[patch] gnu: Add r-glad, r-italicsdata, r-pd-mapping50k-xba240, r-italics, r-manor, r-tilingarray, r-snapcgh, r-quantsmooth, r-beadarraysnp and r-adacgh2.

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3 participants
  • MadalinIonel.Patrascu@mdc-berlin.de
  • Mădălin Ionel Patrașcu
  • Ricardo Wurmus
Owner
unassigned
Submitted by
MadalinIonel.Patrascu@mdc-berlin.de
Severity
normal

Debbugs page

MadalinIonel.Patrascu@mdc-berlin.de wrote 2 years ago
(name . guix-patches@gnu.org)(address . guix-patches@gnu.org)
7175b544a6694ff09d64a005cb0cd6f1@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-glad, r-italicsdata, r-pd-mapping50k-xba240, r-italics, r-manor, r-tilingarray, r-snapcgh, r-quantsmooth, r-beadarraysnp and r-adacgh2): New variables.
Attachment: file
Mădălin Ionel Patrașcu wrote 2 years ago
[PATCH 01/10] gnu: Add r-glad.
(address . 61220@debbugs.gnu.org)
20230202022657.67003-1-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-glad): New variable.
---
gnu/packages/bioconductor.scm | 25 +++++++++++++++++++++++++
1 file changed, 25 insertions(+)

Toggle diff (40 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 711b988e7f..451dcfde86 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6122,6 +6122,31 @@ (define-public r-genomicranges
manipulating genomic intervals and variables defined along a genome.")
(license license:artistic2.0)))
+(define-public r-glad
+ (package
+ (name "r-glad")
+ (version "2.62.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "GLAD" version))
+ (sha256
+ (base32
+ "0gb52ic5r6nkgm2ynm174vcvbmkbhhjgv71lsmxpxzcsb6rr7qj6"))))
+ (properties `((upstream-name . "GLAD")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list gsl
+ r-aws))
+ (native-inputs (list pkg-config))
+ (home-page "http://bioinfo.curie.fr")
+ (synopsis "Gain and loss analysis of DNA")
+ (description
+ "This package helps with the analysis of array @acronym{CGH, comparative
+genomic hybridization} data by detecting of the breakpoints in the genomic profiles
+and assignment of a status (gain, normal or loss) to each chromosomal regions
+identified.")
+ (license license:gpl2)))
+
(define-public r-gostats
(package
(name "r-gostats")

base-commit: 6564a04efaf506a5ef51a7c100144fa31bbe1f31
--
2.39.1
Mădălin Ionel Patrașcu wrote 2 years ago
[PATCH 02/10] gnu: Add r-italicsdata.
(address . 61220@debbugs.gnu.org)
20230202022657.67003-2-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-italicsdata): New variable.
---
gnu/packages/bioconductor.scm | 17 +++++++++++++++++
1 file changed, 17 insertions(+)

Toggle diff (30 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 451dcfde86..ed08807f07 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1431,6 +1431,23 @@ (define-public r-genomationdata
downloaded from Encode.")
(license license:gpl3+)))
+(define-public r-italicsdata
+ (package
+ (name "r-italicsdata")
+ (version "2.36.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "ITALICSData" version 'experiment))
+ (sha256
+ (base32 "09d2igic3b5p7wpq98hb2lffxm1nfq9mwmnqlbdn3jv49pgz3hmw"))))
+ (properties `((upstream-name . "ITALICSData")))
+ (build-system r-build-system)
+ (home-page "http://bioinfo.curie.fr") ;; no https
+ (synopsis "ITALICS data")
+ (description "Data needed to use the ITALICS package.")
+ (license (list license:gpl2+ license:gpl3+)))) ;; expanded from GPL
+
(define-public r-macrophage
(package
(name "r-macrophage")
--
2.39.1
Mădălin Ionel Patrașcu wrote 2 years ago
[PATCH 04/10] gnu: Add r-italics.
(address . 61220@debbugs.gnu.org)
20230202022657.67003-4-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-italics): New variable.
---
gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++
1 file changed, 27 insertions(+)

Toggle diff (40 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index fa8e60a4f4..1efafb1cd3 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4510,6 +4510,33 @@ (define-public r-isoformswitchanalyzer
Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc.")
(license license:gpl2+)))
+(define-public r-italics
+ (package
+ (name "r-italics")
+ (version "2.58.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "ITALICS" version))
+ (sha256
+ (base32 "0g937h9zxkxnm424wh58b46mfasdd7pqy5c04r0a46mx9lxibgbs"))))
+ (properties `((upstream-name . "ITALICS")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-affxparser
+ r-dbi
+ r-glad
+ r-italicsdata
+ r-oligo
+ r-oligoclasses
+ r-pd-mapping50k-xba240))
+ (home-page "http://bioinfo.curie.fr") ;;no https
+ (synopsis "Normalizing of the Affymetrix GeneChip human mapping")
+ (description
+ "This package provides a method to normalize the Affymetrix GeneChip human
+mapping 100K and 500K set.")
+ (license license:gpl2)))
+
;; This is a CRAN package, but it depends on r-biobase and r-limma from Bioconductor.
(define-public r-absfiltergsea
(package
--
2.39.1
Mădălin Ionel Patrașcu wrote 2 years ago
[PATCH 06/10] gnu: Add r-tilingarray.
(address . 61220@debbugs.gnu.org)
20230202022657.67003-6-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-tilingarray): New variable.
---
gnu/packages/bioconductor.scm | 40 +++++++++++++++++++++++++++++++++++
1 file changed, 40 insertions(+)

Toggle diff (53 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 3339c751cb..f692114754 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -14960,6 +14960,46 @@ (define-public r-wavcluster
procedures that induce nucleotide substitutions (e.g. BisSeq).")
(license license:gpl2)))
+(define-public r-tilingarray
+ (package
+ (name "r-tilingarray")
+ (version "1.76.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "tilingArray" version))
+ (sha256
+ (base32
+ "19bkgblpkcp3w3sdyn82c37gkz1sv3r4d546zpbnh36q2pi3l4zd"))))
+ (properties `((upstream-name . "tilingArray")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-affy
+ r-biobase
+ r-genefilter
+ r-pixmap
+ r-rcolorbrewer
+ r-strucchange
+ r-vsn))
+ (home-page "https://bioconductor.org/packages/tilingArray")
+ (synopsis "Transcript mapping with high-density oligonucleotide tiling arrays")
+ (description
+ "The package provides functionality that can be useful for the analysis of
+the high-density tiling microarray data (such as from Affymetrix genechips) or for
+measuring the transcript abundance and the architecture. The main functionalities
+of the package are:
+@enumerate
+@item the class segmentation for representing partitionings of a linear series of
+data;
+@item the function segment for fitting piecewise constant models using a dynamic
+programming algorithm that is both fast and exact;
+@item the function confint for calculating confidence intervals using the strucchange
+package;
+@item the function plotAlongChrom for generating pretty plots;
+@item the function normalizeByReference for probe-sequence dependent response
+adjustment from a (set of) reference hybridizations.
+@end enumerate")
+ (license license:artistic2.0)))
+
(define-public r-timeseriesexperiment
(package
(name "r-timeseriesexperiment")
--
2.39.1
Mădălin Ionel Patrașcu wrote 2 years ago
[PATCH 03/10] gnu: Add r-pd-mapping50k-xba240.
(address . 61220@debbugs.gnu.org)
20230202022657.67003-3-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-pd-mapping50k-xba240): New variable.
---
gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++
1 file changed, 26 insertions(+)

Toggle diff (39 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index ed08807f07..fa8e60a4f4 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -115,6 +115,32 @@ (define-public r-org-bt-eg-db
based on mapping using Entrez Gene identifiers.")
(license license:artistic2.0)))
+(define-public r-pd-mapping50k-xba240
+ (package
+ (name "r-pd-mapping50k-xba240")
+ (version "3.12.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "pd.mapping50k.xba240" version
+ 'annotation))
+ (sha256
+ (base32 "1a1f3lh5ywhyjawdbj2fzban85c8jz70lfcv3pagd5piincjwxq8"))))
+ (properties `((upstream-name . "pd.mapping50k.xba240")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-biostrings
+ r-dbi
+ r-iranges
+ r-oligo
+ r-oligoclasses
+ r-rsqlite
+ r-s4vectors))
+ (home-page "https://bioconductor.org/packages/pd.mapping50k.xba240")
+ (synopsis "Platform design info for Affymetrix Mapping50K_Xba240")
+ (description "This package provides annotations for pd.mapping50k.xba240.")
+ (license license:artistic2.0)))
+
(define-public r-reactome-db
(package
(name "r-reactome-db")
--
2.39.1
Mădălin Ionel Patrașcu wrote 2 years ago
[PATCH 07/10] gnu: Add r-snapcgh.
(address . 61220@debbugs.gnu.org)
20230202022657.67003-7-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-snapcgh): New variable.
---
gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++
1 file changed, 27 insertions(+)

Toggle diff (40 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index f692114754..bce8319dcb 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -18185,6 +18185,33 @@ (define-public r-pathview
large-scale and fully automated analysis.")
(license license:gpl3+)))
+(define-public r-snapcgh
+ (package
+ (name "r-snapcgh")
+ (version "1.68.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "snapCGH" version))
+ (sha256
+ (base32
+ "1zxvl8mkby7yb5kppddag6k9w78d1fm6adx52h4cgrfckn28w64q"))))
+ (properties `((upstream-name . "snapCGH")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-acgh
+ r-cluster
+ r-dnacopy
+ r-glad
+ r-limma
+ r-tilingarray))
+ (home-page "https://bioconductor.org/packages/snapCGH")
+ (synopsis "Segmentation, normalisation and processing of the aCGH data")
+ (description
+ "This package provides methods for segmenting, normalising and processing
+aCGH data. snapCGH also includes plotting functions for visualising raw and
+segmented data for individual and multiple arrays.")
+ (license (list license:gpl2+ license:gpl3+)))) ;; expanded from GPL
+
(define-public r-snpstats
(package
(name "r-snpstats")
--
2.39.1
Mădălin Ionel Patrașcu wrote 2 years ago
[PATCH 08/10] gnu: Add r-quantsmooth.
(address . 61220@debbugs.gnu.org)
20230202022657.67003-8-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-quantsmooth): New variable.
---
gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++
1 file changed, 27 insertions(+)

Toggle diff (40 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index bce8319dcb..07207ebc38 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8738,6 +8738,33 @@ (define-public r-oligo
Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
(license license:lgpl2.0+)))
+(define-public r-quantsmooth
+ (package
+ (name "r-quantsmooth")
+ (version "1.64.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "quantsmooth" version))
+ (sha256
+ (base32 "1adwws3brb01d4g6yidipnd8akkiyc3gpdr876hy57qnmcq8xipp"))))
+ (properties `((upstream-name . "quantsmooth")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-quantreg))
+ (home-page "https://bioconductor.org/packages/quantsmooth")
+ (synopsis "Quantile smoothing and genomic visualization of array data")
+ (description
+ "This package implements quantile smoothing. It contains a dataset used to
+produce human chromosomal ideograms for plotting purposes and a collection of
+arrays that contains data of chromosome 14 of 3 colorectal tumors. The package
+provides functions for painting chromosomal icons, chromosme or chromosomal
+idiogram and other types of plots. Quantsmooth offers options like converting
+chromosomal ids to their numeric form, retrieving the human chromosomal length
+from NCBI data, retrieving regions of interest in a vector of intensities using
+quantile smoothing, determining cytoband position based on the location of the
+probe, and other useful tools.")
+ (license license:gpl2)))
+
(define-public r-qvalue
(package
(name "r-qvalue")
--
2.39.1
Mădălin Ionel Patrașcu wrote 2 years ago
[PATCH 09/10] gnu: Add r-beadarraysnp.
(address . 61220@debbugs.gnu.org)
20230202022657.67003-9-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-beadarraysnp): New variable.
---
gnu/packages/bioconductor.scm | 20 ++++++++++++++++++++
1 file changed, 20 insertions(+)

Toggle diff (33 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 07207ebc38..c509dffb4c 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -17081,6 +17081,26 @@ (define-public r-beachmat
matrices.")
(license license:gpl3)))
+(define-public r-beadarraysnp
+ (package
+ (name "r-beadarraysnp")
+ (version "1.64.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "beadarraySNP" version))
+ (sha256
+ (base32 "06hy89pclbyxjw5yf5i9bc3wr789b9pmhd9sdchgljlijs9vcj6g"))))
+ (properties `((upstream-name . "beadarraySNP")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-biobase r-quantsmooth))
+ (home-page "https://bioconductor.org/packages/beadarraySNP")
+ (synopsis "Normalization and reporting of Illumina SNP bead arrays")
+ (description
+ "This package is importing data from Illumina SNP experiments and it performs
+copy number calculations and reports.")
+ (license license:gpl2)))
+
;; This package includes files that have been taken from kentutils. Some
;; parts of kentutils are not released under a free license, but this package
;; only uses files that are also found in the free parts of kentutils.
--
2.39.1
Mădălin Ionel Patrașcu wrote 2 years ago
[PATCH 05/10] gnu: Add r-manor.
(address . 61220@debbugs.gnu.org)
20230202022657.67003-5-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-manor): New variable.
---
gnu/packages/bioconductor.scm | 23 +++++++++++++++++++++++
1 file changed, 23 insertions(+)

Toggle diff (36 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 1efafb1cd3..3339c751cb 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6518,6 +6518,29 @@ (define-public r-makecdfenv
package that automatically loads that environment.")
(license license:gpl2+)))
+(define-public r-manor
+ (package
+ (name "r-manor")
+ (version "1.70.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "MANOR" version))
+ (sha256
+ (base32 "16b30bmyzml97cjdbh6h9ky5c4h5ws2a3g2xkxnd55sd3jg64jgx"))))
+ (properties `((upstream-name . "MANOR")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-glad))
+ (native-inputs (list r-knitr))
+ (home-page "http://bioinfo.curie.fr/projects/manor/index.html") ;;no https
+ (synopsis "CGH micro-array normalization")
+ (description
+ "This package ofers functions for importation, normalization, visualization,
+and quality control to correct identified sources of variability in array of
+@acronym{CGH, comparative genomic hybridization} experiments.")
+ (license license:gpl2)))
+
+
(define-public r-maser
(package
(name "r-maser")
--
2.39.1
Mădălin Ionel Patrașcu wrote 2 years ago
[PATCH 10/10] gnu: Add r-adacgh2.
(address . 61220@debbugs.gnu.org)
20230202022657.67003-10-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-adacgh2): New variable.
---
gnu/packages/bioconductor.scm | 44 +++++++++++++++++++++++++++++++++++
1 file changed, 44 insertions(+)

Toggle diff (64 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index c509dffb4c..b351936cd8 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -31,6 +31,7 @@
(define-module (gnu packages bioconductor)
#:use-module ((guix licenses) #:prefix license:)
+ #:use-module (guix gexp)
#:use-module (guix packages)
#:use-module (guix download)
#:use-module (guix git-download)
@@ -1800,6 +1801,49 @@ (define-public r-absseq
ranking by fold-change and visualization.")
(license license:gpl3+)))
+(define-public r-adacgh2
+ (package
+ (name "r-adacgh2")
+ (version "2.38.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "ADaCGH2" version))
+ (sha256
+ (base32 "0g9x3lnr56035wq9ijdcri4sz5pwj8184yxm415gmsxrii9xvpfd"))))
+ (properties `((upstream-name . "ADaCGH2")))
+ (build-system r-build-system)
+ (arguments
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-before 'configure 'set-PYTHONPATH
+ (lambda _
+ (setenv "PYTHONPATH"
+ (string-append (getcwd) ":"
+ (getenv "GUIX_PYTHONPATH"))))))))
+ ;; This is needed by toMap.py script which is not compatible with python3
+ (inputs (list python2-minimal))
+ (propagated-inputs
+ (list r-acgh
+ r-bit
+ r-cluster
+ r-dnacopy
+ r-ff
+ r-glad
+ r-snapcgh
+ r-tilingarray
+ r-waveslim))
+ (home-page "https://github.com/rdiaz02/adacgh2")
+ (synopsis "Big data analysis from aCGH experiments")
+ (description
+ "This package analysis and creates plotts of array @acronym{CGH, comparative
+genomic hybridization} data. Also, it allows usage of @acronym{CBS, Circular
+Binary Segementation}, wavelet-based smoothing, HMM, BioHMM, GLAD, CGHseg. Most
+computations are parallelized (either via forking or with clusters, including MPI
+and sockets clusters) and use ff for storing data.")
+ (license license:gpl3+)))
+
(define-public r-adam
(package
(name "r-adam")
--
2.39.1
Ricardo Wurmus wrote 2 years ago
(name . Mădălin Ionel Patrașcu)(address . madalinionel.patrascu@mdc-berlin.de)(address . debbugs-submit@debbugs.gnu.org)(address . 61220@debbugs.gnu.org)
87y1p96cuj.fsf@elephly.net
Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> writes:

Toggle quote (1 lines)
> * gnu/packages/bioconductor.scm (r-adacgh2): New variable.
[…]
Toggle quote (3 lines)
> (define-module (gnu packages bioconductor)
> #:use-module ((guix licenses) #:prefix license:)
> + #:use-module (guix gexp)
[…]
Toggle quote (10 lines)
> + (arguments
> + (list
> + #:phases
> + #~(modify-phases %standard-phases
> + (add-before 'configure 'set-PYTHONPATH
> + (lambda _
> + (setenv "PYTHONPATH"
> + (string-append (getcwd) ":"
> + (getenv "GUIX_PYTHONPATH"))))))))

This phase seems unnecessary.

Toggle quote (3 lines)
> + ;; This is needed by toMap.py script which is not compatible with python3
> + (inputs (list python2-minimal))

The only reason for Python 2 is the outdated “print”, which is not
called as a function but used as a statement. I patched it instead.

--
Ricardo
Ricardo Wurmus wrote 2 years ago
Re: [bug#61220] [PATCH 01/10] gnu: Add r-glad.
(name . Mădălin Ionel Patrașcu)(address . madalinionel.patrascu@mdc-berlin.de)(address . 61220-done@debbugs.gnu.org)
87ttzx6crs.fsf@elephly.net
Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> writes:

Toggle quote (1 lines)
> * gnu/packages/bioconductor.scm (r-glad): New variable.
[…]

Thanks for this patch series.

I applied them all after changes to the description of almost all
packages, and changes to the line comments. I also moved gsl from
propagated-inputs to inputs.

--
Ricardo
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