mirror of
https://codeberg.org/guix/guix.git
synced 2025-10-02 02:15:12 +00:00
Merge branch 'master' into core-updates
This commit is contained in:
Mark H Weaver
commit
a102d359a6
66 changed files with 1928 additions and 363 deletions
|
|
@ -1,10 +1,10 @@
|
|||
;;; GNU Guix --- Functional package management for GNU
|
||||
;;; Copyright © 2014, 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
|
||||
;;; Copyright © 2014, 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
|
||||
;;; Copyright © 2015, 2016, 2017 Ben Woodcroft <donttrustben@gmail.com>
|
||||
;;; Copyright © 2015, 2016 Pjotr Prins <pjotr.guix@thebird.nl>
|
||||
;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
|
||||
;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
|
||||
;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
|
||||
;;; Copyright © 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
|
||||
;;; Copyright © 2016 Marius Bakke <mbakke@fastmail.com>
|
||||
;;; Copyright © 2016 Raoul Bonnal <ilpuccio.febo@gmail.com>
|
||||
;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
|
||||
|
|
@ -71,6 +71,7 @@
|
|||
#:use-module (gnu packages image)
|
||||
#:use-module (gnu packages imagemagick)
|
||||
#:use-module (gnu packages java)
|
||||
#:use-module (gnu packages jemalloc)
|
||||
#:use-module (gnu packages ldc)
|
||||
#:use-module (gnu packages linux)
|
||||
#:use-module (gnu packages logging)
|
||||
|
|
@ -3433,7 +3434,7 @@ sometimes better. Khmer can also identify and fix problems with shotgun
|
|||
data.")
|
||||
;; When building on i686, armhf and mips64el, we get the following error:
|
||||
;; error: ['khmer', 'khmer.tests', 'oxli'] require 64-bit operating system
|
||||
(supported-systems '("x86_64-linux"))
|
||||
(supported-systems '("x86_64-linux" "aarch64-linux"))
|
||||
(license license:bsd-3)))
|
||||
|
||||
(define-public kaiju
|
||||
|
|
@ -5562,6 +5563,11 @@ application of SortMeRNA is filtering rRNA from metatranscriptomic data.")
|
|||
(modify-phases %standard-phases
|
||||
(add-after 'unpack 'enter-source-dir
|
||||
(lambda _ (chdir "source") #t))
|
||||
(add-after 'enter-source-dir 'make-reproducible
|
||||
(lambda _
|
||||
(substitute* "Makefile"
|
||||
(("(COMPILATION_TIME_PLACE=\")(.*)(\")" _ pre mid post)
|
||||
(string-append pre "Built with Guix" post)))))
|
||||
(add-after 'enter-source-dir 'do-not-use-bundled-htslib
|
||||
(lambda _
|
||||
(substitute* "Makefile"
|
||||
|
|
@ -11106,3 +11112,463 @@ for alignment. Pseudoalignment of reads preserves the key information needed
|
|||
for quantification, and kallisto is therefore not only fast, but also as
|
||||
accurate as existing quantification tools.")
|
||||
(license license:bsd-2)))
|
||||
|
||||
(define-public libgff
|
||||
(package
|
||||
(name "libgff")
|
||||
(version "1.0")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append
|
||||
"https://github.com/Kingsford-Group/"
|
||||
"libgff/archive/v" version ".tar.gz"))
|
||||
(file-name (string-append name "-" version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"0vc4nxyhlm6g9vvmx5l4lfs5pnvixsv1hiiy4kddf2y3p6jna8ls"))))
|
||||
(build-system cmake-build-system)
|
||||
(arguments `(#:tests? #f)) ; no tests included
|
||||
(home-page "https://github.com/Kingsford-Group/libgff")
|
||||
(synopsis "Parser library for reading/writing GFF files")
|
||||
(description "This is a simple \"libraryfication\" of the GFF/GTF parsing
|
||||
code that is used in the Cufflinks codebase. The goal of this library is to
|
||||
provide this functionality without the necessity of drawing in a heavy-weight
|
||||
dependency like SeqAn.")
|
||||
(license (license:x11-style "http://www.boost.org/LICENSE_1_0.txt"))))
|
||||
|
||||
(define-public libdivsufsort
|
||||
(package
|
||||
(name "libdivsufsort")
|
||||
(version "2.0.1")
|
||||
(source (origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/y-256/libdivsufsort.git")
|
||||
(commit version)))
|
||||
(sha256
|
||||
(base32
|
||||
"0fgdz9fzihlvjjrxy01md1bv9vh12rkgkwbm90b1hj5xpbaqp7z2"))))
|
||||
(build-system cmake-build-system)
|
||||
(arguments
|
||||
'(#:tests? #f ; there are no tests
|
||||
#:configure-flags
|
||||
;; Needed for rapmap and sailfish.
|
||||
'("-DBUILD_DIVSUFSORT64=ON")))
|
||||
(home-page "https://github.com/y-256/libdivsufsort")
|
||||
(synopsis "Lightweight suffix-sorting library")
|
||||
(description "libdivsufsort is a software library that implements a
|
||||
lightweight suffix array construction algorithm. This library provides a
|
||||
simple and an efficient C API to construct a suffix array and a
|
||||
Burrows-Wheeler transformed string from a given string over a constant-size
|
||||
alphabet. The algorithm runs in O(n log n) worst-case time using only 5n+O(1)
|
||||
bytes of memory space, where n is the length of the string.")
|
||||
(license license:expat)))
|
||||
|
||||
(define-public sailfish
|
||||
(package
|
||||
(name "sailfish")
|
||||
(version "0.10.1")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri
|
||||
(string-append "https://github.com/kingsfordgroup/"
|
||||
"sailfish/archive/v" version ".tar.gz"))
|
||||
(file-name (string-append name "-" version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"1inn60dxiwsz8g9w7kvfhjxj4bwfb0r12dyhpzzhfbig712dkmm0"))
|
||||
(modules '((guix build utils)))
|
||||
(snippet
|
||||
'(begin
|
||||
;; Delete bundled headers for eigen3.
|
||||
(delete-file-recursively "include/eigen3/")
|
||||
#t))))
|
||||
(build-system cmake-build-system)
|
||||
(arguments
|
||||
`(#:configure-flags
|
||||
(list (string-append "-DBOOST_INCLUDEDIR="
|
||||
(assoc-ref %build-inputs "boost")
|
||||
"/include/")
|
||||
(string-append "-DBOOST_LIBRARYDIR="
|
||||
(assoc-ref %build-inputs "boost")
|
||||
"/lib/")
|
||||
(string-append "-DBoost_LIBRARIES="
|
||||
"-lboost_iostreams "
|
||||
"-lboost_filesystem "
|
||||
"-lboost_system "
|
||||
"-lboost_thread "
|
||||
"-lboost_timer "
|
||||
"-lboost_chrono "
|
||||
"-lboost_program_options")
|
||||
"-DBoost_FOUND=TRUE"
|
||||
;; Don't download RapMap---we already have it!
|
||||
"-DFETCHED_RAPMAP=1")
|
||||
;; Tests must be run after installation and the location of the test
|
||||
;; data file must be overridden. But the tests fail. It looks like
|
||||
;; they are not really meant to be run.
|
||||
#:tests? #f
|
||||
#:phases
|
||||
(modify-phases %standard-phases
|
||||
;; Boost cannot be found, even though it's right there.
|
||||
(add-after 'unpack 'do-not-look-for-boost
|
||||
(lambda* (#:key inputs #:allow-other-keys)
|
||||
(substitute* "CMakeLists.txt"
|
||||
(("find_package\\(Boost 1\\.53\\.0") "#"))))
|
||||
(add-after 'unpack 'do-not-assign-to-macro
|
||||
(lambda _
|
||||
(substitute* "include/spdlog/details/format.cc"
|
||||
(("const unsigned CHAR_WIDTH = 1;") ""))))
|
||||
(add-after 'unpack 'prepare-rapmap
|
||||
(lambda* (#:key inputs #:allow-other-keys)
|
||||
(let ((src "external/install/src/rapmap/")
|
||||
(include "external/install/include/rapmap/")
|
||||
(rapmap (assoc-ref inputs "rapmap")))
|
||||
(mkdir-p "/tmp/rapmap")
|
||||
(system* "tar" "xf"
|
||||
(assoc-ref inputs "rapmap")
|
||||
"-C" "/tmp/rapmap"
|
||||
"--strip-components=1")
|
||||
(mkdir-p src)
|
||||
(mkdir-p include)
|
||||
(for-each (lambda (file)
|
||||
(install-file file src))
|
||||
(find-files "/tmp/rapmap/src" "\\.(c|cpp)"))
|
||||
(copy-recursively "/tmp/rapmap/include" include))))
|
||||
(add-after 'unpack 'use-system-libraries
|
||||
(lambda* (#:key inputs #:allow-other-keys)
|
||||
(substitute* '("src/SailfishIndexer.cpp"
|
||||
"src/SailfishUtils.cpp"
|
||||
"src/SailfishQuantify.cpp"
|
||||
"src/FASTAParser.cpp"
|
||||
"include/PCA.hpp"
|
||||
"include/SailfishUtils.hpp"
|
||||
"include/SailfishIndex.hpp"
|
||||
"include/CollapsedEMOptimizer.hpp"
|
||||
"src/CollapsedEMOptimizer.cpp")
|
||||
(("#include \"jellyfish/config.h\"") ""))
|
||||
(substitute* "src/CMakeLists.txt"
|
||||
(("\\$\\{GAT_SOURCE_DIR\\}/external/install/include/jellyfish-2.2..")
|
||||
(string-append (assoc-ref inputs "jellyfish")
|
||||
"/include/jellyfish-" ,(package-version jellyfish)))
|
||||
(("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libjellyfish-2.0.a")
|
||||
(string-append (assoc-ref inputs "jellyfish")
|
||||
"/lib/libjellyfish-2.0.a"))
|
||||
(("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libdivsufsort.a")
|
||||
(string-append (assoc-ref inputs "libdivsufsort")
|
||||
"/lib/libdivsufsort.so"))
|
||||
(("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libdivsufsort64.a")
|
||||
(string-append (assoc-ref inputs "libdivsufsort")
|
||||
"/lib/libdivsufsort64.so")))
|
||||
(substitute* "CMakeLists.txt"
|
||||
;; Don't prefer static libs
|
||||
(("SET\\(CMAKE_FIND_LIBRARY_SUFFIXES.*") "")
|
||||
(("find_package\\(Jellyfish.*") "")
|
||||
(("ExternalProject_Add\\(libjellyfish") "message(")
|
||||
(("ExternalProject_Add\\(libgff") "message(")
|
||||
(("ExternalProject_Add\\(libsparsehash") "message(")
|
||||
(("ExternalProject_Add\\(libdivsufsort") "message("))
|
||||
|
||||
;; Ensure that Eigen headers can be found
|
||||
(setenv "CPLUS_INCLUDE_PATH"
|
||||
(string-append (getenv "CPLUS_INCLUDE_PATH")
|
||||
":"
|
||||
(assoc-ref inputs "eigen")
|
||||
"/include/eigen3")))))))
|
||||
(inputs
|
||||
`(("boost" ,boost)
|
||||
("eigen" ,eigen)
|
||||
("jemalloc" ,jemalloc)
|
||||
("jellyfish" ,jellyfish)
|
||||
("sparsehash" ,sparsehash)
|
||||
("rapmap" ,(origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/COMBINE-lab/RapMap.git")
|
||||
(commit (string-append "sf-v" version))))
|
||||
(file-name (string-append "rapmap-sf-v" version "-checkout"))
|
||||
(sha256
|
||||
(base32
|
||||
"1hv79l5i576ykv5a1srj2p0q36yvyl5966m0fcy2lbi169ipjakf"))
|
||||
(modules '((guix build utils)))
|
||||
;; These files are expected to be excluded.
|
||||
(snippet
|
||||
'(begin (delete-file-recursively "include/spdlog")
|
||||
(for-each delete-file '("include/xxhash.h"
|
||||
"src/xxhash.c"))))))
|
||||
("libdivsufsort" ,libdivsufsort)
|
||||
("libgff" ,libgff)
|
||||
("tbb" ,tbb)
|
||||
("zlib" ,zlib)))
|
||||
(native-inputs
|
||||
`(("pkg-config" ,pkg-config)))
|
||||
(home-page "http://www.cs.cmu.edu/~ckingsf/software/sailfish")
|
||||
(synopsis "Mapping-based isoform quantification from RNA-Seq reads")
|
||||
(description "Sailfish is a tool for genomic transcript quantification
|
||||
from RNA-seq data. It requires a set of target transcripts (either from a
|
||||
reference or de-novo assembly) to quantify. All you need to run sailfish is a
|
||||
fasta file containing your reference transcripts and a (set of) fasta/fastq
|
||||
file(s) containing your reads.")
|
||||
(license license:gpl3+)))
|
||||
|
||||
(define libstadenio-for-salmon
|
||||
(package
|
||||
(name "libstadenio")
|
||||
(version "1.14.8")
|
||||
(source (origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/COMBINE-lab/staden-io_lib.git")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (string-append name "-" version "-checkout"))
|
||||
(sha256
|
||||
(base32
|
||||
"1x8kxxqxl892vwfbprlbyfwkkv7c34ggkc94892x9x0g37x5nbwx"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments '(#:parallel-tests? #f)) ; not supported
|
||||
(inputs
|
||||
`(("zlib" ,zlib)))
|
||||
(native-inputs
|
||||
`(("perl" ,perl))) ; for tests
|
||||
(home-page "https://github.com/COMBINE-lab/staden-io_lib")
|
||||
(synopsis "General purpose trace and experiment file library")
|
||||
(description "This package provides a library of file reading and writing
|
||||
code to provide a general purpose Trace file (and Experiment File) reading
|
||||
interface.
|
||||
|
||||
The following file formats are supported:
|
||||
|
||||
@enumerate
|
||||
@item SCF trace files
|
||||
@item ABI trace files
|
||||
@item ALF trace files
|
||||
@item ZTR trace files
|
||||
@item SFF trace archives
|
||||
@item SRF trace archives
|
||||
@item Experiment files
|
||||
@item Plain text files
|
||||
@item SAM/BAM sequence files
|
||||
@item CRAM sequence files
|
||||
@end enumerate\n")
|
||||
(license license:bsd-3)))
|
||||
|
||||
(define spdlog-for-salmon
|
||||
(package
|
||||
(name "spdlog")
|
||||
(version "0.14.0")
|
||||
(source (origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/COMBINE-lab/spdlog.git")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (string-append name "-" version "-checkout"))
|
||||
(sha256
|
||||
(base32
|
||||
"13730429gwlabi432ilpnja3sfvy0nn2719vnhhmii34xcdyc57q"))))
|
||||
(build-system cmake-build-system)
|
||||
(home-page "https://github.com/COMBINE-lab/spdlog")
|
||||
(synopsis "Very fast C++ logging library")
|
||||
(description "Spdlog is a very fast header-only C++ logging library with
|
||||
performance as its primary goal.")
|
||||
(license license:expat)))
|
||||
|
||||
;; This is a modified variant of bwa for use with Salmon. It installs a
|
||||
;; library to avoid having to build this as part of Salmon.
|
||||
(define bwa-for-salmon
|
||||
(package (inherit bwa)
|
||||
(name "bwa")
|
||||
(version "0.7.12.5")
|
||||
(source (origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/COMBINE-lab/bwa.git")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (string-append "bwa-for-salmon-" version "-checkout"))
|
||||
(sha256
|
||||
(base32
|
||||
"1z2qa64y0c5hky10510x137mnzlhz6k8qf27csw4w9j6qihq95gb"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
'(#:tests? #f ;no "check" target
|
||||
#:phases
|
||||
(modify-phases %standard-phases
|
||||
(replace 'install
|
||||
(lambda* (#:key outputs #:allow-other-keys)
|
||||
(let* ((out (assoc-ref outputs "out"))
|
||||
(bin (string-append out "/bin"))
|
||||
(lib (string-append out "/lib"))
|
||||
(doc (string-append out "/share/doc/bwa"))
|
||||
(man (string-append out "/share/man/man1"))
|
||||
(inc (string-append out "/include/bwa")))
|
||||
(install-file "bwa" bin)
|
||||
(install-file "README.md" doc)
|
||||
(install-file "bwa.1" man)
|
||||
(install-file "libbwa.a" lib)
|
||||
(mkdir-p lib)
|
||||
(mkdir-p inc)
|
||||
(for-each (lambda (file)
|
||||
(install-file file inc))
|
||||
(find-files "." "\\.h$")))
|
||||
#t))
|
||||
;; no "configure" script
|
||||
(delete 'configure))))))
|
||||
|
||||
(define-public salmon
|
||||
(package
|
||||
(name "salmon")
|
||||
(version "0.9.1")
|
||||
(source (origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/COMBINE-lab/salmon.git")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (string-append name "-" version "-checkout"))
|
||||
(sha256
|
||||
(base32
|
||||
"1zi1ff4i7y2ykk0vdzysgwzzzv166vg2x77pj1mf4baclavxj87a"))
|
||||
(modules '((guix build utils)))
|
||||
(snippet
|
||||
'(begin
|
||||
;; Delete bundled headers for eigen3.
|
||||
(delete-file-recursively "include/eigen3/")
|
||||
#t))))
|
||||
(build-system cmake-build-system)
|
||||
(arguments
|
||||
`(#:configure-flags
|
||||
(list (string-append "-DBOOST_INCLUDEDIR="
|
||||
(assoc-ref %build-inputs "boost")
|
||||
"/include/")
|
||||
(string-append "-DBOOST_LIBRARYDIR="
|
||||
(assoc-ref %build-inputs "boost")
|
||||
"/lib/")
|
||||
(string-append "-DBoost_LIBRARIES="
|
||||
"-lboost_iostreams "
|
||||
"-lboost_filesystem "
|
||||
"-lboost_system "
|
||||
"-lboost_thread "
|
||||
"-lboost_timer "
|
||||
"-lboost_chrono "
|
||||
"-lboost_program_options")
|
||||
"-DBoost_FOUND=TRUE"
|
||||
"-DTBB_LIBRARIES=tbb tbbmalloc"
|
||||
;; Don't download RapMap---we already have it!
|
||||
"-DFETCHED_RAPMAP=1")
|
||||
#:phases
|
||||
(modify-phases %standard-phases
|
||||
;; Boost cannot be found, even though it's right there.
|
||||
(add-after 'unpack 'do-not-look-for-boost
|
||||
(lambda* (#:key inputs #:allow-other-keys)
|
||||
(substitute* "CMakeLists.txt"
|
||||
(("find_package\\(Boost 1\\.53\\.0") "#"))))
|
||||
(add-after 'unpack 'do-not-phone-home
|
||||
(lambda _
|
||||
(substitute* "src/Salmon.cpp"
|
||||
(("getVersionMessage\\(\\)") "\"\""))))
|
||||
(add-after 'unpack 'prepare-rapmap
|
||||
(lambda* (#:key inputs #:allow-other-keys)
|
||||
(let ((src "external/install/src/rapmap/")
|
||||
(include "external/install/include/rapmap/")
|
||||
(rapmap (assoc-ref inputs "rapmap")))
|
||||
(mkdir-p src)
|
||||
(mkdir-p include)
|
||||
(for-each (lambda (file)
|
||||
(install-file file src))
|
||||
(find-files (string-append rapmap "/src") "\\.(c|cpp)"))
|
||||
(copy-recursively (string-append rapmap "/include") include)
|
||||
(for-each delete-file '("external/install/include/rapmap/xxhash.h"
|
||||
"external/install/include/rapmap/FastxParser.hpp"
|
||||
"external/install/include/rapmap/concurrentqueue.h"
|
||||
"external/install/include/rapmap/FastxParserThreadUtils.hpp"
|
||||
"external/install/src/rapmap/FastxParser.cpp"
|
||||
"external/install/src/rapmap/xxhash.c")))))
|
||||
(add-after 'unpack 'use-system-libraries
|
||||
(lambda* (#:key inputs #:allow-other-keys)
|
||||
(substitute* "src/CMakeLists.txt"
|
||||
(("\\$\\{GAT_SOURCE_DIR\\}/external/install/include/jellyfish-2.2..")
|
||||
(string-append (assoc-ref inputs "jellyfish")
|
||||
"/include/jellyfish-" ,(package-version jellyfish)))
|
||||
(("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libjellyfish-2.0.a")
|
||||
(string-append (assoc-ref inputs "jellyfish")
|
||||
"/lib/libjellyfish-2.0.a"))
|
||||
(("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libdivsufsort.a")
|
||||
(string-append (assoc-ref inputs "libdivsufsort")
|
||||
"/lib/libdivsufsort.so"))
|
||||
(("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libstaden-read.a")
|
||||
(string-append (assoc-ref inputs "libstadenio-for-salmon")
|
||||
"/lib/libstaden-read.a"))
|
||||
(("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libbwa.a")
|
||||
(string-append (assoc-ref inputs "bwa") "/lib/libbwa.a"))
|
||||
(("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libdivsufsort64.a")
|
||||
(string-append (assoc-ref inputs "libdivsufsort")
|
||||
"/lib/libdivsufsort64.so")))
|
||||
(substitute* "CMakeLists.txt"
|
||||
;; Don't prefer static libs
|
||||
(("SET\\(CMAKE_FIND_LIBRARY_SUFFIXES.*") "")
|
||||
(("set\\(TBB_LIBRARIES") "message(")
|
||||
(("find_package\\(Jellyfish.*") "")
|
||||
(("ExternalProject_Add\\(libcereal") "message(")
|
||||
(("ExternalProject_Add\\(libbwa") "message(")
|
||||
(("ExternalProject_Add\\(libjellyfish") "message(")
|
||||
(("ExternalProject_Add\\(libgff") "message(")
|
||||
(("ExternalProject_Add\\(libtbb") "message(")
|
||||
(("ExternalProject_Add\\(libspdlog") "message(")
|
||||
(("ExternalProject_Add\\(libdivsufsort") "message(")
|
||||
(("ExternalProject_Add\\(libstadenio") "message(")
|
||||
(("ExternalProject_Add_Step\\(") "message("))
|
||||
|
||||
;; Ensure that all headers can be found
|
||||
(setenv "CPLUS_INCLUDE_PATH"
|
||||
(string-append (getenv "CPLUS_INCLUDE_PATH")
|
||||
":"
|
||||
(assoc-ref inputs "bwa")
|
||||
"/include/bwa"
|
||||
":"
|
||||
(assoc-ref inputs "eigen")
|
||||
"/include/eigen3"))
|
||||
(setenv "CPATH"
|
||||
(string-append (assoc-ref inputs "bwa")
|
||||
"/include/bwa"
|
||||
":"
|
||||
(assoc-ref inputs "eigen")
|
||||
"/include/eigen3"))
|
||||
#t))
|
||||
;; CMAKE_INSTALL_PREFIX does not exist when the tests are
|
||||
;; run. It only exists after the install phase.
|
||||
(add-after 'unpack 'fix-tests
|
||||
(lambda _
|
||||
(substitute* "src/CMakeLists.txt"
|
||||
(("DTOPLEVEL_DIR=\\$\\{CMAKE_INSTALL_PREFIX")
|
||||
"DTOPLEVEL_DIR=${GAT_SOURCE_DIR"))
|
||||
#t)))))
|
||||
(inputs
|
||||
`(("boost" ,boost)
|
||||
("bwa" ,bwa-for-salmon)
|
||||
("bzip2" ,bzip2)
|
||||
("cereal" ,cereal)
|
||||
("eigen" ,eigen)
|
||||
("rapmap" ,(origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/COMBINE-lab/RapMap.git")
|
||||
(commit (string-append "salmon-v" version))))
|
||||
(file-name (string-append "rapmap-salmon-v" version "-checkout"))
|
||||
(sha256
|
||||
(base32
|
||||
"1yc12yqsz6f0r8sg1qnk57xg34aqwc9jbqq6gd5ys28xw3plj98p"))))
|
||||
("jemalloc" ,jemalloc)
|
||||
("jellyfish" ,jellyfish)
|
||||
("libgff" ,libgff)
|
||||
("tbb" ,tbb)
|
||||
("libdivsufsort" ,libdivsufsort)
|
||||
("libstadenio-for-salmon" ,libstadenio-for-salmon)
|
||||
("spdlog-for-salmon" ,spdlog-for-salmon)
|
||||
("xz" ,xz)
|
||||
("zlib" ,zlib)))
|
||||
(home-page "https://github.com/COMBINE-lab/salmon")
|
||||
(synopsis "Quantification from RNA-seq reads using lightweight alignments")
|
||||
(description "Salmon is a program to produce highly-accurate,
|
||||
transcript-level quantification estimates from RNA-seq data. Salmon achieves
|
||||
its accuracy and speed via a number of different innovations, including the
|
||||
use of lightweight alignments (accurate but fast-to-compute proxies for
|
||||
traditional read alignments) and massively-parallel stochastic collapsed
|
||||
variational inference.")
|
||||
(license license:gpl3+)))
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue