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-rw-r--r--gn/packages/bioinformatics.scm84
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")