diff options
Diffstat (limited to 'gn/packages')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 388 | ||||
| -rw-r--r-- | gn/packages/genenetwork.scm | 57 | ||||
| -rw-r--r-- | gn/packages/python.scm | 6 |
3 files changed, 428 insertions, 23 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)))) + diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index aec305b..fdcbb7f 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -87,7 +87,6 @@ (description #f) (license #f))) - (define-public genenetwork1 (let ((commit "d622c803b")) (package @@ -141,7 +140,7 @@ (license license:agpl3+)))) (define-public genenetwork2 - (let ((commit "8c9de7e5a2016f1e5b7397be1a8e84396e3a25c5")) + (let ((commit "a8fcff44d3bd768d02e7ed0c80b84d2516bdad2a")) (package (name "genenetwork2") (version (string-append "2.0-" (string-take commit 7) )) @@ -149,12 +148,12 @@ (method git-fetch) (uri (git-reference ;; (url "https://github.com/genenetwork/genenetwork2.git") - (url "https://github.com/pjotrp/genenetwork2.git") + (url "https://github.com/genenetwork/genenetwork2_diet.git") (commit commit))) (file-name (string-append name "-" (string-take commit 7))) (sha256 (base32 - "1kgigzs4rs6zgbqbnm40rcljzz9prlwv7n2n9an57jk58bjgf6v8")))) + "1zs6jgrpwzxmfjz03whnaw8q6h8f53mycl440p058gfn8x7pd618")))) (propagated-inputs `( ;; propagated for development purposes ("python" ,python-2) ;; probably superfluous ("r" ,r) @@ -162,6 +161,7 @@ ("redis" ,redis) ("mysql" ,mysql) ("gemma" ,gemma-git) + ("genenetwork2-files-small" ,genenetwork2-files-small) ("pylmm-gn2" ,pylmm-gn2) ("plink2" ,plink-ng) ("nginx" ,nginx) @@ -195,6 +195,13 @@ (build-system python-build-system) (arguments `(#:python ,python-2 + #:phases + (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" ))) + (substitute* '("etc/default_settings.py") + (("^GENENETWORK_FILES =.*") (string-append "GENENETWORK_FILES = \"" datafiles "\"\n" ))))))) #:tests? #f)) ; no 'setup.py test' (home-page "http://genenetwork.org/") (synopsis "Full genenetwork services") @@ -204,6 +211,48 @@ ;; ./pre-inst-env guix download http://files.genenetwork.org/raw_database/db_webqtl_s.zip ;; 0sscjh0wml2lx0mb43vf4chg9gpbfi7abpjxb34n3kyny9ll557x +(define-public genenetwork2-files-small + (let ((pfff "xx")) + (package + (name "genenetwork2-files-small") + (version "1.0") + (source + (origin + (method url-fetch) + (uri "http://files.genenetwork.org/data_files/gn2_data_s-20160303-C9E672ECED1F51B915DE419B5B2C524E.tar.lz4") + (file-name (string-append name "-" pfff)) + (sha256 + (base32 "058ymx3af6abdhdxyxj0i9qfvb6v7j091frjpp6jh4ahks7r23lj")))) + (build-system trivial-build-system) + (native-inputs `(("lz4" ,lz4) + ("tar" ,tar) + ("source" ,source))) + + (arguments + `(#:modules ((guix build utils)) + #:builder + (let* ((out (assoc-ref %outputs "out")) + (name "gn2_data_s") + (tarfn (string-append name ".tar")) + (targetdir (string-append out "/share/genenetwork2/")) + ) + (begin + (use-modules (guix build utils)) + (let ((source (assoc-ref %build-inputs "source")) + (lz4unpack (string-append (assoc-ref %build-inputs "lz4") "/bin/lz4")) + (tar (string-append (assoc-ref %build-inputs "tar") "/bin/tar")) + ) + (and + (zero? (system* lz4unpack source "-d" tarfn)) + (zero? (system* tar "xf" tarfn)) + (mkdir-p targetdir) + (copy-recursively name targetdir) + )))))) + (home-page "http://genenetwork.org/") + (synopsis "Small file archive to run on genenetwork") + (description "Genenetwork genotype and mapping files.") + (license license:agpl3+)))) + (define-public genenetwork2-database-small (let ((md5 "93e745e9c")) (package diff --git a/gn/packages/python.scm b/gn/packages/python.scm index 7781521..6fff9a3 100644 --- a/gn/packages/python.scm +++ b/gn/packages/python.scm @@ -279,16 +279,14 @@ powerful language for representing information.") (base32 "06qzgwk7j66k8ggx51i6wxx0f0zsppp7w4bh6gjd0cr9rfs86jn7")))) (build-system python-build-system) - (inputs + (propagated-inputs `( ("mysql" ,mysql) ("python-nose" ,python-nose) ("zlib" ,zlib) ("openssl" ,openssl) ("libgcrypt" ,libgcrypt) - )) - (propagated-inputs - `(("python-setuptools" ,python-setuptools) + ("python-setuptools" ,python-setuptools) )) (arguments `(#:tests? #f)) ; wants a running MySQL server |