[PATCH 00/16] Bioinfo stuff

[PATCH 00/16] Bioinfo stuff

[Ricardo Wurmus]

Hi Guix,

this a series of patches to upstream a few package definitions from the
staging module of the guix-bimsb repository.

~~ Ricardo

Ricardo Wurmus (16):
  gnu: Add python-argparse.
  gnu: Add hisat2.
  gnu: Add ribodiff.
  gnu: Add r-compquadform.
  gnu: Add r-seqminer.
  gnu: Add r-raremetals2.
  gnu: Add r-maldiquant.
  gnu: Add r-protgenerics.
  gnu: Add r-mzr.
  gnu: Add r-affyio.
  gnu: Add r-affy.
  gnu: Add r-vsn.
  gnu: Add r-mzid.
  gnu: Add r-pcamethods.
  gnu: Add r-msnbase.
  gnu: Add r-msnid.

 gnu/packages/bioinformatics.scm | 457 ++++++++++++++++++++++++++++++++++++++++
 gnu/packages/python.scm         |  31 ++-
 gnu/packages/statistics.scm     |  23 +-
 3 files changed, 509 insertions(+), 2 deletions(-)

-- 
2.11.0

[PATCH 01/16] gnu: Add python-argparse.

[Ricardo Wurmus]

* gnu/packages/python.scm (python-argparse, python2-argparse): New
variables.
---
 gnu/packages/python.scm | 31 ++++++++++++++++++++++++++++++-
 1 file changed, 30 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index a9792afe2..cf7143be1 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -7,7 +7,7 @@
 ;;; Copyright © 2014, 2015 Federico Beffa <beffa@fbengineering.ch>
 ;;; Copyright © 2015 Omar Radwan <toxemicsquire4@gmail.com>
 ;;; Copyright © 2015 Pierre-Antoine Rault <par@rigelk.eu>
-;;; Copyright © 2015, 2016 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015, 2016 Christopher Allan Webber <cwebber@dustycloud.org>
 ;;; Copyright © 2015 Eric Dvorsak <eric@dvorsak.fr>
 ;;; Copyright © 2015, 2016 David Thompson <davet@gnu.org>
@@ -7863,6 +7863,35 @@ be set via config files and/or environment variables.")
 (define-public python2-configargparse
   (package-with-python2 python-configargparse))
 
+(define-public python-argparse
+  (package
+    (name "python-argparse")
+    (version "1.4.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "argparse" version))
+       (sha256
+        (base32
+         "1r6nznp64j68ih1k537wms7h57nvppq0szmwsaf99n71bfjqkc32"))))
+    (properties `((python2-variant . ,(delay python2-argparse))))
+    (build-system python-build-system)
+    (home-page "https://pypi.python.org/pypi/argparse/")
+    (synopsis "Command-line parsing library")
+    (description "The @code{argparse} module makes it easy to write user
+friendly command line interfaces.  The program defines what arguments it
+requires, and @code{argparse} will figure out how to parse those out of
+@code{sys.argv}.  The @code{argparse} module also automatically generates help
+and usage messages and issues errors when users give the program invalid
+arguments.")
+    (license (package-license python))))
+
+(define-public python2-argparse
+  (package (inherit (package-with-python2
+              (strip-python2-variant python-argparse)))
+    (native-inputs
+     `(("python2-setuptools" ,python2-setuptools)))))
+
 (define-public python-ndg-httpsclient
   (package
     (name "python-ndg-httpsclient")
-- 
2.11.0

[PATCH 02/16] gnu: Add hisat2.

[Ricardo Wurmus]

* gnu/packages/bioinformatics.scm (hisat2): New variable.
---
 gnu/packages/bioinformatics.scm | 63 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 63 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b14b7d4ca..b3aedec63 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2722,6 +2722,69 @@ several alignment strategies enable effective alignment of RNA-seq reads, in
 particular, reads spanning multiple exons.")
     (license license:gpl3+)))
 
+(define-public hisat2
+  (package
+    (name "hisat2")
+    (version "2.0.5")
+    (source
+     (origin
+       (method url-fetch)
+       ;; FIXME: a better source URL is
+       ;; (string-append "ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2"
+       ;;                "/downloads/hisat2-" version "-source.zip")
+       ;; with hash "0lywnr8kijwsc2aw10dwxic0n0yvip6fl3rjlvc8zzwahamy4x7g"
+       ;; but it is currently unavailable.
+       (uri "https://github.com/infphilo/hisat2/archive/cba6e8cb.tar.gz")
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1mf2hdsyv7cd97xm9mp9a4qws02yrj95y6w6f6cdwnq0klp81r50"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f                      ; no check target
+       #:make-flags (list "CC=gcc" "CXX=g++" "allall")
+       #:modules ((guix build gnu-build-system)
+                  (guix build utils)
+                  (srfi srfi-26))
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'make-deterministic
+           (lambda _
+             (substitute* "Makefile"
+               (("`date`") "0"))
+             #t))
+         (delete 'configure)
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (bin (string-append out "/bin/"))
+                    (doc (string-append out "/share/doc/hisat2/")))
+               (for-each
+                (cut install-file <> bin)
+                (find-files "."
+                            "hisat2(-(build|align|inspect)(-(s|l)(-debug)*)*)*$"))
+               (mkdir-p doc)
+               (install-file "doc/manual.inc.html" doc))
+             #t)))))
+    (native-inputs
+     `(("unzip" ,unzip)                 ; needed for archive from ftp
+       ("perl" ,perl)
+       ("pandoc" ,ghc-pandoc)))         ; for documentation
+    (home-page "http://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
+genomes (as well as to a single reference genome).  In addition to using one
+global @dfn{graph FM} (GFM) index that represents a population of human
+genomes, HISAT2 uses a large set of small GFM indexes that collectively cover
+the whole genome.  These small indexes, combined with several alignment
+strategies, enable rapid and accurate alignment of sequencing reads.  This new
+indexing scheme is called a @dfn{Hierarchical Graph FM index} (HGFM).")
+    ;; HISAT2 contains files from Bowtie2, which is released under
+    ;; GPLv2 or later.  The HISAT2 source files are released under
+    ;; GPLv3 or later.
+    (license license:gpl3+)))
+
 (define-public hmmer
   (package
     (name "hmmer")
-- 
2.11.0

[PATCH 03/16] gnu: Add ribodiff.

[Ricardo Wurmus]

* gnu/packages/bioinformatics.scm (ribodiff): New variable.
---
 gnu/packages/bioinformatics.scm | 41 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b3aedec63..cd64d3439 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -468,6 +468,47 @@ frames} (ORFs) using ribosome profiling (ribo-seq) data.  This package
 provides the Ribotaper pipeline.")
     (license license:gpl3+)))
 
+(define-public ribodiff
+  (package
+    (name "ribodiff")
+    (version "0.2.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/ratschlab/RiboDiff/"
+                           "archive/v" version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "0wpbwmfv05wdjxv7ikm664f7s7p7cqr8jnw99zrda0q67rl50aaj"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:python ,python-2
+       #:phases
+       (modify-phases %standard-phases
+         ;; Generate an installable executable script wrapper.
+         (add-after 'unpack 'patch-setup.py
+           (lambda _
+             (substitute* "setup.py"
+               (("^(.*)packages=.*" line prefix)
+                (string-append line "\n"
+                               prefix "scripts=['scripts/TE.py'],\n")))
+             #t)))))
+    (inputs
+     `(("python-numpy" ,python2-numpy)
+       ("python-matplotlib" ,python2-matplotlib)
+       ("python-scipy" ,python2-scipy)
+       ("python-statsmodels" ,python2-statsmodels)))
+    (home-page "http://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
+RNA-Seq data.  It uses a generalized linear model to detect genes showing
+difference in translational profile taking mRNA abundance into account.  It
+facilitates us to decipher the translational regulation that behave
+independently with transcriptional regulation.")
+    (license license:gpl3+)))
+
 (define-public bioawk
   (package
     (name "bioawk")
-- 
2.11.0

[PATCH 04/16] gnu: Add r-compquadform.

[Ricardo Wurmus]

* gnu/packages/statistics.scm (r-compquadform): New variable.
---
 gnu/packages/statistics.scm | 23 ++++++++++++++++++++++-
 1 file changed, 22 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index c00a3d954..41096e8a1 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2015, 2016 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015 Vicente Vera Parra <vicentemvp@gmail.com>
 ;;; Copyright © 2016 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
@@ -4032,3 +4032,24 @@ dispersion modeling and Tweedie power-law families.")
     (description "This R package provides access to the code and data sets
 published by the statistics blog FiveThirtyEight.")
     (license license:expat)))
+
+(define-public r-compquadform
+  (package
+    (name "r-compquadform")
+    (version "1.4.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "CompQuadForm" version))
+       (sha256
+        (base32
+         "0bsgbdblxpv57mbwnf51xyiydp2bqyxkg4zzwqki85cv5xqlrq1n"))))
+    (properties `((upstream-name . "CompQuadForm")))
+    (build-system r-build-system)
+    (home-page "http://cran.r-project.org/web/packages/CompQuadForm")
+    (synopsis "Distribution function of quadratic forms in normal variables")
+    (description
+     "This package provides functions to compute the distribution function of
+quadratic forms in normal variables using Imhof's method, Davies's algorithm,
+Farebrother's algorithm or Liu et al.'s algorithm.")
+    (license license:gpl2+)))
-- 
2.11.0

[PATCH 05/16] gnu: Add r-seqminer.

[Ricardo Wurmus]

* gnu/packages/bioinformatics.scm (r-seqminer): New variable.
---
 gnu/packages/bioinformatics.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index cd64d3439..28a0da80e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8149,3 +8149,25 @@ high-dimensional data like gene expression/RNA sequencing/methylation/brain
 imaging data that can be used in subsequent analyses to adjust for unknown,
 unmodeled, or latent sources of noise.")
     (license license:artistic2.0)))
+
+(define-public r-seqminer
+  (package
+    (name "r-seqminer")
+    (version "5.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "seqminer" version))
+       (sha256
+        (base32
+         "0y0gc5lws3hdxasjb84m532ics6imb7qg9sl1zy62h503jh4j9gw"))))
+    (build-system r-build-system)
+    (inputs
+     `(("zlib" ,zlib)))
+    (home-page "http://seqminer.genomic.codes")
+    (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)")
+    (description
+     "This package provides tools to integrate nucleotide sequencing
+data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.")
+    ;; Any version of the GPL is acceptable
+    (license (list license:gpl2+ license:gpl3+))))
-- 
2.11.0

[PATCH 06/16] gnu: Add r-raremetals2.

[Ricardo Wurmus]

* gnu/packages/bioinformatics.scm (r-raremetals2): New variable.
---
 gnu/packages/bioinformatics.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 28a0da80e..743e8fdce 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8171,3 +8171,34 @@ unmodeled, or latent sources of noise.")
 data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.")
     ;; Any version of the GPL is acceptable
     (license (list license:gpl2+ license:gpl3+))))
+
+(define-public r-raremetals2
+  (package
+    (name "r-raremetals2")
+    (version "0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "http://genome.sph.umich.edu/w/images/"
+                           "b/b7/RareMETALS2_" version ".tar.gz"))
+       (sha256
+        (base32
+         "0z5ljcgvnm06ja9lm85a3cniq7slxcy37aqqkxrdidr79an5fs4s"))))
+    (properties `((upstream-name . "RareMETALS2")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-seqminer" ,r-seqminer)
+       ("r-mvtnorm" ,r-mvtnorm)
+       ("r-compquadform" ,r-compquadform)
+       ("r-getopt" ,r-getopt)))
+    (home-page "http://genome.sph.umich.edu/wiki/RareMETALS2")
+    (synopsis "Analyze gene-level association tests for binary trait")
+    (description
+     "The R package rareMETALS2 is an extension of the R package rareMETALS.
+It was designed to meta-analyze gene-level association tests for binary trait.
+While rareMETALS offers a near-complete solution for meta-analysis of
+gene-level tests for quantitative trait, it does not offer the optimal
+solution for binary trait.  The package rareMETALS2 offers improved features
+for analyzing gene-level association tests in meta-analyses for binary
+trait.")
+    (license license:gpl3)))
-- 
2.11.0

[PATCH 07/16] gnu: Add r-maldiquant.

[Ricardo Wurmus]

* gnu/packages/bioinformatics.scm (r-maldiquant): New variable.
---
 gnu/packages/bioinformatics.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 743e8fdce..74948ec55 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8202,3 +8202,29 @@ solution for binary trait.  The package rareMETALS2 offers improved features
 for analyzing gene-level association tests in meta-analyses for binary
 trait.")
     (license license:gpl3)))
+
+(define-public r-maldiquant
+  (package
+    (name "r-maldiquant")
+    (version "1.16")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "MALDIquant" version))
+       (sha256
+        (base32
+         "067xbmy10mpsvmv77g62chd7wwhdhcfn5hmp5fisbnz2h5rq0q60"))))
+    (properties `((upstream-name . "MALDIquant")))
+    (build-system r-build-system)
+    (home-page "http://cran.r-project.org/web/packages/MALDIquant")
+    (synopsis "Quantitative analysis of mass spectrometry data")
+    (description
+     "This package provides a complete analysis pipeline for matrix-assisted
+laser desorption/ionization-time-of-flight (MALDI-TOF) and other
+two-dimensional mass spectrometry data.  In addition to commonly used plotting
+and processing methods it includes distinctive features, namely baseline
+subtraction methods such as morphological filters (TopHat) or the
+statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak
+alignment using warping functions, handling of replicated measurements as well
+as allowing spectra with different resolutions.")
+    (license license:gpl3+)))
-- 
2.11.0

[PATCH 08/16] gnu: Add r-protgenerics.

[Ricardo Wurmus]

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

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 74948ec55..4a1bd0196 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8228,3 +8228,23 @@ statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak
 alignment using warping functions, handling of replicated measurements as well
 as allowing spectra with different resolutions.")
     (license license:gpl3+)))
+
+(define-public r-protgenerics
+  (package
+    (name "r-protgenerics")
+    (version "1.6.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "ProtGenerics" version))
+       (sha256
+        (base32
+         "0hb3vrrvfx6lcfalmjxm8dmigfmi5nba0pzjfgsrzd35c8mbfc6f"))))
+    (properties `((upstream-name . "ProtGenerics")))
+    (build-system r-build-system)
+    (home-page "https://github.com/lgatto/ProtGenerics")
+    (synopsis "S4 generic functions for proteomics infrastructure")
+    (description
+     "This package provides S4 generic functions needed by Bioconductor
+proteomics packages.")
+    (license license:artistic2.0)))
-- 
2.11.0

[PATCH 09/16] gnu: Add r-mzr.

[Ricardo Wurmus]

* gnu/packages/bioinformatics.scm (r-mzr): New variable.
---
 gnu/packages/bioinformatics.scm | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4a1bd0196..51660026e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8248,3 +8248,35 @@ as allowing spectra with different resolutions.")
      "This package provides S4 generic functions needed by Bioconductor
 proteomics packages.")
     (license license:artistic2.0)))
+
+(define-public r-mzr
+  (package
+    (name "r-mzr")
+    (version "2.8.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "mzR" version))
+       (sha256
+        (base32
+         "0ipmhg6l3pf648rdx5g2ha7l5ppd3cja6afxhdw76x8ga3633x0r"))))
+    (properties `((upstream-name . "mzR")))
+    (build-system r-build-system)
+    (inputs
+     `(("netcdf" ,netcdf)))
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-protgenerics" ,r-protgenerics)
+       ("r-rcpp" ,r-rcpp)
+       ("r-zlibbioc" ,r-zlibbioc)))
+    (home-page "https://github.com/sneumann/mzR/")
+    (synopsis "Parser for mass spectrometry data files")
+    (description
+     "The mzR package provides a unified API to the common file formats and
+parsers available for mass spectrometry data.  It comes with a wrapper for the
+ISB random access parser for mass spectrometry mzXML, mzData and mzML files.
+The package contains the original code written by the ISB, and a subset of the
+proteowizard library for mzML and mzIdentML.  The netCDF reading code has
+previously been used in XCMS.")
+    (license license:artistic2.0)))
-- 
2.11.0

[PATCH 10/16] gnu: Add r-affyio.

[Ricardo Wurmus]

* gnu/packages/bioinformatics.scm (r-affyio): New variable.
---
 gnu/packages/bioinformatics.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 51660026e..6cc808c6a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8280,3 +8280,27 @@ The package contains the original code written by the ISB, and a subset of the
 proteowizard library for mzML and mzIdentML.  The netCDF reading code has
 previously been used in XCMS.")
     (license license:artistic2.0)))
+
+(define-public r-affyio
+  (package
+    (name "r-affyio")
+    (version "1.44.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "affyio" version))
+       (sha256
+        (base32
+         "1svsl4mpk06xm505pap913x69ywks99262krag8y4ygpllj7dfyy"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-zlibbioc" ,r-zlibbioc)))
+    (inputs
+     `(("zlib" ,zlib)))
+    (home-page "https://github.com/bmbolstad/affyio")
+    (synopsis "Tools for parsing Affymetrix data files")
+    (description
+     "This package provides routines for parsing Affymetrix data files based
+upon file format information.  The primary focus is on accessing the CEL and
+CDF file formats.")
+    (license license:lgpl2.0+)))
-- 
2.11.0

[PATCH 11/16] gnu: Add r-affy.

[Ricardo Wurmus]

* gnu/packages/bioinformatics.scm (r-affy): New variable.
---
 gnu/packages/bioinformatics.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 6cc808c6a..9e073843e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8304,3 +8304,29 @@ previously been used in XCMS.")
 upon file format information.  The primary focus is on accessing the CEL and
 CDF file formats.")
     (license license:lgpl2.0+)))
+
+(define-public r-affy
+  (package
+    (name "r-affy")
+    (version "1.52.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "affy" version))
+       (sha256
+        (base32
+         "1snq71ligf0wvaxa6zfrl13ydw0zfhspmhdyfk8q3ba3np4cz344"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-affyio" ,r-affyio)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocinstaller" ,r-biocinstaller)
+       ("r-preprocesscore" ,r-preprocesscore)
+       ("r-zlibbioc" ,r-zlibbioc)))
+    (home-page "http://bioconductor.org/packages/affy")
+    (synopsis "Methods for affymetrix oligonucleotide arrays")
+    (description
+     "This package contains functions for exploratory oligonucleotide array
+analysis.")
+    (license license:lgpl2.0+)))
-- 
2.11.0

[PATCH 12/16] gnu: Add r-vsn.

[Ricardo Wurmus]

* gnu/packages/bioinformatics.scm (r-vsn): New variable.
---
 gnu/packages/bioinformatics.scm | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 9e073843e..82a60dae0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8330,3 +8330,36 @@ CDF file formats.")
      "This package contains functions for exploratory oligonucleotide array
 analysis.")
     (license license:lgpl2.0+)))
+
+(define-public r-vsn
+  (package
+    (name "r-vsn")
+    (version "3.42.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "vsn" version))
+       (sha256
+        (base32
+         "0mgl0azys2g90simf8wx6jdwd7gyg3m4pf12n6w6507jixm2cg97"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-affy" ,r-affy)
+       ("r-biobase" ,r-biobase)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-limma" ,r-limma)))
+    (home-page "http://bioconductor.org/packages/release/bioc/html/vsn.html")
+    (synopsis "Variance stabilization and calibration for microarray data")
+    (description
+     "The package implements a method for normalising microarray intensities,
+and works for single- and multiple-color arrays.  It can also be used for data
+from other technologies, as long as they have similar format.  The method uses
+a robust variant of the maximum-likelihood estimator for an
+additive-multiplicative error model and affine calibration.  The model
+incorporates data calibration step (a.k.a.  normalization), a model for the
+dependence of the variance on the mean intensity and a variance stabilizing
+data transformation.  Differences between transformed intensities are
+analogous to \"normalized log-ratios\".  However, in contrast to the latter,
+their variance is independent of the mean, and they are usually more sensitive
+and specific in detecting differential transcription.")
+    (license license:artistic2.0)))
-- 
2.11.0

[PATCH 13/16] gnu: Add r-mzid.

[Ricardo Wurmus]

* gnu/packages/bioinformatics.scm (r-mzid): New variable.
---
 gnu/packages/bioinformatics.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 82a60dae0..4952bbe33 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8363,3 +8363,33 @@ analogous to \"normalized log-ratios\".  However, in contrast to the latter,
 their variance is independent of the mean, and they are usually more sensitive
 and specific in detecting differential transcription.")
     (license license:artistic2.0)))
+
+(define-public r-mzid
+  (package
+    (name "r-mzid")
+    (version "1.12.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "mzID" version))
+       (sha256
+        (base32
+         "1zn896cpfvqp1qmq5c4vcj933hb8rxwb6gkck1wqvr7393rpqy1q"))))
+    (properties `((upstream-name . "mzID")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-doparallel" ,r-doparallel)
+       ("r-foreach" ,r-foreach)
+       ("r-iterators" ,r-iterators)
+       ("r-plyr" ,r-plyr)
+       ("r-protgenerics" ,r-protgenerics)
+       ("r-rcpp" ,r-rcpp)
+       ("r-xml" ,r-xml)))
+    (home-page "http://bioconductor.org/packages/mzID")
+    (synopsis "Parser for mzIdentML files")
+    (description
+     "This package provides a parser for mzIdentML files implemented using the
+XML package.  The parser tries to be general and able to handle all types of
+mzIdentML files with the drawback of having less pretty output than a vendor
+specific parser.")
+    (license license:gpl2+)))
-- 
2.11.0

[PATCH 14/16] gnu: Add r-pcamethods.

[Ricardo Wurmus]

* gnu/packages/bioinformatics.scm (r-pcamethods): New variable.
---
 gnu/packages/bioinformatics.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4952bbe33..bc7b0be1a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8393,3 +8393,32 @@ XML package.  The parser tries to be general and able to handle all types of
 mzIdentML files with the drawback of having less pretty output than a vendor
 specific parser.")
     (license license:gpl2+)))
+
+(define-public r-pcamethods
+  (package
+    (name "r-pcamethods")
+    (version "1.66.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "pcaMethods" version))
+       (sha256
+        (base32
+         "18mawhxw57pgpn87qha4mwki24gqja7wpqha8q496476vyap11xw"))))
+    (properties `((upstream-name . "pcaMethods")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-rcpp" ,r-rcpp)))
+    (home-page "https://github.com/hredestig/pcamethods")
+    (synopsis "Collection of PCA methods")
+    (description
+     "This package provides Bayesian PCA, Probabilistic PCA, Nipals PCA,
+Inverse Non-Linear PCA and the conventional SVD PCA.  A cluster based method
+for missing value estimation is included for comparison.  BPCA, PPCA and
+NipalsPCA may be used to perform PCA on incomplete data as well as for
+accurate missing value estimation.  A set of methods for printing and plotting
+the results is also provided.  All PCA methods make use of the same data
+structure (pcaRes) to provide a common interface to the PCA results.")
+    (license license:gpl3+)))
-- 
2.11.0

[PATCH 15/16] gnu: Add r-msnbase.

[Ricardo Wurmus]

* gnu/packages/bioinformatics.scm (r-msnbase): New variable.
---
 gnu/packages/bioinformatics.scm | 41 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index bc7b0be1a..abe5c9294 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8422,3 +8422,44 @@ accurate missing value estimation.  A set of methods for printing and plotting
 the results is also provided.  All PCA methods make use of the same data
 structure (pcaRes) to provide a common interface to the PCA results.")
     (license license:gpl3+)))
+
+(define-public r-msnbase
+  (package
+    (name "r-msnbase")
+    (version "2.0.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "MSnbase" version))
+       (sha256
+        (base32
+         "0jjjs29dcwsjaxzfqxy98ycpg3rwxzzchkj77my3cjgdc00sm66n"))))
+    (properties `((upstream-name . "MSnbase")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-affy" ,r-affy)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocparallel" ,r-biocparallel)
+       ("r-digest" ,r-digest)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-impute" ,r-impute)
+       ("r-iranges" ,r-iranges)
+       ("r-maldiquant" ,r-maldiquant)
+       ("r-mzid" ,r-mzid)
+       ("r-mzr" ,r-mzr)
+       ("r-pcamethods" ,r-pcamethods)
+       ("r-plyr" ,r-plyr)
+       ("r-preprocesscore" ,r-preprocesscore)
+       ("r-protgenerics" ,r-protgenerics)
+       ("r-rcpp" ,r-rcpp)
+       ("r-reshape2" ,r-reshape2)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-vsn" ,r-vsn)
+       ("r-xml" ,r-xml)))
+    (home-page "https://github.com/lgatto/MSnbase")
+    (synopsis "Base functions and classes for MS-based proteomics")
+    (description
+     "This package provides basic plotting, data manipulation and processing
+of MS-based proteomics data.")
+    (license license:artistic2.0)))
-- 
2.11.0

[PATCH 16/16] gnu: Add r-msnid.

[Ricardo Wurmus]

* gnu/packages/bioinformatics.scm (r-msnid): New variable.
---
 gnu/packages/bioinformatics.scm | 39 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index abe5c9294..c60bedce4 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8463,3 +8463,42 @@ structure (pcaRes) to provide a common interface to the PCA results.")
      "This package provides basic plotting, data manipulation and processing
 of MS-based proteomics data.")
     (license license:artistic2.0)))
+
+(define-public r-msnid
+  (package
+    (name "r-msnid")
+    (version "1.8.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "MSnID" version))
+       (sha256
+        (base32
+         "0fkk3za39cxi0jyxmagmycjdslr2xf6vg3ylz14jyffqi0blw9d5"))))
+    (properties `((upstream-name . "MSnID")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-data-table" ,r-data-table)
+       ("r-doparallel" ,r-doparallel)
+       ("r-dplyr" ,r-dplyr)
+       ("r-foreach" ,r-foreach)
+       ("r-iterators" ,r-iterators)
+       ("r-msnbase" ,r-msnbase)
+       ("r-mzid" ,r-mzid)
+       ("r-mzr" ,r-mzr)
+       ("r-protgenerics" ,r-protgenerics)
+       ("r-r-cache" ,r-r-cache)
+       ("r-rcpp" ,r-rcpp)
+       ("r-reshape2" ,r-reshape2)))
+    (home-page "http://bioconductor.org/packages/MSnID")
+    (synopsis "Utilities for LC-MSn proteomics identifications")
+    (description
+     "This package extracts MS/MS ID data from mzIdentML (leveraging the mzID
+package) or text files.  After collating the search results from multiple
+datasets it assesses their identification quality and optimize filtering
+criteria to achieve the maximum number of identifications while not exceeding
+a specified false discovery rate.  It also contains a number of utilities to
+explore the MS/MS results and assess missed and irregular enzymatic cleavages,
+mass measurement accuracy, etc.")
+    (license license:artistic2.0)))
-- 
2.11.0

Re: [PATCH 01/16] gnu: Add python-argparse.

[Hartmut Goebel]

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Am 17.01.2017 um 15:11 schrieb Ricardo Wurmus:
> * gnu/packages/python.scm (python-argparse, python2-argparse): New

As of Python >= 2.7 and >= 3.2, the argparse module is maintained within
the Python standard library. Why do we need a this package?


-- 
Regards
Hartmut Goebel

| Hartmut Goebel          | h.goebel@crazy-compilers.com               |
| www.crazy-compilers.com | compilers which you thought are impossible |


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Re: [PATCH 01/16] gnu: Add python-argparse.

[Ricardo Wurmus]

Hartmut Goebel <h.goebel@crazy-compilers.com> writes:

> Am 17.01.2017 um 15:11 schrieb Ricardo Wurmus:
>> * gnu/packages/python.scm (python-argparse, python2-argparse): New
>
> As of Python >= 2.7 and >= 3.2, the argparse module is maintained within
> the Python standard library. Why do we need a this package?

Turns out we don’t!  It used to be required by ribodiff, but that builds
fine without it (and my patch doesn’t include it).

So this should indeed be dropped.

-- 
Ricardo
 
GPG: BCA6 89B6 3655 3801 C3C6  2150 197A 5888 235F ACAC
https://elephly.net

Re: [PATCH 01/16] gnu: Add python-argparse.

[Alex Kost]

Ricardo Wurmus (2017-01-17 15:11 +0100) wrote:

[...]
> +(define-public python-argparse
> +  (package
> +    (name "python-argparse")
> +    (version "1.4.0")
> +    (source
> +     (origin
> +       (method url-fetch)
> +       (uri (pypi-uri "argparse" version))
> +       (sha256
> +        (base32
> +         "1r6nznp64j68ih1k537wms7h57nvppq0szmwsaf99n71bfjqkc32"))))
> +    (properties `((python2-variant . ,(delay python2-argparse))))
> +    (build-system python-build-system)
> +    (home-page "https://pypi.python.org/pypi/argparse/")
> +    (synopsis "Command-line parsing library")
> +    (description "The @code{argparse} module makes it easy to write user
> +friendly command line interfaces.  The program defines what arguments it
> +requires, and @code{argparse} will figure out how to parse those out of
> +@code{sys.argv}.  The @code{argparse} module also automatically generates help
> +and usage messages and issues errors when users give the program invalid
> +arguments.")
> +    (license (package-license python))))
> +
> +(define-public python2-argparse
> +  (package (inherit (package-with-python2
> +              (strip-python2-variant python-argparse)))

I would adjust the indentation here simply by moving "(inherit ..." to
the next line.

> +    (native-inputs
> +     `(("python2-setuptools" ,python2-setuptools)))))
> +
>  (define-public python-ndg-httpsclient
>    (package
>      (name "python-ndg-httpsclient")

-- 
Alex

Re: [PATCH 01/16] gnu: Add python-argparse.

[Alex Kost]

Ricardo Wurmus (2017-01-17 16:26 +0100) wrote:

> Hartmut Goebel <h.goebel@crazy-compilers.com> writes:
>
>> Am 17.01.2017 um 15:11 schrieb Ricardo Wurmus:
>>> * gnu/packages/python.scm (python-argparse, python2-argparse): New
>>
>> As of Python >= 2.7 and >= 3.2, the argparse module is maintained within
>> the Python standard library. Why do we need a this package?
>
> Turns out we don’t!  It used to be required by ribodiff, but that builds
> fine without it (and my patch doesn’t include it).
>
> So this should indeed be dropped.

Oops, then ignore my previous message about indentation :-)

-- 
Alex

Re: [PATCH 02/16] gnu: Add hisat2.

[Leo Famulari]

On Tue, Jan 17, 2017 at 03:11:27PM +0100, Ricardo Wurmus wrote:
> * gnu/packages/bioinformatics.scm (hisat2): New variable.

> +       #:make-flags (list "CC=gcc" "CXX=g++" "allall")

"allall"... We can categorize this alongside -Weverything! ;)

> +         (add-after 'unpack 'make-deterministic
> +           (lambda _
> +             (substitute* "Makefile"
> +               (("`date`") "0"))

I'd take the value of SOURCE_DATE_EPOCH from the environment, but it's
not very important.

Re: [PATCH 02/16] gnu: Add hisat2.

[Ricardo Wurmus]

Leo Famulari <leo@famulari.name> writes:

> On Tue, Jan 17, 2017 at 03:11:27PM +0100, Ricardo Wurmus wrote:
>> * gnu/packages/bioinformatics.scm (hisat2): New variable.
>
>> +       #:make-flags (list "CC=gcc" "CXX=g++" "allall")
>
> "allall"... We can categorize this alongside -Weverything! ;)
>
>> +         (add-after 'unpack 'make-deterministic
>> +           (lambda _
>> +             (substitute* "Makefile"
>> +               (("`date`") "0"))
>
> I'd take the value of SOURCE_DATE_EPOCH from the environment, but it's
> not very important.

Oh, I’m sorry.  I have just pushed based on Marius’s review and didn’t
see your message in time.  I’ll keep SOURCE_DATE_EPOCH in mind for
future cases.

--
Ricardo

GPG: BCA6 89B6 3655 3801 C3C6  2150 197A 5888 235F ACAC
https://elephly.net

Re: [PATCH 06/16] gnu: Add r-raremetals2.

[Ludovic Courtès]

Ricardo Wurmus <rekado@elephly.net> skribis:

> * gnu/packages/bioinformatics.scm (r-raremetals2): New variable.

[...]

> +    (home-page "http://genome.sph.umich.edu/wiki/RareMETALS2")
> +    (synopsis "Analyze gene-level association tests for binary trait")
> +    (description
> +     "The R package rareMETALS2 is an extension of the R package rareMETALS.
> +It was designed to meta-analyze gene-level association tests for binary trait.
> +While rareMETALS offers a near-complete solution for meta-analysis of
> +gene-level tests for quantitative trait, it does not offer the optimal
> +solution for binary trait.  The package rareMETALS2 offers improved features
> +for analyzing gene-level association tests in meta-analyses for binary
> +trait.")
> +    (license license:gpl3)))

The only piece of licensing info I could find is this line in
‘DESCRIPTION’:

  License: GPL3

Does that mean “version 3 only” or “any later version”?

Otherwise LGTM, thanks!

Ludo’.

Re: [PATCH 15/16] gnu: Add r-msnbase.

[Ludovic Courtès]

Ricardo Wurmus <rekado@elephly.net> skribis:

> * gnu/packages/bioinformatics.scm (r-msnbase): New variable.

[...]

> +    (synopsis "Base functions and classes for MS-based proteomics")
> +    (description
> +     "This package provides basic plotting, data manipulation and processing
> +of MS-based proteomics data.")

Please expand “MS” at least in the description.

Otherwise LGTM, thanks!

Re: [PATCH 15/16] gnu: Add r-msnbase.

[Ludovic Courtès]

I quickly looked at the other patches in the series and didn’t notice
anything particular.  I’d say go ahead!

Ludo’.

Re: [PATCH 06/16] gnu: Add r-raremetals2.

[Ricardo Wurmus]

Ludovic Courtès <ludo@gnu.org> writes:

> Ricardo Wurmus <rekado@elephly.net> skribis:
>
>> * gnu/packages/bioinformatics.scm (r-raremetals2): New variable.
>
> [...]
>
>> +    (home-page "http://genome.sph.umich.edu/wiki/RareMETALS2")
>> +    (synopsis "Analyze gene-level association tests for binary trait")
>> +    (description
>> +     "The R package rareMETALS2 is an extension of the R package rareMETALS.
>> +It was designed to meta-analyze gene-level association tests for binary trait.
>> +While rareMETALS offers a near-complete solution for meta-analysis of
>> +gene-level tests for quantitative trait, it does not offer the optimal
>> +solution for binary trait.  The package rareMETALS2 offers improved features
>> +for analyzing gene-level association tests in meta-analyses for binary
>> +trait.")
>> +    (license license:gpl3)))
>
> The only piece of licensing info I could find is this line in
> ‘DESCRIPTION’:
>
>   License: GPL3
>
> Does that mean “version 3 only” or “any later version”?

It means “version 3 only”.  To indicate “any later version” the
DESCRIPTION file would have to state “GPL (>= 3)”.  The importer knows
about these conventions and generally does the right thing.  (It didn’t
always do that in the past, though.)

-- 
Ricardo

GPG: BCA6 89B6 3655 3801 C3C6  2150 197A 5888 235F ACAC
https://elephly.net

Re: [PATCH 06/16] gnu: Add r-raremetals2.

[Ludovic Courtès]

Ricardo Wurmus <rekado@elephly.net> skribis:

> Ludovic Courtès <ludo@gnu.org> writes:
>
>> Ricardo Wurmus <rekado@elephly.net> skribis:
>>
>>> * gnu/packages/bioinformatics.scm (r-raremetals2): New variable.
>>
>> [...]
>>
>>> +    (home-page "http://genome.sph.umich.edu/wiki/RareMETALS2")
>>> +    (synopsis "Analyze gene-level association tests for binary trait")
>>> +    (description
>>> +     "The R package rareMETALS2 is an extension of the R package rareMETALS.
>>> +It was designed to meta-analyze gene-level association tests for binary trait.
>>> +While rareMETALS offers a near-complete solution for meta-analysis of
>>> +gene-level tests for quantitative trait, it does not offer the optimal
>>> +solution for binary trait.  The package rareMETALS2 offers improved features
>>> +for analyzing gene-level association tests in meta-analyses for binary
>>> +trait.")
>>> +    (license license:gpl3)))
>>
>> The only piece of licensing info I could find is this line in
>> ‘DESCRIPTION’:
>>
>>   License: GPL3
>>
>> Does that mean “version 3 only” or “any later version”?
>
> It means “version 3 only”.  To indicate “any later version” the
> DESCRIPTION file would have to state “GPL (>= 3)”.  The importer knows
> about these conventions and generally does the right thing.  (It didn’t
> always do that in the past, though.)

Oh, perfect then.

Ludo’.