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01/01: gnu: salmon: Update to 0.13.1.
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From: |
guix-commits |
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Subject: |
01/01: gnu: salmon: Update to 0.13.1. |
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Date: |
Thu, 23 May 2019 10:34:43 -0400 (EDT) |
rekado pushed a commit to branch master
in repository guix.
commit a9150d4c236f71aa74988360487d0e30e49c749a
Author: Ricardo Wurmus <address@hidden>
Date: Thu May 23 16:32:21 2019 +0200
gnu: salmon: Update to 0.13.1.
* gnu/packages/bioinformatics.scm (salmon): Update to 0.13.1.
[arguments]: Adjust "do-not-look-for-boost" build phase; adjust
"prepare-rapmap" phase; adjust "use-system-libraries" phase.
[inputs]: Remove bwa, jellyfish, spdlog-for-salmon.
[native-inputs]: Add pkg-config.
(spdlog-for-salmon, bwa-for-salmon): Remove variables.
---
gnu/packages/bioinformatics.scm | 135 +++++++++-------------------------------
1 file changed, 29 insertions(+), 106 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e3c24ae..0a30d09 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -11783,80 +11783,19 @@ The following file formats are supported:
@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")
+ (version "0.13.1")
(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"))
+ (file-name (git-file-name name version))
(sha256
(base32
- "1zi1ff4i7y2ykk0vdzysgwzzzv166vg2x77pj1mf4baclavxj87a"))
+ "1i2z4aivicmiixdz9bxalp7vmfzi3k92fxa63iqa8kgvfw5a4aq5"))
(modules '((guix build utils)))
(snippet
'(begin
@@ -11890,7 +11829,7 @@ performance as its primary goal.")
(add-after 'unpack 'do-not-look-for-boost
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "CMakeLists.txt"
- (("find_package\\(Boost 1\\.53\\.0") "#"))
+ (("find_package\\(Boost 1\\.59\\.0") "#"))
#t))
(add-after 'unpack 'do-not-phone-home
(lambda _
@@ -11904,66 +11843,51 @@ performance as its primary goal.")
(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 "/src") src)
(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")))
+ "external/install/src/rapmap/xxhash.c"))
+ (delete-file-recursively
"external/install/include/rapmap/spdlog"))
#t))
(add-after 'unpack 'use-system-libraries
(lambda* (#:key inputs #:allow-other-keys)
+ (substitute* "CMakeLists.txt"
+ ;; Don't prefer static libs
+ (("SET\\(CMAKE_FIND_LIBRARY_SUFFIXES.*") "")
+ (("set\\(TBB_LIBRARIES") "message(")
+ ;; Don't download anything
+ (("DOWNLOAD_COMMAND") "DOWNLOAD_COMMAND echo")
+ (("externalproject_add\\(libcereal") "message(")
+ (("externalproject_add\\(libgff") "message(")
+ (("externalproject_add\\(libtbb") "message(")
+ (("externalproject_add\\(libdivsufsort") "message(")
+ (("externalproject_add\\(libstadenio") "message(")
+ (("externalproject_add_step\\(") "message("))
(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"))
+ (("add_dependencies") "#")
+
(("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libstaden-read.a")
+ (string-append (assoc-ref inputs "libstadenio-for-salmon")
+ "/lib/libstaden-read.so"))
(("\\$\\{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("))
+ "/lib/libdivsufsort64.so"))
+ (("lib/libdivsufsort.a") "/lib/libdivsufsort.so"))
;; 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")
+ (string-append (assoc-ref inputs "eigen")
"/include/eigen3"))
#t))
;; CMAKE_INSTALL_PREFIX does not exist when the tests are
@@ -11976,7 +11900,6 @@ performance as its primary goal.")
#t)))))
(inputs
`(("boost" ,boost)
- ("bwa" ,bwa-for-salmon)
("bzip2" ,bzip2)
("cereal" ,cereal)
("eigen" ,eigen)
@@ -11988,16 +11911,16 @@ performance as its primary goal.")
(file-name (string-append "rapmap-salmon-v" version
"-checkout"))
(sha256
(base32
-
"1yc12yqsz6f0r8sg1qnk57xg34aqwc9jbqq6gd5ys28xw3plj98p"))))
+
"1biplxf0csc7a8h1wf219b0vmjkvw6wk2zylhdklb577kgmihdms"))))
("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)))
+ (native-inputs
+ `(("pkg-config" ,pkg-config)))
(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,