From 5f0f9e2bc4f10c7219990614f89f79408fcb9f35 Mon Sep 17 00:00:00 2001 From: pjotrp Date: Tue, 23 Feb 2016 09:05:47 +0000 Subject: gn2: added database download --- gn/packages/genenetwork.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) (limited to 'gn/packages') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 2f755a6..1b52a5d 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -202,3 +202,35 @@ ;; ./pre-inst-env guix download http://files.genenetwork.org/raw_database/db_webqtl_s.zip ;; 0sscjh0wml2lx0mb43vf4chg9gpbfi7abpjxb34n3kyny9ll557x + +(define-public genenetwork2-database-small + (let ((md5 "93e745e9c")) + (package + (name "genenetwork2-database-small") + (version "1.0") + (source + (origin + (method url-fetch) + (uri "http://files.genenetwork.org/raw_database/db_webqtl_s.zip") + (file-name (string-append name "-" md5)) + (sha256 + (base32 "0sscjh0wml2lx0mb43vf4chg9gpbfi7abpjxb34n3kyny9ll557x")))) + (build-system trivial-build-system) + (native-inputs `(("unzip" ,unzip) + ("source" ,source))) + + (arguments + `(#:modules ((guix build utils)) + #:builder (begin + (use-modules (guix build utils)) + (let ((source (assoc-ref %build-inputs "source")) + (unzip (string-append (assoc-ref %build-inputs "unzip") "/bin/unzip")) + ) + (and (mkdir "db") + (zero? (system* unzip source "-d" "db")) + (chdir "db")))))) + (home-page "http://genenetwork.org/") + (synopsis "Small database to run on genenetwork") + (description "Genenetwork installation + database.") + (license license:agpl3+)))) + -- cgit v1.2.3 From bfee81246e891fc7d4b7b19cd0375168f83624ad Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Wed, 23 Mar 2016 17:42:12 -0500 Subject: Fixed hash --- gn/packages/bioinformatics.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gn/packages') diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 1aee0ef..f3a1e87 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -372,7 +372,7 @@ association studies (GWAS).") (file-name (string-append name "-" commit)) (sha256 (base32 - "09hvy9mf4dnmkb8qg49viffzrxk53m2kr4r955m84dxaa5pdrjhd")))) + "1fimy5959q24wdk9jm83574fpywrarwvf9cd162vs6lriirq0cq5")))) (propagated-inputs `( ("python" ,python-2) ;; probably superfluous ("r" ,r) -- cgit v1.2.3 From 7dbdfa3d6930096d27e12003b9677c537febc74f Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Wed, 23 Mar 2016 18:00:55 -0500 Subject: GN2 fix --- gn/packages/bioinformatics.scm | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) (limited to 'gn/packages') diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index f3a1e87..aa5432a 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -359,20 +359,21 @@ association studies (GWAS).") (license license:agpl3+)))) (define-public genenetwork2 - (let ((commit "9e9475053")) + (let ((commit "234aa9820eeaa3e4611239de31de1ba526d8bf09")) (package (name "genenetwork2") - (version (string-append "2.0-" commit )) + (version (string-append "2.0-" (string-take commit 7) )) (source (origin (method git-fetch) (uri (git-reference ;; (url "https://github.com/genenetwork/genenetwork2.git") - (url "https://github.com/pjotrp/genenetwork2.git") + ;; (url "https://github.com/pjotrp/genenetwork2.git") + (url "https://github.com/genenetwork/genenetwork2_diet.git") (commit commit))) - (file-name (string-append name "-" commit)) + (file-name (string-append name "-" (string-take commit 7))) (sha256 (base32 - "1fimy5959q24wdk9jm83574fpywrarwvf9cd162vs6lriirq0cq5")))) + "10knws2azy53bar615r0b1dk6nr9lrl0x25k7vsc6jm879wcp91b")))) (propagated-inputs `( ("python" ,python-2) ;; probably superfluous ("r" ,r) -- cgit v1.2.3 From 390831e540aa2f4d00fdb74be5e0bccce02fa7ef Mon Sep 17 00:00:00 2001 From: pjotrp Date: Wed, 23 Mar 2016 18:16:20 -0500 Subject: GN2 fix --- gn/packages/bioinformatics.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gn/packages') diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index aa5432a..3629963 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -404,7 +404,7 @@ association studies (GWAS).") ("python2-scipy" ,python2-scipy) ("python2-simplejson" ,python2-simplejson) ("python2-pyyaml" ,python2-pyyaml) - ("python-xlsxwriter" ,python-xlsxwriter) + ("python2-xlsxwriter" ,python-xlsxwriter) ;; python-yolk is not needed ("plink" ,plink) ("qtlreaper" ,qtlreaper) -- cgit v1.2.3 From d81eb54552568897e9a3c9cd52b352b2c0644565 Mon Sep 17 00:00:00 2001 From: pjotrp Date: Wed, 23 Mar 2016 18:28:27 -0500 Subject: This runs with gn-stable --- gn/packages/bioinformatics.scm | 68 +----------------------------------------- gn/packages/genenetwork.scm | 2 +- 2 files changed, 2 insertions(+), 68 deletions(-) (limited to 'gn/packages') diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 0798822..3a82c18 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -77,7 +77,7 @@ (propagated-inputs `(("python" ,python-2) ("r" ,r) - ("r-dnacopy" ,r-dnacopy) + ;; ("r-dnacopy" ,r-dnacopy) <-- missing in Pjotr's tree ("bedtools" ,bedtools) ("samtools" ,samtools))) (arguments @@ -1048,72 +1048,6 @@ subset of samtools functionality, including view, index, sort, markdup, and depth.") (license license:gpl2+)))) -(define-public genenetwork2 - (let ((commit "234aa9820eeaa3e4611239de31de1ba526d8bf09")) - (package - (name "genenetwork2") - (version (string-append "2.0-" (string-take commit 7) )) - (source (origin - (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 - "10knws2azy53bar615r0b1dk6nr9lrl0x25k7vsc6jm879wcp91b")))) - (propagated-inputs `( - ("python" ,python-2) ;; probably superfluous - ("r" ,r) - )) - (inputs `( - ("mysql" ,mysql) - ("gemma" ,gemma-git) - ("plink2" ,plink-ng) - ("nginx" ,nginx) - ("python2-flask" ,python2-flask) - ("python2-htmlgen-gn" ,python2-htmlgen-gn) - ("python2-jinja2" ,python2-jinja2) - ("python2-sqlalchemy" ,python2-sqlalchemy) - ("python2-flask-sqlalchemy" ,python2-flask-sqlalchemy) - ("python2-setuptools" ,python2-setuptools) - ("python2-scipy" ,python2-scipy) - ;; looks like python-numarray is not needed - ("python2-mysqlclient" ,python2-mysqlclient) - ("python2-numarray" ,python2-numarray) - ("python2-numpy" ,python2-numpy) - ("python2-pandas" ,python2-pandas) - ("python2-parallel" ,python2-parallel) - ("python2-passlib" ,python2-passlib) - ("python2-piddle" ,python2-piddle) - ("python2-redis" ,python2-redis) - ("python2-requests" ,python2-requests) - ("python2-rpy2" ,python2-rpy2) - ("python2-scipy" ,python2-scipy) - ("python2-simplejson" ,python2-simplejson) - ("python2-pyyaml" ,python2-pyyaml) - ("python2-xlsxwriter" ,python-xlsxwriter) - ;; python-yolk is not needed - ("plink" ,plink) - ("qtlreaper" ,qtlreaper) - ("r-qtl" ,r-qtl) - )) - (build-system python-build-system) - (arguments - `(("perl" ,perl) ; Needed to run the java command. - ("jdk" ,icedtea "jdk"))) - (native-inputs - `(("ant" ,ant) ; TODO: Most Java packages need Ant, but in this case, IDK.. - ("jdk" ,icedtea "jdk") - ;;("htsjdk" ,htsjdk) ; It is based on htsjdk, but it ships its own copy. - ("unzip" ,unzip))) - (home-page "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/") - (synopsis "A quality control tool for high throughput sequence data") - (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")) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 79ad3fe..1382cfb 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -223,7 +223,7 @@ ;; ./pre-inst-env guix download http://files.genenetwork.org/raw_database/db_webqtl_s.zip ;; 0sscjh0wml2lx0mb43vf4chg9gpbfi7abpjxb34n3kyny9ll557x -(define-public genenetwork2-files-small1 +(define-public genenetwork2-files-small (let ((pfff "xx")) (package (name "genenetwork2-files-small") -- cgit v1.2.3 From a0c613babbabf0418a4f69a5437fe4caf074a1d7 Mon Sep 17 00:00:00 2001 From: pjotrp Date: Thu, 24 Mar 2016 12:00:00 -0500 Subject: Updated erlang by Leo --- gn/packages/erlang.scm | 100 +++++++++++++++++++++---------------------------- 1 file changed, 42 insertions(+), 58 deletions(-) (limited to 'gn/packages') diff --git a/gn/packages/erlang.scm b/gn/packages/erlang.scm index ebf98cf..117057b 100644 --- a/gn/packages/erlang.scm +++ b/gn/packages/erlang.scm @@ -22,17 +22,14 @@ #:use-module (guix packages) #:use-module (guix download) #:use-module (guix build-system gnu) - #:use-module (guix build-system trivial) - #:use-module (gnu packages base) - #:use-module (gnu packages compression) #:use-module (gnu packages ncurses) #:use-module (gnu packages perl) #:use-module (gnu packages tls)) (define-public erlang - ;; Keep in sync with 'erlang-manpages'! (package (name "erlang") + ;; When updating, remember to update the hash of erlang-manpages! (version "18.3") (source (origin (method url-fetch) @@ -45,7 +42,17 @@ "1hy9slq9gjvwdb504dmvp6rax90isnky6chqkyq5v4ybl4lq3azx")))) (build-system gnu-build-system) (native-inputs - `(("perl" ,perl))) + `(("perl" ,perl) + + ;; Erlang's documentation is distributed in a separate tarball. + ("erlang-manpages" + ,(origin + (method url-fetch) + (uri (string-append "http://erlang.org/download/otp_doc_man_" + version ".tar.gz")) + (sha256 + (base32 + "1hpcr7a3dx2y9gnb53bvb4g6lyvbwigadl9s3f978s01x40f32wp")))))) (inputs `(("ncurses" ,ncurses) ("openssl" ,openssl))) @@ -54,28 +61,28 @@ (list (string-append "--with-ssl=" (assoc-ref %build-inputs "openssl"))) #:phases (modify-phases %standard-phases - (add-after 'patch-source-shebangs 'patch-source-env - (lambda _ - (let ((escripts - (append - (find-files "." "\\.escript") - (find-files "lib/stdlib/test/escript_SUITE_data/") - '("erts/lib_src/utils/make_atomics_api" - "erts/preloaded/src/add_abstract_code" - "lib/diameter/bin/diameterc" - "lib/reltool/examples/display_args" - "lib/reltool/examples/mnesia_core_dump_viewer" - "lib/snmp/src/compile/snmpc.src" - "make/verify_runtime_dependencies" - "make/emd2exml.in")))) - (substitute* escripts - (("/usr/bin/env") (which "env")))))) (add-after 'unpack 'path-to-rm (lambda _ (substitute* "erts/configure" (("/bin/rm") (which "rm"))) (substitute* "lib/odbc/configure" (("/bin/rm") (which "rm"))))) + (add-after 'patch-source-shebangs 'patch-source-env + (lambda _ + (let ((escripts + (append + (find-files "." "\\.escript") + (find-files "lib/stdlib/test/escript_SUITE_data/") + '("erts/lib_src/utils/make_atomics_api" + "erts/preloaded/src/add_abstract_code" + "lib/diameter/bin/diameterc" + "lib/reltool/examples/display_args" + "lib/reltool/examples/mnesia_core_dump_viewer" + "lib/snmp/src/compile/snmpc.src" + "make/verify_runtime_dependencies" + "make/emd2exml.in")))) + (substitute* escripts + (("/usr/bin/env") (which "env")))))) (add-before 'configure 'set-erl-top (lambda _ (setenv "ERL_TOP" (getcwd)))) @@ -83,7 +90,20 @@ ;; This only works after install. (lambda _ (substitute* (string-append (assoc-ref %outputs "out") "/bin/erl") - (("sed") (which "sed")))))) + (("sed") (which "sed"))))) + (add-after 'install 'install-doc + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (manpages (assoc-ref inputs "erlang-manpages")) + (share (string-append out "/share/"))) + (mkdir-p share) + (with-directory-excursion share + (and + (zero? (system* "tar" "xvf" manpages)) + ;; Delete superfluous files. + (for-each delete-file '("COPYRIGHT" + "PR.template" + "README")))))))) #:test-target "release_tests")) (home-page "http://erlang.org/") (synopsis "The Erlang programming language") @@ -94,39 +114,3 @@ availability. Some of its uses are in telecoms, banking, e-commerce, computer telephony and instant messaging. Erlang's runtime system has built-in support for concurrency, distribution and fault tolerance.") (license license:asl2.0))) - -(define-public erlang-manpages - ;; Keep in sync with 'erlang'! - (package - (name "erlang-manpages") - (version (package-version erlang)) - (source (origin - (method url-fetch) - (uri (string-append "http://erlang.org/download/otp_doc_man_" - version ".tar.gz")) - (sha256 - (base32 - "1hpcr7a3dx2y9gnb53bvb4g6lyvbwigadl9s3f978s01x40f32wp")))) - (build-system trivial-build-system) - (arguments - '(#:modules ((guix build utils)) - #:builder - (begin - (use-modules (guix build utils)) - (let* ((gz (assoc-ref %build-inputs "gzip")) - (tar (assoc-ref %build-inputs "tar")) - (out (assoc-ref %outputs "out")) - (man (string-append out "/share/man"))) - (setenv "PATH" (string-append tar "/bin:" gz "/bin")) - (mkdir-p man) - (with-directory-excursion man - (zero? (system* "tar" "xvf" - (assoc-ref %build-inputs "source")))) - (delete-file (string-append man "/PR.template")) - (delete-file (string-append man "/README")))))) - (native-inputs `(("tar" ,tar) - ("gzip" ,gzip))) - (synopsis "Man pages of Erlang") - (description "This provides the man pages of Erlang.") - (home-page (package-home-page erlang)) - (license license:asl2.0))) -- cgit v1.2.3 From d45beef0f30b6e4a20f099e9b264b69d078d6947 Mon Sep 17 00:00:00 2001 From: pjotrp Date: Thu, 24 Mar 2016 16:35:21 -0500 Subject: Added elixir --- gn/packages/elixir.scm | 61 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 61 insertions(+) create mode 100644 gn/packages/elixir.scm (limited to 'gn/packages') diff --git a/gn/packages/elixir.scm b/gn/packages/elixir.scm new file mode 100644 index 0000000..fbf8a9b --- /dev/null +++ b/gn/packages/elixir.scm @@ -0,0 +1,61 @@ +;;; GNU Guix --- Functional package management for GNU +;;; Copyright © 2016 Pjotr Prins +;;; Copyright © 2016 Leo Famulari +;;; +;;; This file is part of GNU Guix. +;;; +;;; GNU Guix is free software; you can redistribute it and/or modify it +;;; under the terms of the GNU General Public License as published by +;;; the Free Software Foundation; either version 3 of the License, or (at +;;; your option) any later version. +;;; +;;; GNU Guix is distributed in the hope that it will be useful, but +;;; WITHOUT ANY WARRANTY; without even the implied warranty of +;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +;;; GNU General Public License for more details. +;;; +;;; You should have received a copy of the GNU General Public License +;;; along with GNU Guix. If not, see . + +(define-module (gn packages elixir) + #:use-module ((guix licenses) #:prefix license:) + #:use-module (guix packages) + #:use-module (guix download) + #:use-module (guix build-system gnu) + #:use-module (gn packages erlang) + #:use-module (gnu packages ncurses) + #:use-module (gnu packages perl) + #:use-module (gnu packages tls)) + +(define-public elixir + (package + (name "elixir") + (version "1.2.3") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/elixir-lang/elixir/archive/v" + version ".tar.gz")) + (sha256 + (base32 + "09s8469830s4070i0m04fxdhqimkdyc5k9jylm5vpfz9l3z4wvl8")))) + (build-system gnu-build-system) + (inputs + `(("erlang" ,erlang))) + (arguments + `(#:phases (modify-phases %standard-phases + (delete 'configure) + ;; (replace 'check + ;; (lambda _ + ;; (zero? (system* "make" "test"))))))) + ) + #:make-flags (list (string-append "PREFIX=" %output)) + #:tests? #f)) ;; 2845 tests, 12 failures + (home-page "http://elixir-lang.org/") + (synopsis "The Elixir programming language") +(description "Elixir is a dynamic, functional language designed for +building scalable and maintainable applications. Elixir leverages the +Erlang VM, known for running low-latency, distributed and +fault-tolerant systems, while also being successfully used in web +development and the embedded software domain.") + (license license:asl2.0))) -- cgit v1.2.3 From 5cf3ef6444d42ddc7e5ee8bd184b4ccbba5d500e Mon Sep 17 00:00:00 2001 From: pjotrp Date: Thu, 24 Mar 2016 17:20:08 -0500 Subject: elixir: fix filename --- gn/packages/elixir.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gn/packages') diff --git a/gn/packages/elixir.scm b/gn/packages/elixir.scm index fbf8a9b..58e1ee0 100644 --- a/gn/packages/elixir.scm +++ b/gn/packages/elixir.scm @@ -36,6 +36,7 @@ (uri (string-append "https://github.com/elixir-lang/elixir/archive/v" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 "09s8469830s4070i0m04fxdhqimkdyc5k9jylm5vpfz9l3z4wvl8")))) -- cgit v1.2.3 From f537772b8b48f5fa05606afd1573ff003f991ce0 Mon Sep 17 00:00:00 2001 From: pjotrp Date: Thu, 24 Mar 2016 17:48:13 -0500 Subject: Elixir fix path --- gn/packages/elixir.scm | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) (limited to 'gn/packages') diff --git a/gn/packages/elixir.scm b/gn/packages/elixir.scm index 58e1ee0..2f9bcc3 100644 --- a/gn/packages/elixir.scm +++ b/gn/packages/elixir.scm @@ -45,7 +45,12 @@ `(("erlang" ,erlang))) (arguments `(#:phases (modify-phases %standard-phases - (delete 'configure) + (delete 'configure) + (add-before + 'build 'rewrite-path + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "bin/elixir" + (("ERL_EXEC=\"erl\"") (string-append "ERL_EXEC=" (which "erl")))))) ;; (replace 'check ;; (lambda _ ;; (zero? (system* "make" "test"))))))) -- cgit v1.2.3