From 7affda5295cb6bab9cd336be0fea70e1c2bf24d2 Mon Sep 17 00:00:00 2001 From: pjotrp Date: Sun, 26 Feb 2017 19:13:31 +0000 Subject: Added comments on guix viability - removed r-wcna and r-preprocesscore as they are in Guix now --- gn/packages/4store.scm | 2 +- gn/packages/bioinformatics.scm | 84 +++--------------------------------------- gn/packages/cwl.scm | 2 +- gn/packages/genenetwork.scm | 4 +- gn/packages/glfw.scm | 2 +- gn/packages/gtest.scm | 2 +- gn/packages/hyphy.scm | 2 +- gn/packages/ldc.scm | 4 +- gn/packages/mongodb.scm | 2 +- gn/packages/perl.scm | 2 +- gn/packages/python.scm | 26 ++++++------- gn/packages/ruby.scm | 6 +-- 12 files changed, 33 insertions(+), 105 deletions(-) diff --git a/gn/packages/4store.scm b/gn/packages/4store.scm index 41e3249..ec09112 100644 --- a/gn/packages/4store.scm +++ b/gn/packages/4store.scm @@ -39,7 +39,7 @@ #:use-module (gnu packages file) #:use-module (gnu packages xml)) -(define-public 4store +(define-public 4store ; guix ready (let ((commit "c5a56d7c7504551a1f2fff6c16c4d9a440e4a317")) (package (name "4store") diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 6be95dc..efb9470 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -397,7 +397,7 @@ combinatorial configurations.\" G Ehrlich - Journal of the ACM (JACM), replacement for strverscmp.") (license license:gpl3+)))) -(define-public fastahack +(define-public fastahack ; guix ready (let ((commit "c68cebb4f2e5d5d2b70cf08fbdf1944e9ab2c2dd")) (package (name "fastahack") @@ -430,7 +430,7 @@ automatically handles index file generation and use.") ;; A part of the program is licensed GPLv2. (license (list license:non-copyleft license:gpl2))))) -(define-public vcflib +(define-public vcflib ; guix duplicat, see below? (let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb")) (package (name "vcflib") @@ -523,7 +523,7 @@ format, and a collection of command-line utilities for executing complex manipulations on VCF files.") (license license:expat)))) -(define-public bash-tap +(define-public bash-tap ; guix license issue (package (name "bash-tap") (version "1.0.2") @@ -565,7 +565,7 @@ in-process output capturing.") ;; The author didn't specify a license. (license license:public-domain))) -(define-public freebayes +(define-public freebayes ; guix dependent package issues (let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb") (revision "1")) (package @@ -701,78 +701,6 @@ 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 - (name "r-biocpreprocesscore") - (version "1.34.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "preprocessCore" version)) - (sha256 - (base32 - "0bcfi26ahs4ybagvz29vlp1wldhhbwwh73xz6v6xb07nakyzb6cf")))) - (properties - `((upstream-name . "BiocpreprocessCore") - (r-repository . bioconductor))) - (build-system r-build-system) - (home-page "http://bioconductor.org/packages/preprocessCore") - (synopsis "Preprocess functions for Bioconductor") - (description - "A library of core preprocessing routines.") - (license license:lgpl2.0+))) - -(define-public r-wgcna - (let ((commit "425bc170cc0873ddbd414675ac40f6d4d724c7cb")) -(package - (name "r-wgcna") - (version (string-append "1.49-" commit)) - (source (origin - (method git-fetch) - (uri (git-reference - ;; (url "https://github.com/genenetwork/WGCNA.git") - (url "https://github.com/pjotrp/WGCNA.git") - (commit commit))) - (file-name (string-append name "-" commit)) - (sha256 - (base32 - "1zqnsb8s3065rq1y2y3l79zi8wmdwjkcjls96ypycrb7pmdil58j")))) - (properties `((upstream-name . "WGCNA"))) - (build-system r-build-system) - (propagated-inputs - `( ;; ("r-annotationdbi" ,r-annotationdbi) - ; ("r-biocparallel" ,r-biocparallel) - ("r-doparallel" ,r-doparallel) - ("r-dynamictreecut" ,r-dynamictreecut) - ("r-fastcluster" ,r-fastcluster) - ("r-foreach" ,r-foreach) - ("r-go-db" ,r-go-db) - ; ("r-grdevices" ,r-grdevices) - ("r-hmisc" ,r-hmisc) - ("r-impute" ,r-impute) - ("r-matrixstats" ,r-matrixstats) - ; ("r-parallel" ,r-parallel) - ("r-biocpreprocesscore" ,r-biocpreprocesscore) - ; ("r-splines" ,r-splines) - ; ("r-stats" ,r-stats) - ; ("r-survival" ,r-survival) - ; ("r-utils" ,r-utils) - )) - (arguments - `( - #:tests? #f)) ; no 'setup.py test' - (home-page - "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/") - (synopsis - "Weighted gene correlation network analysis (wgcna)") - (description - "Functions necessary to perform Weighted Correlation Network -Analysis on high-dimensional data. Includes functions for rudimentary -data cleaning, construction of correlation networks, module -identification, summarization, and relating of variables and modules -to sample traits. Also includes a number of utility functions for -data manipulation and visualization.") - (license license:gpl2+)))) - (define-public plink2 (package (name "plink2") @@ -879,7 +807,7 @@ integration with gPLINK and Haploview, there is some support for the subsequent visualization, annotation and storage of results.") (license license:gpl3+)))) -(define-public gemma-git +(define-public gemma-git ; guix candidate (let ((commit "2de4bfab3")) (package (name "gemma-git") @@ -921,7 +849,7 @@ mixed model and some of its close relatives for genome-wide association studies (GWAS).") (license license:gpl3)))) -(define-public vcflib +(define-public vcflib ; duplicate? See above (let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb")) (package (name "vcflib") diff --git a/gn/packages/cwl.scm b/gn/packages/cwl.scm index 8c41187..2acac7c 100644 --- a/gn/packages/cwl.scm +++ b/gn/packages/cwl.scm @@ -15,7 +15,7 @@ #:use-module (guix build-system trivial) #:use-module (srfi srfi-1)) -(define-public python-cwltool +(define-public python-cwltool ; guix: needs work (package (name "python-cwltool") (version "1.0.20150916041152") diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index dfbba02..7ee798e 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -87,7 +87,7 @@ (description #f) (license #f))) -(define-public qtlreaper +(define-public qtlreaper ; guix obsolete - but used in GN2 (let ((commit "71fbbe2b35e4f54937be2d54d09fb71d25fe5fad")) (package (name "qtlreaper") @@ -122,7 +122,7 @@ bootstrap resampling to estimate the confidence region for the location of a putative QTL.") (license license:gpl2+)))) -(define-public genenetwork1 +(define-public genenetwork1 ; guix incomplete (let ((commit "d622c803b")) (package (name "genenetwork1") diff --git a/gn/packages/glfw.scm b/gn/packages/glfw.scm index 30342f0..6eb3a75 100644 --- a/gn/packages/glfw.scm +++ b/gn/packages/glfw.scm @@ -42,7 +42,7 @@ #:use-module (gnu packages version-control) #:use-module (gnu packages linux)) -(define-public glfw +(define-public glfw ; guix opengl (package (name "glfw") (version "3.1.2") diff --git a/gn/packages/gtest.scm b/gn/packages/gtest.scm index f8b34e9..708df09 100644 --- a/gn/packages/gtest.scm +++ b/gn/packages/gtest.scm @@ -49,7 +49,7 @@ #:use-module (gnu packages zip) #:use-module (gnu packages linux)) -(define-public gtest +(define-public gtest ; guix check (let ((revision "1") (commit "13206d6f53aaff844f2d3595a01ac83a29e383db")) (package diff --git a/gn/packages/hyphy.scm b/gn/packages/hyphy.scm index fea73a4..e5c120a 100644 --- a/gn/packages/hyphy.scm +++ b/gn/packages/hyphy.scm @@ -42,7 +42,7 @@ #:use-module (gnu packages version-control) #:use-module (gnu packages linux)) -(define-public hyphy +(define-public hyphy ; guix: check (package (name "hyphy") (version "2.2.6") diff --git a/gn/packages/ldc.scm b/gn/packages/ldc.scm index 438cfd3..e39d746 100644 --- a/gn/packages/ldc.scm +++ b/gn/packages/ldc.scm @@ -33,7 +33,7 @@ #:use-module (gnu packages textutils) #:use-module (gnu packages zip)) -(define-public ldc-0.17.2 +(define-public ldc-0.17.2 ; guix in main line (package (inherit ldcmain:ldc) (name "ldc") @@ -116,7 +116,7 @@ (base32 "0n7gvalxwfmia4gag53r9qhcnk2cqrw3n4icj1yri0zkgc27pm60")))))))) -(define-public ldc-1.1.0-patched +(define-public ldc-1.1.0-patched ; guix in main line w.o. patch (let ((version2 "1.1.0")) ; version for libraries (package (inherit ldcmain:ldc) diff --git a/gn/packages/mongodb.scm b/gn/packages/mongodb.scm index cc4196e..79c2b75 100644 --- a/gn/packages/mongodb.scm +++ b/gn/packages/mongodb.scm @@ -27,7 +27,7 @@ #:use-module (gnu packages pkg-config) #:use-module (gnu packages python)) -(define-public mongodb +(define-public mongodb ; guix fix tests and maybe non-free (package (name "mongodb") (version "3.3.3") diff --git a/gn/packages/perl.scm b/gn/packages/perl.scm index 75256fe..c1b7946 100644 --- a/gn/packages/perl.scm +++ b/gn/packages/perl.scm @@ -39,7 +39,7 @@ #:use-module (gnu packages web) #:use-module (guix build-system perl)) -(define-public perl-time-parsedate +(define-public perl-time-parsedate ; guix: old lib and tests failing - works though (package (name "perl-time-parsedate") (version "2015.103") diff --git a/gn/packages/python.scm b/gn/packages/python.scm index fedc2ed..393de4c 100644 --- a/gn/packages/python.scm +++ b/gn/packages/python.scm @@ -42,7 +42,7 @@ #:use-module (guix build-system trivial) #:use-module (srfi srfi-1)) -(define-public speedtest-cli +(define-public speedtest-cli ; guix submitted (package (name "speedtest-cli") (version "1.0.2") @@ -63,7 +63,7 @@ "Command line interface for testing internet bandwidth using speedtest.net") (license license:asl2.0))) -(define-public python-flask-sqlalchemy +(define-public python-flask-sqlalchemy-in-mainline ; guix main line (package (name "python-flask-sqlalchemy") (version "2.1") @@ -88,10 +88,10 @@ "Adds SQLAlchemy support to your Flask application") (license license:bsd-3))) -(define-public python2-flask-sqlalchemy +(define-public python2-flask-sqlalchemy ; guix? (package-with-python2 python-flask-sqlalchemy)) -(define-public python-xlsxwriter +(define-public python-xlsxwriter ; guix ready (package (name "python-xlsxwriter") (version "0.8.4") @@ -116,7 +116,7 @@ (define-public python2-xlsxwriter (package-with-python2 python-xlsxwriter)) -(define-public python-rdflib-jsonld +(define-public python-rdflib-jsonld ; guix ready (package (name "python-rdflib-jsonld") (version "0.3") @@ -195,7 +195,7 @@ powerful language for representing information.") `(#:python ,python-2 #:tests? #f))))) ; 3 tests fail, also outside Guix -(define-public python-avro +(define-public python-avro ; guix ready - used by CWL (package (name "python-avro") (version "1.7.7") @@ -222,7 +222,7 @@ powerful language for representing information.") (define-public python2-avro (package-with-python2 python-avro)) -(define-public python-shellescape +(define-public python-shellescape ; guix ready (package (name "python-shellescape") (version "3.4.1") @@ -251,7 +251,7 @@ powerful language for representing information.") (define-public python2-shellescape (package-with-python2 python-shellescape)) -(define-public python-mysqlclient +(define-public python-mysqlclient ; guix ready (package (name "python-mysqlclient") (version "1.3.7") @@ -284,7 +284,7 @@ powerful language for representing information.") (package-with-python2 python-mysqlclient)) -(define-public python2-htmlgen-gn +(define-public python2-htmlgen-gn ; guix obsolete (package (name "python2-htmlgen-gn") (version "2.2.2") @@ -339,7 +339,7 @@ project)") (description #f) (license #f))) -(define-public python2-pil +(define-public python2-pil ; guix obsolete (package (name "python2-pil") (version "1.1.6") @@ -400,7 +400,7 @@ capabilities to the Python interpreter.") "file://README" "See 'README' in the distribution.")))) -(define-public python2-piddle-gn +(define-public python2-piddle-gn ; guix obsolete (package (name "python2-piddle") (version "1.0.15-gn") @@ -428,7 +428,7 @@ version ".tgz")) (description #f) (license #f))) -(define-public python2-parallel +(define-public python2-parallel ; guix fix number of things (package (name "python2-parallel") (version "1.6.4") @@ -456,7 +456,7 @@ version ".tgz")) (description #f) (license #f))) -(define-public python2-numarray +(define-public python2-numarray ; guix: obsolete lib (package (name "python2-numarray") (version "1.5.2") diff --git a/gn/packages/ruby.scm b/gn/packages/ruby.scm index 41743d9..5307e1c 100644 --- a/gn/packages/ruby.scm +++ b/gn/packages/ruby.scm @@ -96,7 +96,7 @@ a focus on simplicity and productivity.") (home-page "https://ruby-lang.org") (license license:ruby))) -(define-public bio-vcf +(define-public bio-vcf ; guix ready with tests (package (name "bio-vcf") (version "0.9.2") @@ -121,7 +121,7 @@ filtering and output rewriting (JSON, RDF etc.)") "http://github.com/pjotrp/bioruby-vcf") (license expat))) -(define-public bio-table +(define-public bio-table ; guix ready with tests (package (name "bio-table") (version "1.0.0") @@ -228,7 +228,7 @@ for an example.") (home-page "https://github.com/knu/webrobots") (license #f))) -(define-public ruby-mechanize +(define-public ruby-mechanize ; guix maybe ready (package (name "ruby-mechanize") (version "2.7.5") -- cgit v1.2.3