg/intervaltree/archive/" + "dbb4c513d1ad3baac516fc1484c995daf9b42838" ".tar.gz")) + (file-name "intervaltree-src.tar.gz") + (sha256 + (base32 "19prwpn2wxsrijp5svfqvfcxl5nj7zdhm3jycd5kqhl9nifpmcks")))) + ("smithwaterman-src" + ,(origin + (method url-fetch) + (uri (string-append "https://github.com/ekg/smithwaterman/archive/" + "203218b47d45ac56ef234716f1bd4c741b289be1" ".tar.gz")) + (file-name "smithwaterman-src.tar.gz") + (sha256 + (base32 "1lkxy4xkjn96l70jdbsrlm687jhisgw4il0xr2dm33qwcclzzm3b")))) + ("multichoose-src" + ,(origin + (method url-fetch) + (uri (string-append "https://github.com/ekg/multichoose/archive/" + "73d35daa18bf35729b9ba758041a9247a72484a5" ".tar.gz")) + (file-name "multichoose-src.tar.gz") + (sha256 + (base32 "07aizwdabmlnjaq4p3v0vsasgz1xzxid8xcxcw3paq8kh9c1099i")))) + ("fsom-src" + ,(origin + (method url-fetch) + (uri (string-append "https://github.com/ekg/fsom/archive/" + "a6ef318fbd347c53189384aef7f670c0e6ce89a3" ".tar.gz")) + (file-name "fsom-src.tar.gz") + (sha256 + (base32 "0q6b57ppxfvsm5cqmmbfmjpn5qvx2zi5pamvp3yh8gpmmz8cfbl3")))) + ("filevercmp-src" + ,(origin + (method url-fetch) + (uri (string-append "https://github.com/ekg/filevercmp/archive/" + "1a9b779b93d0b244040274794d402106907b71b7" ".tar.gz")) + (file-name "filevercmp-src.tar.gz") + (sha256 + (base32 "0yp5jswf5j2pqc6517x277s4s6h1ss99v57kxw9gy0jkfl3yh450")))) + ("fastahack-src" + ,(origin + (method url-fetch) + (uri (string-append "https://github.com/ekg/fastahack/archive/" + "c68cebb4f2e5d5d2b70cf08fbdf1944e9ab2c2dd" ".tar.gz")) + (file-name "fastahack-src.tar.gz") + (sha256 + (base32 "0j25lcl3jk1kls66zzxjfyq5ir6sfcvqrdwfcva61y3ajc9ssay2")))))) + (arguments + `(#:tests? #f + #: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")))))) + (and + (unpack "intervaltree-src" "intervaltree") + (unpack "fastahack-src" "fastahack") + (unpack "filevercmp-src" "filevercmp") + (unpack "fsom-src" "fsom") + (unpack "intervaltree-src" "intervaltree") + (unpack "multichoose-src" "multichoose") + (unpack "smithwaterman-src" "smithwaterman") + (unpack "tabixpp-src" "tabixpp"))))) + (add-after 'unpack-submodule-sources 'fix-makefile + (lambda* (#:key inputs #:allow-other-keys) + (substitute* '("Makefile") + (("^GIT_VERSION.*") "GIT_VERSION = v1.0.0")))) + (replace + 'build + (lambda* (#:key inputs make-flags #:allow-other-keys) + (with-directory-excursion "tabixpp" + (zero? (system* "make"))) + (zero? (system* "make" "CC=gcc" + (string-append "CFLAGS=\"" "-Itabixpp " + "-I" (assoc-ref inputs "htslib") "/include " "\"") "all")))) + (replace + 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin")) + (lib (string-append (assoc-ref outputs "out") "/lib"))) + (for-each (lambda (file) + (install-file file bin)) + (find-files "bin" ".*")) + (install-file "libvcflib.a" lib))))))) + (home-page "https://github.com/vcflib/vcflib/") + (synopsis "Library for parsing and manipulating VCF files") + (description "Vcflib provides methods to manipulate and interpret +sequence variation as it can be described by VCF. It is both an API for parsing +and operating on records of genomic variation as it can be described by the VCF +format, and a collection of command-line utilities for executing complex +manipulations on VCF files.") + (license license:expat)))) + |