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staging.scm
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;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2015-2024 Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
;;; Copyright © 2017 CM Massimo <carlomaria.massimo@mdc-berlin.de>
;;; Copyright © 2018, 2019, 2021 Marcel Schilling <marcel.schilling@uni-luebeck.de>
;;; Copyright © 2019, 2020 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
;;;
;;; This file is NOT part of GNU Guix, but is supposed to be used with GNU
;;; Guix and thus has the same license.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; GNU Guix is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
(define-module (bimsb packages staging)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix packages)
#:use-module (guix gexp)
#:use-module (guix deprecation)
#:use-module (guix download)
#:use-module (guix git-download)
#:use-module (guix hg-download)
#:use-module (guix utils)
#:use-module (guix build utils)
#:use-module (guix build-system ant)
#:use-module (guix build-system cmake)
#:use-module (guix build-system gnu)
#:use-module (guix build-system perl)
#:use-module (guix build-system python)
#:use-module (guix build-system pyproject)
#:use-module (guix build-system r)
#:use-module (gnu packages)
#:use-module (gnu packages algebra)
#:use-module (gnu packages autotools)
#:use-module ((gnu packages base) #:hide (which))
#:use-module (gnu packages bash)
#:use-module (gnu packages boost)
#:use-module (gnu packages check)
#:use-module (gnu packages compression)
#:use-module (gnu packages cmake)
#:use-module (gnu packages cran)
#:use-module (gnu packages curl)
#:use-module (gnu packages dlang)
#:use-module (gnu packages bioinformatics)
#:use-module (gnu packages bioconductor)
#:use-module (gnu packages databases)
#:use-module (gnu packages datastructures)
#:use-module (gnu packages docbook)
#:use-module (gnu packages documentation)
#:use-module (gnu packages fabric-management)
#:use-module (gnu packages gawk)
#:use-module (gnu packages gcc)
#:use-module (gnu packages gd)
#:use-module (gnu packages ghostscript)
#:use-module (gnu packages gtk)
#:use-module (gnu packages guile)
#:use-module (gnu packages graph)
#:use-module (gnu packages haskell)
#:use-module (gnu packages haskell-xyz)
#:use-module (gnu packages image)
#:use-module (gnu packages imagemagick)
#:use-module (gnu packages java)
#:use-module (gnu packages jemalloc)
#:use-module (gnu packages linux)
#:use-module (gnu packages llvm)
#:use-module (gnu packages logging)
#:use-module (gnu packages machine-learning)
#:use-module (gnu packages maths)
#:use-module (gnu packages mpi)
#:use-module (gnu packages multiprecision)
#:use-module (gnu packages perl)
#:use-module (gnu packages perl-check)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages popt)
#:use-module (gnu packages protobuf)
#:use-module (gnu packages python)
#:use-module (gnu packages python-build)
#:use-module (gnu packages python-crypto)
#:use-module (gnu packages python-science)
#:use-module (gnu packages python-web)
#:use-module (gnu packages python-xyz)
#:use-module (gnu packages qt)
#:use-module (gnu packages readline)
#:use-module (gnu packages ruby)
#:use-module (gnu packages serialization)
#:use-module (gnu packages shells)
#:use-module (gnu packages statistics)
#:use-module (gnu packages swig)
#:use-module (gnu packages tbb)
#:use-module (gnu packages tex)
#:use-module (gnu packages time)
#:use-module (gnu packages tls)
#:use-module (gnu packages valgrind)
#:use-module (gnu packages video)
#:use-module (gnu packages web)
#:use-module (gnu packages wxwidgets)
#:use-module (gnu packages xml)
#:use-module (gnu packages xorg)
#:use-module (past packages bioinformatics)
#:use-module (guix-science packages rstudio)
#:use-module ((srfi srfi-1) #:select (alist-delete)))
(define-public rstudio-server
(@ (guix-science packages rstudio) rstudio-server))
(define-public rstudio-server-bimsb
(deprecated-package "rstudio-server-bimsb"
(@ (guix-science packages rstudio) rstudio-server-multi-version)))
(define-public rstudio
(@ (guix-science packages rstudio) rstudio))
(define-public transat
(package
(name "transat")
(version "2.0")
(source
(origin
(method url-fetch/tarbomb)
;; FIXME: without this field "url-fetch/tarbomb" fails
(file-name (string-append name "-" version ".tgz"))
(uri (string-append "http://www.e-rna.org/transat/download/"
"transat_v" version ".tgz"))
(sha256
(base32
"0z754slkl6ijz3g8d7wjyqwaq1gb4cx3csfx4gyrvlg14wagjpm6"))))
(build-system cmake-build-system)
(arguments
`(#:tests? #f ; no tests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'change-dir
(lambda _ (chdir "src") #t))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(bin (string-append out "/bin")))
(mkdir-p bin)
(install-file "Transat" bin)
#t))))))
(home-page "http://www.e-rna.org/transat/")
(synopsis "Detect conserved helices of functional RNA structures")
(description "Transat detects conserved helices of high
statistical significance in functional RNA, including pseudo-knotted,
transient and alternative structures. Given a multiple sequence
alignment, Transat will recover all possible helices and determine the
statistical probability of the helix existing based on its
phylogeny-based evolutionary likelihood.")
(license license:gpl3+)))
(define-public rnadecoder
(package
(name "rnadecoder")
(version "1.0")
(source
(origin
(method url-fetch)
;; FIXME: there are no versioned tarballs
(uri (string-append "http://www.e-rna.org/rnadecoder/download/"
"rnadecoder.tar.bz2"))
(sha256
(base32
"1ml1bbil0gm2w9knx85kvkjwm7598313a5jy9fmavbsmwx7p3v0j"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; no tests
#:phases
(modify-phases %standard-phases
(delete 'patch-source-shebangs)
(delete 'configure)
(delete 'build)
(delete 'patch-shebangs)
(add-after 'unpack 'change-dir
(lambda _ (chdir "bin") #t))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(bin (string-append out "/bin")))
(mkdir-p bin)
(install-file "RNA-decoder" bin)
#t))))))
(home-page "http://www.e-rna.org/rnadecoder/")
(synopsis "Find and fold RNA secondary structures in protein-coding regions")
(description "RNA-Decoder is a comparative method to find and fold
RNA secondary structures in protein-coding regions. It explicitly
takes the known protein-coding context of an RNA-sequence alignment
into account in order to predict evolutionarily conserved
secondary-structure elements, which may span both coding and
non-coding regions.")
(license license:gpl3+)))
(define-public rapidstorm
(let ((commit "f912ad5689220c32844fd8faa36d521a89271e60")
(revision "0"))
(package
(name "rapidstorm")
(version (git-version "3.3.1" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/stevewolter/rapidSTORM.git")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"0kngg83g6f4kcj2b656mgg4kgh2frinwwbgh5gjxkfiw01573rsi"))))
(build-system gnu-build-system)
(arguments
`(#:make-flags (list "XSLT_FLAGS=--nonet --novalid"
"BIB2XML=touch")
;; There is one test and it fails because runtest cannot be
;; found. It also says this:
;; Test setup error: test unit with name 'gaussian_psf'
;; registered multiple times in the test suite 'Master
;; Test Suite'
#:tests? #f
#:configure-flags
(list "--enable-documentation=no")
#:phases
(modify-phases %standard-phases
(add-before 'build 'build-guilabels
(lambda _
(with-directory-excursion "doc"
(invoke "xsltproc"
"--nonet"
"--novalid"
"--path" ".:"
"--xinclude"
"-o" "guilabels.h" "rapidstorm_guilabels.xsl"
"./rapidstorm.xml"))))
(add-after 'unpack 'fix-doc
(lambda _
;; TODO: something's wrong with entities. Not sure what,
;; so I'll just remove them for now.
(substitute* '("doc/rapidstorm.xml"
"doc/ui.xml"
"doc/usage-examples.xml"
"doc/input-options.xml"
"doc/engine_options.xml"
"doc/output-options.xml"
"doc/fundamentals.xml")
(("%version;") "")
(("&marketingversion;") "TODO")
(("&publicationyear;") "2016")
(("&publicationdate;") "2016")
(("ä") "a")
(("ü") "u")
(("é") "e")
(("%isopub;") "")
(("%isonum;") "")
(("%isogrk1;") "")
(("%isolat1;") "")
(("&lgr;") "l")
(("&mgr;") "m")
(("&Dgr;") "D")
(("&sgr;") "s")
(("&ohgr;") "oh")
(("…") "...")
(("·") ""))
#t))
(add-after 'unpack 'fix-build-system
(lambda _
(substitute* "Makefile.am"
(("doxygen-doc") ""))
(with-output-to-file "README" (const #t))
#t)))))
(inputs
`(("boost" ,boost)
;; FIXME: the build fails when protobuf is used:
;; tsf/Output.cpp: In member function ?virtual dStorm::output::Output::RunRequirements dStorm::tsf::{anonymous}::Output::announce_run(const dStorm::output::Output::RunAnnouncement&)?:
;; tsf/Output.cpp:85:56: error: variable ?google::protobuf::io::CodedOutputStream coded_output? has initializer but incomplete type
;; google::protobuf::io::CodedOutputStream coded_output(file.get());
;;("protobuf" ,protobuf)
("eigen" ,eigen)
("gsl" ,gsl)
("tinyxml" ,tinyxml)
("libtiff" ,libtiff)
("wxwidgets" ,wxwidgets-2)
("graphicsmagick" ,graphicsmagick)
("zlib" ,zlib)))
(native-inputs
`(("autoconf" ,autoconf)
("autoconf-archive" ,autoconf-archive)
("automake" ,automake)
("libtool" ,libtool)
("pkg-config" ,pkg-config)
;; For documentation
("docbook-xml" ,docbook-xml-4.2)
("docbook-xsl" ,docbook-xsl)
("doxygen" ,doxygen)
("libxslt" ,libxslt)
("texlive" ,texlive-tiny)
("zip" ,zip)))
(home-page "https://stevewolter.github.io/rapidSTORM/")
(synopsis "Process single-molecule localization microscopy data")
(description "RapidSTORM provides fast and highly configurable
data processing for single-molecule localization microscopy such as
dSTORM. It provides both two-dimensional and three-dimensional,
multi-color data analysis as well as a wide range of filtering and
image generation capabilities.")
;; Documentation is under fdl1.3+, most of rapidstorm is released
;; under GPL; parts are released under LGPL.
(license (list license:gpl3+
license:lgpl3+
license:fdl1.3+)))))
(define-public circ-explorer
(package
(name "circ-explorer")
(version "1.1.10")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/YangLab/CIRCexplorer.git")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"1d98xmc5pmbzgrzpmb68q20p2qphaa2qfrsnhmqj4nsss25gh1aa"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'patch-imports
(lambda _
(substitute* "circ/CIRCexplorer.py"
(("from genomic_interval import Interval")
"from circ.genomic_interval import Interval"))
(substitute* (find-files "test" "\\.py")
(("from utils import")
"from .utils import")))))))
(inputs
(list python-pysam python-docopt))
(native-inputs
(list python-setuptools))
(home-page "https://github.com/YangLab/CIRCexplorer")
(synopsis "Tool to identify circular RNAs")
(description "CIRCexplorer implements a combined strategy to
identify genomic junction reads from back spliced exons and intron
lariats.")
(license license:expat)))
(define-public python-fastcluster
(package
(inherit r-fastcluster)
(name "python-fastcluster")
(build-system python-build-system)
(arguments
`(#:tests? #f
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'chdir
(lambda _ (chdir "src/python") #t)))))
(propagated-inputs
`(("python-numpy" ,python-numpy)))))
(define-public python-biomagic
(deprecated-package "python-biomagic" python-magic-impute))
(define-public mageck
(package
(name "mageck")
(version "0.5.9.3")
(source (origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/mageck/"
(version-major+minor version)
"/mageck-" version ".tar.gz"))
(sha256
(base32
"1rvbvwr1jsnijy6pplqgzcz0k05ksbparvl6zkdfxfxfg80142ql"))
(snippet
'(begin
(delete-file "bin/RRA")
(delete-file "bin/mageckGSEA")))))
(build-system python-build-system)
(arguments
(list
#:use-setuptools? #f
#:modules '((guix build python-build-system)
(guix build utils)
(srfi srfi-1)
(ice-9 match))
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'use-python3
(lambda _
(substitute* "bin/mageck"
(("python2") "python"))))
(add-before 'build 'build-rra-and-gsea
(lambda _
(with-directory-excursion "rra"
(invoke "make"))
(with-directory-excursion "gsea"
(invoke "make"))))
(delete 'check)
(add-after 'wrap 'check
(lambda _
(let ((tests '(("demo1" "run.sh")
("demo2" "runmageck.sh")
("demo3" "run.sh")
("demo4" "run.sh"))))
(setenv "PATH"
(string-append #$output "/bin:"
(getenv "PATH")))
(for-each (match-lambda
((dir script)
(with-directory-excursion (string-append "demo/" dir)
(invoke "bash" script))))
tests)))))))
(inputs
(list python-numpy
python-scipy
python-matplotlib
python-statsmodels
python-pyqt
r-minimal
r-xtable
r-gplots))
(home-page "http://mageck.sourceforge.net")
(synopsis "Model-based analysis of genome-wide CRISPR-Cas9 Knockout")
(description
"Model-based Analysis of Genome-wide CRISPR-Cas9
Knockout (MAGeCK) is a computational tool to identify important genes
from the recent genome-scale CRISPR-Cas9 knockout screens
technology. Its features include:
@enumerate
@item Simple, easy to use pipeline to screen genes in Genome-wide
CRISPR-Cas9 Knockout experiments;
@item High sensitivity and low false discovery rate;
@item Fully utilize the screening data by performing both positive and
negative screening in one dataset;
@item Provide statistical evaluation in genes, sgRNAs and pathways;
@item Require as few as 2 samples;
@item Identify cell-type specific targets;
@item A set of visualization features that generate publication
standard figures.
@end enumerate\n")
;; It's unclear which BSD variant it is, because no copy of the
;; license text is included.
(license license:bsd-3)))
(define-public squid
(deprecated-package "squid" eddylab-squid))
(define-public python-multicore-tsne
(let ((commit "e1a40182068d4815e7fbe523db266caab20773ff")
(revision "1"))
(package
(name "python-multicore-tsne")
(version (git-version "0" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/DmitryUlyanov/Multicore-TSNE.git")
(commit commit)))
(sha256
(base32
"1k5vvsak19ap75rvanll0k71j5fi4kpyj83rl1006v4h04hwv1x6"))))
(build-system python-build-system)
;; Tests need python-cffi and pypi/psutils (the latter not in
;; guix)
(arguments `(#:tests? #f))
(native-inputs
`(("cmake" ,cmake)))
(home-page "https://github.com/DmitryUlyanov/Multicore-TSNE")
(synopsis "Parallel t-SNE implementation with Python and Torch wrappers")
(description
"This package contains a multicore Barnes-Hut implementation of
the t-SNE algorithm. The implementation is described here:
@url{http://lvdmaaten.github.io/publications/papers/JMLR_2014.pdf}.")
(license license:bsd-3))))
(define-public footprint-pipeline
(package
(name "footprint-pipeline")
(version "1.0.1")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/aslihankarabacak/FootprintPipeline/")
(commit "6ff3646e71203e1147f0c9e99dab930905fb6763")))
(file-name (git-file-name name version))
(sha256
(base32
"1bzl5v09jz1lxlp6nhc3cnfg9kl74gs90vrdyj51l02jzcxahx4f"))))
(build-system gnu-build-system)
(arguments
(list
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'fix-build-system
(lambda _
;; The checks for R packages fail.
(substitute* "configure.ac"
(("AX_R_PACKAGE.*") "echo skip\n"))
(delete-file "configure")
(with-output-to-file "VERSION"
(lambda () (display #$version)))))
(add-after 'configure 'fix-broken-shebang
(lambda _
(substitute* "run_footprinting.R.in"
(("@RSCRIPT@") (which "Rscript")))))
(add-after 'install 'wrap-executable
(lambda _
(wrap-program (string-append #$output "/bin/find_footprints.sh")
`("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))))))))
(inputs
(list r-minimal
r-mixtools
r-gtools
r-genomicranges
perl
samtools-1.1
bedtools-2.18))
(native-inputs (list autoconf automake))
(home-page "https://ohlerlab.mdc-berlin.de/software/Reproducible_footprinting_139/")
(synopsis "Find transcription factor footprints in ATAC-seq or DNase-seq data")
(description "This is a pipeline to find transcription factor
footprints in ATAC-seq or DNase-seq data.")
(license license:gpl2+)))
(define-public samstat
(package
(name "samstat")
(version "1.5.1")
(source (origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/samstat/"
"samstat-" version ".tar.gz"))
(sha256
(base32
"0hq5fsialpdv4dnhzws3nwiwzhhlhnf1438vg8h81yr63f84dw66"))))
(build-system gnu-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'embed-samtools-path
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "src/io.c"
(("samtools")
(string-append (assoc-ref inputs "samtools")
"/bin/samtools")))
#t)))))
(inputs
`(("samtools" ,samtools)))
(home-page "http://samstat.sourceforge.net/")
(synopsis "Sequence statistics for next generation sequencing")
(description "SAMStat displays various properties of
next-generation genomic sequencing reads stored in SAM/BAM format.")
(license license:gpl3+)))
(define-public python-ont-tombo
(deprecated-package "python-ont-tombo"
(@ (gnu packages bioinformatics) tombo)))
(define-public kissplice
(package
(name "kissplice")
(version "2.4.0-p1")
(source (origin
(method url-fetch)
(uri (string-append "ftp://pbil.univ-lyon1.fr/pub/logiciel/"
"kissplice/download/kissplice-"
version ".tar.gz"))
(sha256
(base32
"1xvn2rjb8c009i6xrsx904i0kbyb7wyqhgsw5ax0xcfh9i29nmpl"))))
(build-system cmake-build-system)
(inputs
`(("zlib" ,zlib)
("python" ,python-2)))
(home-page "http://kissplice.prabi.fr/")
(synopsis "De-novo calling alternative splicing events from RNA-seq data")
(description "This package provides a program whose purpose is to
detect alternative splicing events from RNA-seq data.")
(license license:cecill)))
(define-public idr-legacy
(package
(name "idr-legacy")
(version "0")
(source (origin
(method url-fetch)
(uri "https://docs.google.com/uc?export=download&id=0B_ssVVyXv8ZSX3luT0xhV3ZQNWc")
(file-name (string-append "idr-legacy-" version ".tar.gz"))
(sha256
(base32
"1d4zxh860in3sf6nkwwz427srh8p3hx35a7x1izbf73hlfbjk6a5"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; there are no tests
#:phases
(modify-phases %standard-phases
(delete 'configure)
(delete 'build)
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(share (string-append out "/share/idr-legacy")))
(substitute* '("batch-consistency-plot.r"
"batch-consistency-plot-merged2.r"
"batch-consistency-analysis.r")
(("source\\(\"functions-all-clayton-12-13.r\"\\)")
(string-append "source(\"" share "/functions-all-clayton-12-13.r\")")))
(mkdir-p share)
(copy-recursively "." share)
#t))))))
(propagated-inputs
`(("bash" ,bash)
("coreutils" ,coreutils)
("gawk" ,gawk)
("grep" ,grep)
("r-minimal" ,r-minimal)))
(home-page "https://sites.google.com/site/anshulkundaje/projects/idr/deprecated")
(synopsis "Legacy pipeline for measuring the Irreproducible Discovery Rate")
(description "The IDR (Irreproducible Discovery Rate) framework is
a unified approach to measure the reproducibility of findings
identified from replicate experiments and provide highly stable
thresholds based on reproducibility. This package provides the
original implementation of a pipeline using this method.")
(license license:gpl2+)))
(define-public openmpi-with-hwloc2
(package (inherit openmpi)
(name "openmpi-with-hwloc2")
(arguments
(substitute-keyword-arguments (package-arguments openmpi)
((#:configure-flags flags)
`(cons* "--enable-orterun-prefix-by-default"
"--with-orte"
,flags))))
(inputs
`(("hwloc" ,hwloc-2 "lib")
,@(package-inputs openmpi)))))
(define-public openmpi-psm-only
(package (inherit openmpi)
(name "openmpi-psm-only")
(arguments
(substitute-keyword-arguments (package-arguments openmpi)
((#:configure-flags flags)
`(cons* "--enable-orterun-prefix-by-default"
"--with-orte"
"--with-psm"
,flags))))
(inputs
`(("hwloc" ,hwloc-2 "lib")
("psm" ,psm)
,@(alist-delete "psm2" (package-inputs openmpi))))))
(define-public openmpi-psm2-only
(package (inherit openmpi)
(name "openmpi-psm2-only")
(arguments
(substitute-keyword-arguments (package-arguments openmpi)
((#:configure-flags flags)
`(cons* "--enable-orterun-prefix-by-default"
"--with-orte"
"--with-psm2"
,flags))))
(inputs
`(("hwloc" ,hwloc-2 "lib")
("psm2" ,psm2)
,@(alist-delete "psm" (package-inputs openmpi))))))
(define-public r-dsa
(let ((commit "f181f549fd86feb58955f11e53ee38da67ac4f5e")
(revision "1"))
(package
(name "r-dsa")
(version (git-version "1.0" revision commit))
(source (origin
(method url-fetch)
(uri (string-append
"https://github.com/zhandong/DSA/raw/" commit "/"
"Package/version_" version "/"
"DSA_" version ".tar.gz"))
(sha256
(base32
"1m2g760lwyxzqm7vxp5j1haw2qldgysbfj86w27h15adj604129z"))))
(build-system r-build-system)
(home-page "https://github.com/zhandong/DSA")
(synopsis "Digital sorting algorithm")
(description
"This package provides functions to implement the @dfn{Digital sorting
algorithm} (DSA) for extracting cell-type specific gene expression profiles
from mixed tissue samples.")
(license license:gpl2))))