From 7241b44ad497d6a59c5cc55af2375ba4ba02143d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 16 Jan 2020 06:08:43 +0100
Subject: gnu: r-biocstyle: Update to 2.14.4.
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.14.4.
---
gnu/packages/bioinformatics.scm | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
(limited to 'gnu/packages/bioinformatics.scm')
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0e4cb5b1db..0f7c7b7403 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015, 2016, 2017, 2018 Ben Woodcroft <donttrustben@gmail.com>
;;; Copyright © 2015, 2016 Pjotr Prins <pjotr.guix@thebird.nl>
;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
@@ -7272,13 +7272,13 @@ also known as views, in a controlled vocabulary.")
(define-public r-biocstyle
(package
(name "r-biocstyle")
- (version "2.14.2")
+ (version "2.14.4")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocStyle" version))
(sha256
(base32
- "0nc1cbzp5zdwc0rss4r6v7cpgynmmnj3sczwmajr58nabkndwsvf"))))
+ "1x71in059zql40f4c87bd1gf96r945kdvwbq61jmch9d3d8nwxbb"))))
(properties
`((upstream-name . "BiocStyle")))
(build-system r-build-system)
--
cgit v1.2.3
From fdf69f1ee0f604041028b325c6e9fec9577adb23 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 16 Jan 2020 06:09:16 +0100
Subject: gnu: r-s4vectors: Update to 0.24.2.
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.24.2.
---
gnu/packages/bioinformatics.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
(limited to 'gnu/packages/bioinformatics.scm')
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0f7c7b7403..03ddd30004 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7345,13 +7345,13 @@ checks on R packages that are to be submitted to the Bioconductor repository.")
(define-public r-s4vectors
(package
(name "r-s4vectors")
- (version "0.24.1")
+ (version "0.24.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "S4Vectors" version))
(sha256
(base32
- "1rr7ml3gn83g8fbvhgvryyzlh4p3qgpwcrsz6ii4y7gh1hqxggpx"))))
+ "1s1h00k2ki7sd0hz4l8n41xr6ixszag7lm0ryrbb08idgcy16ipn"))))
(properties
`((upstream-name . "S4Vectors")))
(build-system r-build-system)
--
cgit v1.2.3
From f7b5c1a02ff4fe4694252bf44e1650af93f4130b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 16 Jan 2020 06:09:21 +0100
Subject: gnu: r-iranges: Update to 2.20.2.
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.20.2.
---
gnu/packages/bioinformatics.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
(limited to 'gnu/packages/bioinformatics.scm')
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 03ddd30004..b72259042d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7372,13 +7372,13 @@ S4Vectors package itself.")
(define-public r-iranges
(package
(name "r-iranges")
- (version "2.20.1")
+ (version "2.20.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "IRanges" version))
(sha256
(base32
- "0qssp04wfrc1r92hd3szy03n8sdz8vrqjdxa2mcrsc0k0n9bchz5"))))
+ "1jhnxb9yacmj2z82b6992gihjvj1a0gnjwbjiagyyx03fqnv23kg"))))
(properties
`((upstream-name . "IRanges")))
(build-system r-build-system)
--
cgit v1.2.3
From d64124df89d61bf3429eb7bd7f50179be6740dd8 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 16 Jan 2020 06:09:27 +0100
Subject: gnu: r-delayedarray: Update to 0.12.2.
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.12.2.
---
gnu/packages/bioinformatics.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
(limited to 'gnu/packages/bioinformatics.scm')
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b72259042d..32eea9d153 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7783,13 +7783,13 @@ tab-delimited (tabix) files.")
(define-public r-delayedarray
(package
(name "r-delayedarray")
- (version "0.12.1")
+ (version "0.12.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "DelayedArray" version))
(sha256
(base32
- "1yr4i2x127v814nxg53aibp77p3vg76f3n3hgknpwx3snfhc81xs"))))
+ "09lackgix5jpm16k0mz2zkibflfb4wzidbz4q32mlxmklf40037q"))))
(properties
`((upstream-name . "DelayedArray")))
(build-system r-build-system)
--
cgit v1.2.3
From 7699e3228960457707f103e8e9e0db60de3891c5 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 15 Jan 2020 22:18:35 +0100
Subject: gnu: kentutils: Build with OpenSSL 1.0.
* gnu/packages/bioinformatics.scm (kentutils)[inputs]: Change from OPENSSL to
OPENSSL-1.0.
---
gnu/packages/bioinformatics.scm | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
(limited to 'gnu/packages/bioinformatics.scm')
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 32eea9d153..381c9dfe11 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -11322,7 +11322,7 @@ models. TADbit is complemented by TADkit for visualizing 3D models.")
("libpng" ,libpng)
("mariadb" ,mariadb "lib")
("mariadb-dev" ,mariadb "dev")
- ("openssl" ,openssl)))
+ ("openssl" ,openssl-1.0)))
(home-page "http://genome.cse.ucsc.edu/index.html")
(synopsis "Assorted bioinformatics utilities")
(description "This package provides the kentUtils, a selection of
--
cgit v1.2.3
From f1fa954a7daa500c60172d524e35b8cf53eb398e Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sat, 18 Jan 2020 12:40:25 +0100
Subject: gnu: edirect: Use HTTPS home page.
* gnu/packages/bioinformatics.scm (edirect)[home-page]: Use HTTPS.
---
gnu/packages/bioinformatics.scm | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
(limited to 'gnu/packages/bioinformatics.scm')
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 381c9dfe11..4a84273dd2 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2796,7 +2796,7 @@ quantitative phenotypes.")
("perl-www-robotrules" ,perl-www-robotrules)
("perl-xml-simple" ,perl-xml-simple)
("perl" ,perl)))
- (home-page "http://www.ncbi.nlm.nih.gov/books/NBK179288/")
+ (home-page "https://www.ncbi.nlm.nih.gov/books/NBK179288/")
(synopsis "Tools for accessing the NCBI's set of databases")
(description
"Entrez Direct (EDirect) is a method for accessing the National Center
--
cgit v1.2.3
From 99db6db7be7a51a6250584dfe896afd797c73812 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Tue, 21 Jan 2020 23:50:29 +0100
Subject: gnu: Use HTTPS for bioconductor.org.
* gnu/packages/bioinformatics.scm (r-homo-sapiens)[source]: Use HTTPS.
* gnu/packages/bioconductor.scm (r-bsgenome-mmusculus-ucsc-mm9-masked,
r-cghcall, r-diffbind, r-cghbase, r-ripseeker, r-chippeakanno,
r-qdnaseq, r-marray, r-multtest)[home-page]: Likewise.
* gnu/packages/graph.scm (r-rgraphviz)[home-page]: Likewise.
---
gnu/packages/bioconductor.scm | 18 +++++++++---------
gnu/packages/bioinformatics.scm | 2 +-
gnu/packages/graph.scm | 2 +-
3 files changed, 11 insertions(+), 11 deletions(-)
(limited to 'gnu/packages/bioinformatics.scm')
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index ef34b99649..e2b4f6ea7f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -297,7 +297,7 @@ provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
`(("r-bsgenome" ,r-bsgenome)
("r-bsgenome-mmusculus-ucsc-mm9"
,r-bsgenome-mmusculus-ucsc-mm9)))
- (home-page "http://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/")
+ (home-page "https://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/")
(synopsis "Full masked genome sequences for Mouse")
(description
"This package provides full genome sequences for Mus musculus (Mouse) as
@@ -1400,7 +1400,7 @@ problems in genomics, brain imaging, astrophysics, and data mining.")
("r-s4vectors" ,r-s4vectors)
("r-summarizedexperiment" ,r-summarizedexperiment)
("r-systempiper" ,r-systempiper)))
- (home-page "http://bioconductor.org/packages/DiffBind")
+ (home-page "https://bioconductor.org/packages/DiffBind")
(synopsis "Differential binding analysis of ChIP-Seq peak data")
(description
"This package computes differentially bound sites from multiple
@@ -1429,7 +1429,7 @@ occupancy (overlap) analysis and plotting functions.")
("r-rsamtools" ,r-rsamtools)
("r-genomicalignments" ,r-genomicalignments)
("r-rtracklayer" ,r-rtracklayer)))
- (home-page "http://bioconductor.org/packages/RIPSeeker")
+ (home-page "https://bioconductor.org/packages/RIPSeeker")
(synopsis
"Identifying protein-associated transcripts from RIP-seq experiments")
(description
@@ -1458,7 +1458,7 @@ processing to visualization and annotation.")
("r-biocgenerics" ,r-biocgenerics)
("r-biobase" ,r-biobase)
("r-mass" ,r-mass)))
- (home-page "http://bioconductor.org/packages/multtest")
+ (home-page "https://bioconductor.org/packages/multtest")
(synopsis "Resampling-based multiple hypothesis testing")
(description
"This package can do non-parametric bootstrap and permutation
@@ -1569,7 +1569,7 @@ determining dependencies between variables, code improvement suggestions.")
("r-seqinr" ,r-seqinr)
("r-summarizedexperiment" ,r-summarizedexperiment)
("r-venndiagram" ,r-venndiagram)))
- (home-page "http://bioconductor.org/packages/ChIPpeakAnno")
+ (home-page "https://bioconductor.org/packages/ChIPpeakAnno")
(synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
(description
"The package includes functions to retrieve the sequences around the peak,
@@ -1594,7 +1594,7 @@ enrichedGO (addGeneIDs).")
(build-system r-build-system)
(propagated-inputs
`(("r-limma" ,r-limma)))
- (home-page "http://bioconductor.org/packages/marray")
+ (home-page "https://bioconductor.org/packages/marray")
(synopsis "Exploratory analysis for two-color spotted microarray data")
(description "This package contains class definitions for two-color spotted
microarray data. It also includes functions for data input, diagnostic plots,
@@ -1615,7 +1615,7 @@ normalization and quality checking.")
(propagated-inputs
`(("r-biobase" ,r-biobase)
("r-marray" ,r-marray)))
- (home-page "http://bioconductor.org/packages/CGHbase")
+ (home-page "https://bioconductor.org/packages/CGHbase")
(synopsis "Base functions and classes for arrayCGH data analysis")
(description "This package contains functions and classes that are needed by
the @code{arrayCGH} packages.")
@@ -1638,7 +1638,7 @@ the @code{arrayCGH} packages.")
("r-impute" ,r-impute)
("r-dnacopy" ,r-dnacopy)
("r-snowfall" ,r-snowfall)))
- (home-page "http://bioconductor.org/packages/CGHcall")
+ (home-page "https://bioconductor.org/packages/CGHcall")
(synopsis "Base functions and classes for arrayCGH data analysis")
(description "This package contains functions and classes that are needed by
@code{arrayCGH} packages.")
@@ -1667,7 +1667,7 @@ the @code{arrayCGH} packages.")
("r-matrixstats" ,r-matrixstats)
("r-r-utils" ,r-r-utils)
("r-rsamtools" ,r-rsamtools)))
- (home-page "http://bioconductor.org/packages/QDNAseq")
+ (home-page "https://bioconductor.org/packages/QDNAseq")
(synopsis "Quantitative DNA sequencing for chromosomal aberrations")
(description "The genome is divided into non-overlapping fixed-sized bins,
number of sequence reads in each counted, adjusted with a simultaneous
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4a84273dd2..edfccacb4e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10161,7 +10161,7 @@ the earlier snpMatrix package, allowing for uncertainty in genotypes.")
(method url-fetch)
;; We cannot use bioconductor-uri here because this tarball is
;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "http://www.bioconductor.org/packages/"
+ (uri (string-append "https://www.bioconductor.org/packages/"
"release/data/annotation/src/contrib/"
"Homo.sapiens_"
version ".tar.gz"))
diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index 4095926af3..982def62c6 100644
--- a/gnu/packages/graph.scm
+++ b/gnu/packages/graph.scm
@@ -183,7 +183,7 @@ model.")
`(("r-graph" ,r-graph)))
(native-inputs
`(("pkg-config" ,pkg-config)))
- (home-page "http://bioconductor.org/packages/Rgraphviz")
+ (home-page "https://bioconductor.org/packages/Rgraphviz")
(synopsis "Plotting capabilities for R graph objects")
(description
"This package interfaces R with the graphviz library for plotting R graph
--
cgit v1.2.3
From 568bd2e3822b3ad6d8190f1dc04c5a6e43dcb2fa Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Tue, 21 Jan 2020 00:49:36 +0100
Subject: gnu: dendropy: Update home page.
* gnu/packages/bioinformatics.scm (dendropy)[home-page]: Update.
---
gnu/packages/bioinformatics.scm | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
(limited to 'gnu/packages/bioinformatics.scm')
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index edfccacb4e..18f07e5dc2 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2439,7 +2439,7 @@ accessing bigWig files.")
(base32
"097hfyv2kaf4x92i4rjx0paw2cncxap48qivv8zxng4z7nhid0x9"))))
(build-system python-build-system)
- (home-page "http://packages.python.org/DendroPy/")
+ (home-page "https://dendropy.org/")
(synopsis "Library for phylogenetics and phylogenetic computing")
(description
"DendroPy is a library for phylogenetics and phylogenetic computing: reading,
--
cgit v1.2.3
From b56f2b6366a387ff42d7a33998f08527df60875e Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Tue, 21 Jan 2020 00:55:32 +0100
Subject: gnu: express-beta-diversity: Update home page.
The original is not coming back:
<https://github.com/dparks1134/ExpressBetaDiversity/issues/11>.
* gnu/packages/bioinformatics.scm (express-beta-diversity)[home-page]:
Use source code repository as home page.
---
gnu/packages/bioinformatics.scm | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
(limited to 'gnu/packages/bioinformatics.scm')
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 18f07e5dc2..81ffbb7cf8 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2916,7 +2916,7 @@ ChIP-Seq, and analysis of metagenomic data.")
#t))))))
(inputs
`(("python" ,python-2)))
- (home-page "http://kiwi.cs.dal.ca/Software/ExpressBetaDiversity")
+ (home-page "https://github.com/dparks1134/ExpressBetaDiversity")
(synopsis "Taxon- and phylogenetic-based beta diversity measures")
(description
"Express Beta Diversity (EBD) calculates ecological beta diversity
--
cgit v1.2.3
From b725655fce8444049f886955a143b005642f811a Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Tue, 21 Jan 2020 01:28:41 +0100
Subject: gnu: grit: Update home page.
* gnu/packages/bioinformatics.scm (grit)[home-page]: Use source code
repository as home page.
---
gnu/packages/bioinformatics.scm | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
(limited to 'gnu/packages/bioinformatics.scm')
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 81ffbb7cf8..a0a5597ab5 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3313,7 +3313,8 @@ association studies (GWAS).")
("python-networkx" ,python2-networkx)))
(native-inputs
`(("python-cython" ,python2-cython)))
- (home-page "http://grit-bio.org")
+ ;; The canonical <http://grit-bio.org> home page times out as of 2020-01-21.
+ (home-page "https://github.com/nboley/grit")
(synopsis "Tool for integrative analysis of RNA-seq type assays")
(description
"GRIT is designed to use RNA-seq, TES, and TSS data to build and quantify
--
cgit v1.2.3
From 030fe2fb7e2a75985fe289ef81ba7e03bf022365 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Tue, 21 Jan 2020 01:32:10 +0100
Subject: gnu: miso: Update home page.
* gnu/packages/bioinformatics.scm (miso)[home-page]: Update.
---
gnu/packages/bioinformatics.scm | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
(limited to 'gnu/packages/bioinformatics.scm')
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a0a5597ab5..6695c2fc16 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4596,7 +4596,7 @@ assembled metagenomic sequence.")
;; Use setuptools, or else the executables are not
;; installed.
(("distutils.core") "setuptools")
- ;; use "gcc" instead of "cc" for compilation
+ ;; Use "gcc" instead of "cc" for compilation.
(("^defines")
"cc.set_executables(
compiler='gcc',
@@ -4606,8 +4606,8 @@ linker_so='gcc -shared'); defines"))
#t))))
(build-system python-build-system)
(arguments
- `(#:python ,python-2 ; only Python 2 is supported
- #:tests? #f)) ; no "test" target
+ `(#:python ,python-2 ; only Python 2 is supported
+ #:tests? #f)) ; no "test" target
(inputs
`(("samtools" ,samtools)
("python-numpy" ,python2-numpy)
@@ -4615,9 +4615,9 @@ linker_so='gcc -shared'); defines"))
("python-scipy" ,python2-scipy)
("python-matplotlib" ,python2-matplotlib)))
(native-inputs
- `(("python-mock" ,python2-mock) ;for tests
- ("python-pytz" ,python2-pytz))) ;for tests
- (home-page "http://genes.mit.edu/burgelab/miso/index.html")
+ `(("python-mock" ,python2-mock) ; for tests
+ ("python-pytz" ,python2-pytz))) ; for tests
+ (home-page "https://www.genes.mit.edu/burgelab/miso/index.html")
(synopsis "Mixture of Isoforms model for RNA-Seq isoform quantitation")
(description
"MISO (Mixture-of-Isoforms) is a probabilistic framework that quantitates
--
cgit v1.2.3
From 5832b88c45d2625f282d7057524a1d2664d0f8d0 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Tue, 21 Jan 2020 01:41:59 +0100
Subject: gnu: prodigal: Update home page.
* gnu/packages/bioinformatics.scm (prodigal)[home-page]: Use source code repository as home page.
---
gnu/packages/bioinformatics.scm | 6 ++++--
1 file changed, 4 insertions(+), 2 deletions(-)
(limited to 'gnu/packages/bioinformatics.scm')
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 6695c2fc16..c51aa89218 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4992,6 +4992,8 @@ different command-line tools:
(define-public prodigal
(package
(name "prodigal")
+ ;; Check for a new home page when updating this package:
+ ;; https://github.com/hyattpd/Prodigal/issues/36#issuecomment-536617588
(version "2.6.3")
(source (origin
(method git-fetch)
@@ -5004,14 +5006,14 @@ different command-line tools:
"1fs1hqk83qjbjhrvhw6ni75zakx5ki1ayy3v6wwkn3xvahc9hi5s"))))
(build-system gnu-build-system)
(arguments
- `(#:tests? #f ;no check target
+ `(#:tests? #f ; no check target
#:make-flags (list (string-append "INSTALLDIR="
(assoc-ref %outputs "out")
"/bin"))
#:phases
(modify-phases %standard-phases
(delete 'configure))))
- (home-page "http://prodigal.ornl.gov")
+ (home-page "https://github.com/hyattpd/Prodigal")
(synopsis "Protein-coding gene prediction for Archaea and Bacteria")
(description
"Prodigal runs smoothly on finished genomes, draft genomes, and
--
cgit v1.2.3
From 0eeaf1ac3cd5ea21cf126017b639efd964a759f5 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Tue, 21 Jan 2020 01:43:36 +0100
Subject: gnu: raxml: Update home page.
* gnu/packages/bioinformatics.scm (raxml)[home-page]: Update.
---
gnu/packages/bioinformatics.scm | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
(limited to 'gnu/packages/bioinformatics.scm')
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c51aa89218..48f181db1b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5171,7 +5171,7 @@ extremely diverse sets of genomes.")
#t)))))
(inputs
`(("openmpi" ,openmpi)))
- (home-page "http://sco.h-its.org/exelixis/web/software/raxml/index.html")
+ (home-page "https://cme.h-its.org/exelixis/web/software/raxml/index.html")
(synopsis "Randomized Axelerated Maximum Likelihood phylogenetic trees")
(description
"RAxML is a tool for phylogenetic analysis and post-analysis of large
--
cgit v1.2.3
From 0388046068e2c80afe201bf0a55795dfa8454c01 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Tue, 21 Jan 2020 01:44:54 +0100
Subject: gnu: sra-tools: Update home page.
* gnu/packages/bioinformatics.scm (sra-tools)[home-page]: Update.
---
gnu/packages/bioinformatics.scm | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
(limited to 'gnu/packages/bioinformatics.scm')
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 48f181db1b..f4eec88b42 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6042,7 +6042,8 @@ sequence itself can be retrieved from these databases.")
("fuse" ,fuse)
("hdf5" ,hdf5)
("zlib" ,zlib)))
- (home-page "http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software")
+ (home-page
+ "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software")
(synopsis "Tools and libraries for reading and writing sequencing data")
(description
"The SRA Toolkit from NCBI is a collection of tools and libraries for
--
cgit v1.2.3
From 72607005e465e4f7635f7a4f584457be9e6c9d77 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Tue, 21 Jan 2020 01:47:30 +0100
Subject: gnu: r-gage: Update home page.
* gnu/packages/bioinformatics.scm (r-gage)[home-page]: Update.
---
gnu/packages/bioinformatics.scm | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
(limited to 'gnu/packages/bioinformatics.scm')
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f4eec88b42..8454b3e25c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9784,7 +9784,8 @@ microarrays or GRanges for sequencing data.")
`(("r-annotationdbi" ,r-annotationdbi)
("r-graph" ,r-graph)
("r-keggrest" ,r-keggrest)))
- (home-page "http://www.biomedcentral.com/1471-2105/10/161")
+ (home-page (string-append "https://bmcbioinformatics.biomedcentral.com/"
+ "articles/10.1186/1471-2105-10-161"))
(synopsis "Generally applicable gene-set enrichment for pathway analysis")
(description
"GAGE is a published method for gene set (enrichment or GSEA) or pathway
--
cgit v1.2.3
From a19fb6a43648f6a3556d8139794ebd8646e792b8 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Tue, 21 Jan 2020 01:59:49 +0100
Subject: gnu: Use HTTPS for (gnu packages bioinformatics) home pages.
* gnu/packages/bioinformatics (bamm, ribodiff, python-biopython)
(discrover, hisat, hisat2, htseq, fastqc, htslib, python2-pbcore, roary)
(sortmerna, r-qtl, multiqc, r-deseq, r-fastseg, sambamba, trim-galore)
(gess, kentutils, bismark, kallisto, sailfish, python-hicexplorer)
(pplacer, python2-checkm-genome, r-velocyto)[home-page]: Use HTTPS.
---
gnu/packages/bioinformatics.scm | 58 ++++++++++++++++++++---------------------
1 file changed, 29 insertions(+), 29 deletions(-)
(limited to 'gnu/packages/bioinformatics.scm')
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 8454b3e25c..e8dac2a12b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -261,7 +261,7 @@ structure of the predicted RNA.")
("coreutils" ,coreutils)))
(propagated-inputs
`(("python-numpy" ,python2-numpy)))
- (home-page "http://ecogenomics.github.io/BamM/")
+ (home-page "https://ecogenomics.github.io/BamM/")
(synopsis "Metagenomics-focused BAM file manipulator")
(description
"BamM is a C library, wrapped in python, to efficiently generate and
@@ -726,7 +726,7 @@ provides the Ribotaper pipeline.")
(native-inputs
`(("python-mock" ,python2-mock)
("python-nose" ,python2-nose)))
- (home-page "http://public.bmi.inf.ethz.ch/user/zhongy/RiboDiff/")
+ (home-page "https://public.bmi.inf.ethz.ch/user/zhongy/RiboDiff/")
(synopsis "Detect translation efficiency changes from ribosome footprints")
(description "RiboDiff is a statistical tool that detects the protein
translational efficiency change from Ribo-Seq (ribosome footprinting) and
@@ -1056,7 +1056,7 @@ provide a coordinated and extensible framework to do computational biology.")
(lambda _ (setenv "HOME" "/tmp") #t)))))
(propagated-inputs
`(("python-numpy" ,python-numpy)))
- (home-page "http://biopython.org/")
+ (home-page "https://biopython.org/")
(synopsis "Tools for biological computation in Python")
(description
"Biopython is a set of tools for biological computation including parsers
@@ -2676,7 +2676,7 @@ data and settings.")
texlive-latex-pgf ; tikz
texlive-latex-verbatimbox)))
("imagemagick" ,imagemagick)))
- (home-page "http://dorina.mdc-berlin.de/public/rajewsky/discrover/")
+ (home-page "https://dorina.mdc-berlin.de/public/rajewsky/discrover/")
(synopsis "Discover discriminative nucleotide sequence motifs")
(description "Discrover is a motif discovery method to find binding sites
of nucleic acid binding proteins.")
@@ -3381,7 +3381,7 @@ estimates transcript expression.")
;; Non-portable SSE instructions are used so building fails on platforms
;; other than x86_64.
(supported-systems '("x86_64-linux"))
- (home-page "http://ccb.jhu.edu/software/hisat/index.shtml")
+ (home-page "https://ccb.jhu.edu/software/hisat/index.shtml")
(synopsis "Hierarchical indexing for spliced alignment of transcripts")
(description
"HISAT is a fast and sensitive spliced alignment program for mapping
@@ -3435,7 +3435,7 @@ particular, reads spanning multiple exons.")
`(("unzip" ,unzip) ; needed for archive from ftp
("perl" ,perl)
("pandoc" ,ghc-pandoc))) ; for documentation
- (home-page "http://ccb.jhu.edu/software/hisat2/index.shtml")
+ (home-page "https://ccb.jhu.edu/software/hisat2/index.shtml")
(synopsis "Graph-based alignment of genomic sequencing reads")
(description "HISAT2 is a fast and sensitive alignment program for mapping
next-generation sequencing reads (both DNA and RNA) to a population of human
@@ -3495,7 +3495,7 @@ HMMs).")
(inputs
`(("python-pysam" ,python-pysam)
("python-matplotlib" ,python-matplotlib)))
- (home-page "http://www-huber.embl.de/users/anders/HTSeq/")
+ (home-page "https://htseq.readthedocs.io/")
(synopsis "Analysing high-throughput sequencing data with Python")
(description
"HTSeq is a Python package that provides infrastructure to process data
@@ -3970,7 +3970,7 @@ VCF.")
("java-jbzip2" ,java-jbzip2)))
(native-inputs
`(("unzip" ,unzip)))
- (home-page "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/")
+ (home-page "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/")
(synopsis "Quality control tool for high throughput sequence data")
(description
"FastQC aims to provide a simple way to do some quality control
@@ -4049,7 +4049,7 @@ performance.")
`(("zlib" ,zlib)))
(native-inputs
`(("perl" ,perl)))
- (home-page "http://www.htslib.org")
+ (home-page "https://www.htslib.org")
(synopsis "C library for reading/writing high-throughput sequencing data")
(description
"HTSlib is a C library for reading/writing high-throughput sequencing
@@ -4743,7 +4743,7 @@ interrupted by stop codons. OrfM finds and prints these ORFs.")
`(("python-nose" ,python2-nose)
("python-sphinx" ,python2-sphinx)
("python-pyxb" ,python2-pyxb)))
- (home-page "http://pacificbiosciences.github.io/pbcore/")
+ (home-page "https://pacificbiosciences.github.io/pbcore/")
(synopsis "Library for reading and writing PacBio data files")
(description
"The pbcore package provides Python APIs for interacting with PacBio data
@@ -5127,7 +5127,7 @@ partial genes, and identifies translation initiation sites.")
("r-minimal" ,r-minimal)
("r-ggplot2" ,r-ggplot2)
("coreutils" ,coreutils)))
- (home-page "http://sanger-pathogens.github.io/Roary")
+ (home-page "https://sanger-pathogens.github.io/Roary/")
(synopsis "High speed stand-alone pan genome pipeline")
(description
"Roary is a high speed stand alone pan genome pipeline, which takes
@@ -6269,7 +6269,7 @@ of these reads to align data quickly through a hash-based indexing scheme.")
#t))))))
(inputs
`(("zlib" ,zlib)))
- (home-page "http://bioinfo.lifl.fr/RNA/sortmerna")
+ (home-page "https://bioinfo.lifl.fr/RNA/sortmerna/")
(synopsis "Biological sequence analysis tool for NGS reads")
(description
"SortMeRNA is a biological sequence analysis tool for filtering, mapping
@@ -8237,7 +8237,7 @@ throughput genetic sequencing data sets using regression methods.")
(base32
"03lmvydln8b7666b6w46qbryhf83vsd11d4y2v95rfgvqgq66l1i"))))
(build-system r-build-system)
- (home-page "http://rqtl.org/")
+ (home-page "https://rqtl.org/")
(synopsis "R package for analyzing QTL experiments in genetics")
(description "R/qtl is an extension library for the R statistics
system. It is used to analyze experimental crosses for identifying
@@ -8313,7 +8313,7 @@ libraries for systems that do not have these available via other means.")
(propagated-inputs
`(("r-optparse" ,r-optparse)
("r-rcolorbrewer" ,r-rcolorbrewer)))
- (home-page "http://www.e-rna.org/r-chie/index.cgi")
+ (home-page "https://www.e-rna.org/r-chie/index.cgi")
(synopsis "Analysis framework for RNA secondary structure")
(description
"The R4RNA package aims to be a general framework for the analysis of RNA
@@ -8933,7 +8933,7 @@ replacement for strverscmp.")
(("['\"]matplotlib.*?['\"]")
"'matplotlib'"))
#t)))))
- (home-page "http://multiqc.info")
+ (home-page "https://multiqc.info")
(synopsis "Aggregate bioinformatics analysis reports")
(description
"MultiQC is a tool to aggregate bioinformatics results across many
@@ -9603,7 +9603,7 @@ classes.")
("r-locfit" ,r-locfit)
("r-mass" ,r-mass)
("r-rcolorbrewer" ,r-rcolorbrewer)))
- (home-page "http://www-huber.embl.de/users/anders/DESeq")
+ (home-page "https://www-huber.embl.de/users/anders/DESeq/")
(synopsis "Differential gene expression analysis")
(description
"This package provides tools for estimating variance-mean dependence in
@@ -9732,7 +9732,7 @@ by the user, helping with quick and reproducible access.")
("r-genomicranges" ,r-genomicranges)
("r-iranges" ,r-iranges)
("r-s4vectors" ,r-s4vectors)))
- (home-page "http://www.bioinf.jku.at/software/fastseg/index.html")
+ (home-page "https://www.bioinf.jku.at/software/fastseg/index.html")
(synopsis "Fast segmentation algorithm for genetic sequencing data")
(description
"Fastseg implements a very fast and efficient segmentation algorithm.
@@ -10897,7 +10897,7 @@ droplet sequencing. It has been particularly tailored for Drop-seq.")
(inputs
`(("lz4" ,lz4)
("htslib" ,htslib-for-sambamba)))
- (home-page "http://lomereiter.github.io/sambamba")
+ (home-page "https://lomereiter.github.io/sambamba/")
(synopsis "Tools for working with SAM/BAM data")
(description "Sambamba is a high performance modern robust and
fast tool (and library), written in the D programming language, for
@@ -11014,7 +11014,7 @@ with narrow binding events such as transcription factor ChIP-seq.")
("cutadapt" ,cutadapt)))
(native-inputs
`(("unzip" ,unzip)))
- (home-page "http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/")
+ (home-page "https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/")
(synopsis "Wrapper around Cutadapt and FastQC")
(description "Trim Galore! is a wrapper script to automate quality and
adapter trimming as well as quality control, with some added functionality to
@@ -11076,7 +11076,7 @@ matplotlib.use('Agg')
("python2-numpy" ,python2-numpy)
("python2-networkx" ,python2-networkx)
("python2-biopython" ,python2-biopython)))
- (home-page "http://compbio.uthscsa.edu/GESS_Web/")
+ (home-page "https://compbio.uthscsa.edu/GESS_Web/")
(synopsis "Detect exon-skipping events from raw RNA-seq data")
(description
"GESS is an implementation of a novel computational method to detect de
@@ -11328,7 +11328,7 @@ models. TADbit is complemented by TADkit for visualizing 3D models.")
("mariadb" ,mariadb "lib")
("mariadb-dev" ,mariadb "dev")
("openssl" ,openssl-1.0)))
- (home-page "http://genome.cse.ucsc.edu/index.html")
+ (home-page "https://genome.cse.ucsc.edu/index.html")
(synopsis "Assorted bioinformatics utilities")
(description "This package provides the kentUtils, a selection of
bioinformatics utilities used in combination with the UCSC genome
@@ -11488,7 +11488,7 @@ Browser.")
(sha256
(base32 "138mwsr4nf5qif4mrxx286mpnagxd1xwl6k8aidrjgknaqg88zyr"))))
("uglify-js" ,uglify-js)))
- (home-page "http://www.bioinformatics.babraham.ac.uk/projects/bismark/")
+ (home-page "https://www.bioinformatics.babraham.ac.uk/projects/bismark/")
(synopsis "Map bisulfite treated sequence reads and analyze methylation")
(description "Bismark is a program to map bisulfite treated sequencing
reads to a genome of interest and perform methylation calls in a single step.
@@ -11591,7 +11591,7 @@ using nucleotide or amino-acid sequence data.")
`(("hdf5" ,hdf5)
("htslib" ,htslib)
("zlib" ,zlib)))
- (home-page "http://pachterlab.github.io/kallisto/")
+ (home-page "https://pachterlab.github.io/kallisto/")
(synopsis "Near-optimal RNA-Seq quantification")
(description
"Kallisto is a program for quantifying abundances of transcripts from
@@ -11766,7 +11766,7 @@ dependency like SeqAn.")
("zlib" ,zlib)))
(native-inputs
`(("pkg-config" ,pkg-config)))
- (home-page "http://www.cs.cmu.edu/~ckingsf/software/sailfish")
+ (home-page "https://www.cs.cmu.edu/~ckingsf/software/sailfish/")
(synopsis "Mapping-based isoform quantification from RNA-Seq reads")
(description "Sailfish is a tool for genomic transcript quantification
from RNA-seq data. It requires a set of target transcripts (either from a
@@ -13569,7 +13569,7 @@ such as Hi-C contact matrices.")
("python-six" ,python-six)
("python-tables" ,python-tables)
("python-unidecode" ,python-unidecode)))
- (home-page "http://hicexplorer.readthedocs.io")
+ (home-page "https://hicexplorer.readthedocs.io")
(synopsis "Process, analyze and visualize Hi-C data")
(description
"HiCExplorer is a powerful and easy to use set of tools to process,
@@ -14651,7 +14651,7 @@ to maximize phylogenetic likelihood or posterior probability according to a
reference alignment. Pplacer is designed to be fast, to give useful
information about uncertainty, and to offer advanced visualization and
downstream analysis.")
- (home-page "http://matsen.fhcrc.org/pplacer")
+ (home-page "https://matsen.fhcrc.org/pplacer/")
(license license:gpl3))))
;; This package is installed alongside 'pplacer'. It is a separate package so
@@ -14707,14 +14707,14 @@ downstream analysis.")
(build-system python-build-system)
(arguments
`(#:python ,python-2
- #:tests? #f)) ; some tests are interactive
+ #:tests? #f)) ; some tests are interactive
(propagated-inputs
`(("python-dendropy" ,python2-dendropy)
("python-matplotlib" ,python2-matplotlib)
("python-numpy" ,python2-numpy)
("python-pysam" ,python2-pysam)
("python-scipy" ,python2-scipy)))
- (home-page "http://pypi.python.org/pypi/checkm/")
+ (home-page "https://pypi.org/project/Checkm/")
(synopsis "Assess the quality of putative genome bins")
(description
"CheckM provides a set of tools for assessing the quality of genomes
@@ -15366,7 +15366,7 @@ pairs.")
("r-rsamtools" ,r-rsamtools)
("r-edger" ,r-edger)
("r-igraph" ,r-igraph)))
- (home-page "http://velocyto.org")
+ (home-page "https://velocyto.org")
(synopsis "RNA velocity estimation in R")
(description
"This package provides basic routines for estimation of gene-specific
--
cgit v1.2.3