From e6c2e0459a71e6c0fc108bf34bee94c1b59c983b Mon Sep 17 00:00:00 2001 From: pjotrp Date: Thu, 3 Mar 2016 14:04:12 +0000 Subject: Added genenetwork2-files-small --- gn/packages/genenetwork.scm | 46 +++++++++++++++++++++++++++++++++++++++++---- 1 file changed, 42 insertions(+), 4 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index aec305b..54c9fce 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 "3d55e84c81ae6c10765c79b6dfa18ccf30e98b53")) (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")))) + "0pmf96hsmxpiczkh4c2zpq5zz6byklhw4vjrazn9qvrgh78aqyab")))) (propagated-inputs `( ;; propagated for development purposes ("python" ,python-2) ;; probably superfluous ("r" ,r) @@ -204,6 +203,45 @@ ;; ./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")) + ;; (targetdir (string-append out "/gn2_data_s")) + ) + (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 ;; (mkdir targetdir) + (zero? (system* lz4unpack source "-d" "xx.tar")) + (zero? (system* tar "xf" "xx.tar")) + (copy-recursively "gn2_data_s" (string-append out "/gn2_data_s")) + )))))) + (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 -- cgit v1.2.3 From 6332603b4492b36a79d0744289a50f7081a52a24 Mon Sep 17 00:00:00 2001 From: pjotrp Date: Fri, 4 Mar 2016 11:07:37 +0000 Subject: GN2 is now a self contained package (except for the database) --- gn/packages/genenetwork.scm | 25 ++++++++++++++++++------- 1 file changed, 18 insertions(+), 7 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 54c9fce..fdcbb7f 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -140,7 +140,7 @@ (license license:agpl3+)))) (define-public genenetwork2 - (let ((commit "3d55e84c81ae6c10765c79b6dfa18ccf30e98b53")) + (let ((commit "a8fcff44d3bd768d02e7ed0c80b84d2516bdad2a")) (package (name "genenetwork2") (version (string-append "2.0-" (string-take commit 7) )) @@ -153,7 +153,7 @@ (file-name (string-append name "-" (string-take commit 7))) (sha256 (base32 - "0pmf96hsmxpiczkh4c2zpq5zz6byklhw4vjrazn9qvrgh78aqyab")))) + "1zs6jgrpwzxmfjz03whnaw8q6h8f53mycl440p058gfn8x7pd618")))) (propagated-inputs `( ;; propagated for development purposes ("python" ,python-2) ;; probably superfluous ("r" ,r) @@ -161,6 +161,7 @@ ("redis" ,redis) ("mysql" ,mysql) ("gemma" ,gemma-git) + ("genenetwork2-files-small" ,genenetwork2-files-small) ("pylmm-gn2" ,pylmm-gn2) ("plink2" ,plink-ng) ("nginx" ,nginx) @@ -194,6 +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") @@ -224,7 +232,9 @@ `(#:modules ((guix build utils)) #:builder (let* ((out (assoc-ref %outputs "out")) - ;; (targetdir (string-append out "/gn2_data_s")) + (name "gn2_data_s") + (tarfn (string-append name ".tar")) + (targetdir (string-append out "/share/genenetwork2/")) ) (begin (use-modules (guix build utils)) @@ -232,10 +242,11 @@ (lz4unpack (string-append (assoc-ref %build-inputs "lz4") "/bin/lz4")) (tar (string-append (assoc-ref %build-inputs "tar") "/bin/tar")) ) - (and ;; (mkdir targetdir) - (zero? (system* lz4unpack source "-d" "xx.tar")) - (zero? (system* tar "xf" "xx.tar")) - (copy-recursively "gn2_data_s" (string-append out "/gn2_data_s")) + (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") -- cgit v1.2.3 From a4a9f2eec7a770a52bbeda64169ba9e3b1ff2583 Mon Sep 17 00:00:00 2001 From: pjotrp Date: Sat, 5 Mar 2016 16:07:32 +0000 Subject: Guix paths to the tools --- gn/packages/bioinformatics.scm | 2 +- gn/packages/genenetwork.scm | 20 +++++++++++++++++--- gn/packages/python.scm | 2 ++ 3 files changed, 20 insertions(+), 4 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 295a2b3..c04c928 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -305,8 +305,8 @@ 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) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index fdcbb7f..c952792 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) @@ -190,7 +194,6 @@ ;; python-yolk is not needed ("plink" ,plink) ("qtlreaper" ,qtlreaper) - ("r-qtl" ,r-qtl) )) (build-system python-build-system) (arguments @@ -199,9 +202,20 @@ (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 -- cgit v1.2.3 From 2f4d42ad812517b931bc71e979824b09f6c6004a Mon Sep 17 00:00:00 2001 From: pjotrp Date: Mon, 7 Mar 2016 11:25:53 +0000 Subject: python2-pil was missing from gn2 --- gn/packages/genenetwork.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index c952792..3d62d55 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -185,6 +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) -- cgit v1.2.3 From 1b16196348f91b6b7655550766a79418428977c1 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Wed, 9 Mar 2016 11:42:16 -0500 Subject: fix --- gn/packages/genenetwork.scm | 3 --- 1 file changed, 3 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 3d62d55..1b46117 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -154,9 +154,6 @@ (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) -- cgit v1.2.3 From a9ae940435ffa67b04598a215280c42dd185e964 Mon Sep 17 00:00:00 2001 From: pjotrp Date: Wed, 9 Mar 2016 17:59:12 +0100 Subject: spaces --- gn/packages/genenetwork.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 1b46117..1382cfb 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -150,7 +150,7 @@ ;; (url "https://github.com/genenetwork/genenetwork2.git") (url "https://github.com/genenetwork/genenetwork2_diet.git") (commit commit))) - (file-name (string-append name "-" (string-take commit 7))) + (file-name (string-append name "-" (string-take commit 7))) (sha256 (base32 "1zs6jgrpwzxmfjz03whnaw8q6h8f53mycl440p058gfn8x7pd618")))) -- cgit v1.2.3