[bug#61220] [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.

[bug#61220] [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.

[MadalinIonel.Patrascu]

[-- Attachment #1: Type: text/plain, Size: 188 bytes --]

* 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 #2: Type: text/html, Size: 583 bytes --]

[bug#61220] [PATCH 01/10] gnu: Add r-glad.

[Mădălin Ionel Patrașcu]

* gnu/packages/bioconductor.scm (r-glad): New variable.
---
 gnu/packages/bioconductor.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

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

[bug#61220] [PATCH 02/10] gnu: Add r-italicsdata.

[Mădălin Ionel Patrașcu]

* gnu/packages/bioconductor.scm (r-italicsdata): New variable.
---
 gnu/packages/bioconductor.scm | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

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

[bug#61220] [PATCH 03/10] gnu: Add r-pd-mapping50k-xba240.

[Mădălin Ionel Patrașcu]

* gnu/packages/bioconductor.scm (r-pd-mapping50k-xba240): New variable.
---
 gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

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

[bug#61220] [PATCH 04/10] gnu: Add r-italics.

[Mădălin Ionel Patrașcu]

* gnu/packages/bioconductor.scm (r-italics): New variable.
---
 gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

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

[bug#61220] [PATCH 05/10] gnu: Add r-manor.

[Mădălin Ionel Patrașcu]

* gnu/packages/bioconductor.scm (r-manor): New variable.
---
 gnu/packages/bioconductor.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

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

[bug#61220] [PATCH 06/10] gnu: Add r-tilingarray.

[Mădălin Ionel Patrașcu]

* gnu/packages/bioconductor.scm (r-tilingarray): New variable.
---
 gnu/packages/bioconductor.scm | 40 +++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)

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

[bug#61220] [PATCH 07/10] gnu: Add r-snapcgh.

[Mădălin Ionel Patrașcu]

* gnu/packages/bioconductor.scm (r-snapcgh): New variable.
---
 gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

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

[bug#61220] [PATCH 08/10] gnu: Add r-quantsmooth.

[Mădălin Ionel Patrașcu]

* gnu/packages/bioconductor.scm (r-quantsmooth): New variable.
---
 gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

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

[bug#61220] [PATCH 09/10] gnu: Add r-beadarraysnp.

[Mădălin Ionel Patrașcu]

* gnu/packages/bioconductor.scm (r-beadarraysnp): New variable.
---
 gnu/packages/bioconductor.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

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

[bug#61220] [PATCH 10/10] gnu: Add r-adacgh2.

[Mădălin Ionel Patrașcu]

* gnu/packages/bioconductor.scm (r-adacgh2): New variable.
---
 gnu/packages/bioconductor.scm | 44 +++++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

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

[bug#61220] [PATCH 10/10] gnu: Add r-adacgh2.

[Ricardo Wurmus]

Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> writes:

> * gnu/packages/bioconductor.scm (r-adacgh2): New variable.
[…]
>  (define-module (gnu packages bioconductor)
>    #:use-module ((guix licenses) #:prefix license:)
> +  #:use-module (guix gexp)
[…]
> +    (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.

> +    ;; 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

bug#61220: [PATCH 01/10] gnu: Add r-glad.

[Ricardo Wurmus]

Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> writes:

> * 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