gnu: Add salmon.
* gnu/packages/bioinformatics.scm (libstadenio-for-salmon, spdlog-for-salmon, bwa-for-salmon, salmon): New variables.
This commit is contained in:
Ricardo Wurmus
parent
8d77a085a7
commit
7762646d95
1 changed files with 263 additions and 0 deletions
|
|
@ -11307,3 +11307,266 @@ 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
|
fasta file containing your reference transcripts and a (set of) fasta/fastq
|
||||||
file(s) containing your reads.")
|
file(s) containing your reads.")
|
||||||
(license license:gpl3+)))
|
(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+)))
|
||||||
|
|
|
||||||
Reference in a new issue