diff options
Diffstat (limited to 'gn/packages/bioinformatics.scm')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 84 |
1 files changed, 6 insertions, 78 deletions
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") |