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authorpjotrp2016-03-11 09:03:57 +0000
committerpjotrp2016-03-11 09:03:57 +0000
commitcd6dea3c1cc7489d02b93d66dee135ba040f19f7 (patch)
tree6f12f810366b89d6f103a83ff6dbe538cf160553 /gn/packages
parentc6ecd9efe0587d0b4828a4e2167799abe6764319 (diff)
parent34ae8b6d400fcce50f9848441ddf4e302b9d1057 (diff)
downloadguix-bioinformatics-cd6dea3c1cc7489d02b93d66dee135ba040f19f7.tar.gz
Merge conflict
Diffstat (limited to 'gn/packages')
-rw-r--r--gn/packages/bioinformatics.scm461
-rw-r--r--gn/packages/llvm.scm4
2 files changed, 385 insertions, 80 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index d865117..11a624f 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -13,17 +13,25 @@
;; #:use-module (guix build-system ruby)
#:use-module (guix build-system r)
#:use-module (guix build-system trivial)
+ #:use-module (gn packages statistics)
#:use-module (gnu packages)
+ #:use-module (gnu packages autotools)
#:use-module (gnu packages algebra)
#:use-module (gnu packages base)
#:use-module (gnu packages bioinformatics)
#:use-module (gnu packages boost)
#:use-module (gnu packages compression)
#:use-module (gnu packages databases)
+ #:use-module (gnu packages check)
#:use-module (gnu packages cmake)
+ #:use-module (gnu packages compression)
#:use-module (gnu packages cpio)
+ #:use-module (gnu packages curl)
+ #:use-module (gnu packages doxygen)
+ #:use-module (gnu packages datastructures)
#:use-module (gnu packages check)
#:use-module (gnu packages file)
+ #:use-module (gnu packages gawk)
#:use-module (gnu packages gcc)
#:use-module (gnu packages graphviz)
#:use-module (gnu packages java)
@@ -31,7 +39,11 @@
#:use-module (gnu packages ldc)
#:use-module (gnu packages machine-learning)
#:use-module (gnu packages maths)
+ #:use-module (gnu packages mpi)
#:use-module (gnu packages ncurses)
+ #:use-module (gnu packages node)
+ #:use-module (gnu packages parallel)
+ #:use-module (gnu packages pcre)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages popt)
@@ -41,13 +53,13 @@
#:use-module (gnu packages statistics)
#:use-module (gnu packages tbb)
#:use-module (gnu packages textutils)
+ #:use-module (gnu packages time)
+ #:use-module (gnu packages tls)
#:use-module (gnu packages vim)
#:use-module (gnu packages web)
#:use-module (gnu packages xml)
#:use-module (gnu packages zip)
#:use-module (gnu packages bootstrap)
- #:use-module (gn packages python)
- #:use-module (gn packages statistics)
#:use-module (srfi srfi-1))
(define-public freec
@@ -100,6 +112,350 @@ data. For whole genome sequencing data analysis, the program can also use
mappability data (files created by GEM). ")
(license license:gpl2+)))
+(define-public tabixpp
+ (package
+ (name "tabixpp")
+ (version "1.0.0")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/ekg/tabixpp/archive/v"
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "1s0lgks7qlvlhvcjhi2wm18nnza1bwcnic44ij7z8wfg88h4ivwn"))))
+ (build-system gnu-build-system)
+ (inputs
+ `(("htslib" ,htslib)
+ ("zlib" ,zlib)))
+ (arguments
+ `(#:tests? #f ; There are no tests to run.
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure) ; There is no configure phase.
+ ;; The build phase needs overriding the location of htslib.
+ (replace 'build
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((htslib-ref (assoc-ref inputs "htslib")))
+ (zero?
+ (system* "make"
+ (string-append "HTS_LIB=" htslib-ref "/lib/libhts.a")
+ "HTS_HEADERS=" ; No need to check for headers here.
+ (string-append "LIBPATH=-L. -L" htslib-ref "/include"))))))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+ (install-file "tabix++" bin)))))))
+ (home-page "https://github.com/ekg/tabixpp")
+ (synopsis "C++ wrapper around tabix project")
+ (description "This is a C++ wrapper around the Tabix project which abstracts
+some of the details of opening and jumping in tabix-indexed files.")
+ (license license:expat)))
+
+;; This version works with FreeBayes while the released version doesn't. The
+;; released creates a variable with the name "vcf" somewhere, which is also the
+;; name of a namespace in vcflib.
+(define-public tabixpp-freebayes
+ (let ((commit "bbc63a49acc52212199f92e9e3b8fba0a593e3f7"))
+ (package (inherit tabixpp)
+ (name "tabixpp-freebayes")
+ (version (string-append "0-1." (string-take commit 7)))
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/ekg/tabixpp/archive/"
+ commit ".tar.gz"))
+ (file-name (string-append name "-" version "-checkout.tar.gz"))
+ (sha256
+ (base32 "1s06wmpgj4my4pik5kp2lc42hzzazbp5ism2y4i2ajp2y1c68g77")))))))
+
+(define-public smithwaterman
+ ;; TODO: Upgrading smithwaterman breaks FreeBayes.
+ (let ((commit "203218b47d45ac56ef234716f1bd4c741b289be1"))
+ (package
+ (name "smithwaterman")
+ (version (string-append "0-1." (string-take commit 7)))
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/ekg/smithwaterman/archive/"
+ commit ".tar.gz"))
+ (file-name (string-append name "-" version "-checkout.tar.gz"))
+ (sha256
+ (base32 "1lkxy4xkjn96l70jdbsrlm687jhisgw4il0xr2dm33qwcclzzm3b"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; There are no tests to run.
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure) ; There is no configure phase.
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+ (install-file "smithwaterman" bin)))))))
+ (home-page "https://github.com/ekg/smithwaterman")
+ (synopsis "Implementation of the Smith-Waterman algorithm")
+ (description "Implementation of the Smith-Waterman algorithm.")
+ ;; The project contains a license file for the GPLv2. The source files
+ ;; do not contain a license notice, so GPLv2-only is assumed here.
+ (license license:gpl2))))
+
+(define-public multichoose
+ (package
+ (name "multichoose")
+ (version "1.0.3")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/ekg/multichoose/archive/v"
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "0xy86vvr3qrs4l81qis7ia1q2hnqv0xcb4a1n60smxbhqqis5w3l"))))
+ (build-system gnu-build-system)
+ (native-inputs
+ `(("python" ,python-2)
+ ("node" ,node)))
+ (arguments
+ `(#:tests? #f ; There are no tests to run.
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure) ; There is no configure phase.
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+ ;; TODO: There are Python modules for these programs too.
+ (install-file "multichoose" bin)
+ (install-file "multipermute" bin)))))))
+ (home-page "https://github.com/ekg/multichoose")
+ (synopsis "Library for efficient loopless multiset combination generation
+algorithm")
+ (description "A library implements an efficient loopless multiset
+combination generation algorithm which is (approximately) described in
+\"Loopless algorithms for generating permutations, combinations, and other
+combinatorial configurations.\" G Ehrlich - Journal of the ACM (JACM),
+1973. (Algorithm 7.)")
+ (license license:expat)))
+
+(define-public fsom
+ (let ((commit "a6ef318fbd347c53189384aef7f670c0e6ce89a3"))
+ (package
+ (name "fsom")
+ (version (string-append "0-1." (string-take commit 7)))
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/ekg/fsom/archive/"
+ "a6ef318fbd347c53189384aef7f670c0e6ce89a3" ".tar.gz"))
+ (file-name (string-append name "-" version "-checkout.tar.gz"))
+ (sha256
+ (base32 "0q6b57ppxfvsm5cqmmbfmjpn5qvx2zi5pamvp3yh8gpmmz8cfbl3"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; There are no tests to run.
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure) ; There is no configure phase.
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+ (install-file "fsom" bin)))))))
+ (home-page "https://github.com/ekg/fsom")
+ (synopsis "Program for managing SOM (Self-Organizing Maps) neural networks")
+ (description "Program for managing SOM (Self-Organizing Maps) neural networks.")
+ (license license:gpl3))))
+
+(define-public filevercmp
+ (let ((commit "1a9b779b93d0b244040274794d402106907b71b7"))
+ (package
+ (name "filevercmp")
+ (version (string-append "0-1." (string-take commit 7)))
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/ekg/filevercmp/archive/"
+ commit ".tar.gz"))
+ (file-name "filevercmp-src.tar.gz")
+ (sha256
+ (base32 "0yp5jswf5j2pqc6517x277s4s6h1ss99v57kxw9gy0jkfl3yh450"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; There are no tests to run.
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure) ; There is no configure phase.
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+ (install-file "filevercmp" bin)))))))
+ (home-page "https://github.com/ekg/filevercmp")
+ (synopsis "Program to compare version strings")
+ (description "A program to compare version strings. It intends to be a
+replacement for strverscmp.")
+ (license license:gpl3+))))
+
+(define-public fastahack
+ (let ((commit "c68cebb4f2e5d5d2b70cf08fbdf1944e9ab2c2dd"))
+ (package
+ (name "fastahack")
+ (version (string-append "0-1." (string-take commit 7)))
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/ekg/fastahack/archive/"
+ commit ".tar.gz"))
+ (file-name (string-append name "-" version "-checkout.tar.gz"))
+ (sha256
+ (base32 "0j25lcl3jk1kls66zzxjfyq5ir6sfcvqrdwfcva61y3ajc9ssay2"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; There are no tests to run.
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure) ; There is no configure phase.
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+ (install-file "fastahack" bin)))))))
+ (home-page "https://github.com/ekg/fastahack")
+ (synopsis "Program for indexing and sequence extraction from FASTA files")
+ (description "Fastahack is a small application for indexing and extracting
+sequences and subsequences from FASTA files. The included Fasta.cpp library
+provides a FASTA reader and indexer that can be embeddedinto applications which
+would benefit from directly reading subsequences from FASTA files. The library
+automatically handles index file generation and use.")
+ ;; There is no specific license for fastahack.
+ ;; A part of the program is licensed GPLv2.
+ (license (list license:non-copyleft license:gpl2)))))
+
+(define-public vcflib
+ (let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb"))
+ (package
+ (name "vcflib")
+ (version (string-append "1.0.2-1." (string-take commit 7)))
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/vcflib/vcflib/archive/"
+ "5ac091365fdc716cc47cc5410bb97ee5dc2a2c92" ".tar.gz"))
+ (file-name "vcflib-5ac0913.tar.gz")
+ (sha256
+ (base32 "0ywshwpif059z5h0g7zzrdfzzdj2gr8xvwlwcsdxrms3p9iy35h8"))))
+ (build-system gnu-build-system)
+ (native-inputs
+ `(("htslib" ,htslib)
+ ("zlib" ,zlib)
+ ("python" ,python-2)
+ ("perl" ,perl)
+ ("r" ,r)
+ ("node" ,node)
+ ("tabixpp-src" ,(package-source tabixpp-freebayes))
+ ("smithwaterman-src" ,(package-source smithwaterman))
+ ("multichoose-src" ,(package-source multichoose))
+ ("fsom-src" ,(package-source fsom))
+ ("filevercmp-src" ,(package-source filevercmp))
+ ("fastahack-src" ,(package-source fastahack))
+ ("intervaltree-src"
+ ,(origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/ekg/intervaltree/archive/"
+ "dbb4c513d1ad3baac516fc1484c995daf9b42838" ".tar.gz"))
+ (file-name "intervaltree-src.tar.gz")
+ (sha256
+ (base32 "19prwpn2wxsrijp5svfqvfcxl5nj7zdhm3jycd5kqhl9nifpmcks"))))))
+ (arguments
+ `(#:tests? #f
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (delete 'check)
+ (add-after 'unpack 'unpack-submodule-sources
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((unpack (lambda (source target)
+ (with-directory-excursion target
+ (zero? (system* "tar" "xvf"
+ (assoc-ref inputs source)
+ "--strip-components=1"))))))
+ (and
+ (unpack "intervaltree-src" "intervaltree")
+ (unpack "fastahack-src" "fastahack")
+ (unpack "filevercmp-src" "filevercmp")
+ (unpack "fsom-src" "fsom")
+ (unpack "multichoose-src" "multichoose")
+ (unpack "smithwaterman-src" "smithwaterman")
+ (unpack "tabixpp-src" "tabixpp")))))
+ (add-after 'unpack-submodule-sources 'fix-makefile
+ (lambda* (#:key inputs #:allow-other-keys)
+ (substitute* '("Makefile")
+ (("^GIT_VERSION.*") "GIT_VERSION = v1.0.0"))))
+ (replace
+ 'build
+ (lambda* (#:key inputs make-flags #:allow-other-keys)
+ (with-directory-excursion "tabixpp"
+ (zero? (system* "make")))
+ (zero? (system* "make" "CC=gcc"
+ (string-append "CFLAGS=\"" "-Itabixpp "
+ "-I" (assoc-ref inputs "htslib") "/include " "\"") "all"))))
+ (replace
+ 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
+ ;;(include (string-append (assoc-ref outputs "out") "/include"))
+ (lib (string-append (assoc-ref outputs "out") "/lib")))
+ (for-each (lambda (file)
+ (install-file file bin))
+ (find-files "bin" ".*"))
+ ;; The header files do not correspond to libvcflib.a, therefore
+ ;; I left them out.
+ ;;(for-each (lambda (file)
+ ;; (install-file file include))
+ ;; (find-files "src" "\\.h$"))
+ (install-file "libvcflib.a" lib)))))))
+ (home-page "https://github.com/vcflib/vcflib/")
+ (synopsis "Library for parsing and manipulating VCF files")
+ (description "Vcflib provides methods to manipulate and interpret
+sequence variation as it can be described by VCF. It is both an API for parsing
+and operating on records of genomic variation as it can be described by the VCF
+format, and a collection of command-line utilities for executing complex
+manipulations on VCF files.")
+ (license license:expat))))
+
+(define-public bash-tap
+ (package
+ (name "bash-tap")
+ (version "1.0.2")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/illusori/bash-tap/archive/"
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "0qs1qi38bl3ns4mpagcawv618dsk2q1lgrbddgvs0wl3ia12cyz5"))))
+ (build-system trivial-build-system)
+ (native-inputs `(("source" ,source)
+ ("tar" ,tar)
+ ("gzip" ,gzip)))
+ (arguments
+ `(#:modules ((guix build utils))
+ #:builder (begin
+ (use-modules (guix build utils))
+ (let ((tar (string-append (assoc-ref %build-inputs "tar") "/bin/tar"))
+ (path (string-append (assoc-ref %build-inputs "gzip") "/bin"))
+ (bin (string-append %output "/bin"))
+ (source (string-append (assoc-ref %build-inputs "source"))))
+ (setenv "PATH" path)
+ (mkdir-p bin)
+ (with-directory-excursion bin
+ (zero? (system* tar "xvf" source
+ "--strip-components=1"
+ "--no-anchored"
+ "bash-tap"
+ "bash-tap-bootstrap"
+ "bash-tap-mock")))))))
+ (home-page "http://www.illusori.co.uk/projects/bash-tap/")
+ (synopsis "Bash port of a Test::More/Test::Builder-style TAP-compliant
+test library")
+ (description "Bash TAP is a TAP-compliant Test::More-style testing library
+for Bash shell scripts and functions. Along with the Test::More-style testing
+helpers it provides helper functions for mocking commands and functions and
+in-process output capturing.")
+ ;; The author didn't specify a license.
+ (license license:public-domain)))
+
(define-public freebayes
(let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb")
(revision "1"))
@@ -116,7 +472,8 @@ mappability data (files created by GEM). ")
(base32 "1sbzwmcbn78ybymjnhwk7qc5r912azy5vqz2y7y81616yc3ba2a2"))))
(build-system gnu-build-system)
(inputs
- `(("zlib" ,zlib)))
+ `(("zlib" ,zlib)
+ ("htslib" ,htslib)))
(native-inputs
`(("bc" ,bc) ; Needed for running tests.
("samtools" ,samtools) ; Needed for running tests.
@@ -124,35 +481,19 @@ mappability data (files created by GEM). ")
("procps" ,procps) ; Needed for running tests.
("bamtools" ,bamtools)
("cmake" ,cmake)
- ("htslib" ,htslib)
("python" ,python-2)
+ ("node" ,node)
("r" ,r)
("perl" ,perl)
- ("bamtools-src"
- ,(origin
- (method url-fetch)
- (uri (string-append "https://github.com/ekg/bamtools/archive/"
- "e77a43f5097ea7eee432ee765049c6b246d49baa" ".tar.gz"))
- (file-name "bamtools-src.tar.gz")
- (sha256
- (base32 "0rqymka21g6lfjfgxzr40pxz4c4fcl77jpy1np1li70pnc7h2cs1"))))
- ("vcflib-src"
- ,(origin
- (method url-fetch)
- (uri (string-append "https://github.com/vcflib/vcflib/archive/"
- "5ac091365fdc716cc47cc5410bb97ee5dc2a2c92" ".tar.gz"))
- (file-name "vcflib-5ac0913.tar.gz")
- (sha256
- (base32 "0ywshwpif059z5h0g7zzrdfzzdj2gr8xvwlwcsdxrms3p9iy35h8"))))
+ ("bamtools-src" ,(package-source bamtools))
+ ("vcflib-src" ,(package-source vcflib))
;; These are submodules for the vcflib version used in freebayes
- ("tabixpp-src"
- ,(origin
- (method url-fetch)
- (uri (string-append "https://github.com/ekg/tabixpp/archive/"
- "bbc63a49acc52212199f92e9e3b8fba0a593e3f7" ".tar.gz"))
- (file-name "tabixpp-src.tar.gz")
- (sha256
- (base32 "1s06wmpgj4my4pik5kp2lc42hzzazbp5ism2y4i2ajp2y1c68g77"))))
+ ("tabixpp-src" ,(package-source tabixpp-freebayes))
+ ("smithwaterman-src" ,(package-source smithwaterman))
+ ("multichoose-src" ,(package-source multichoose))
+ ("fsom-src" ,(package-source fsom))
+ ("filevercmp-src" ,(package-source filevercmp))
+ ("fastahack-src" ,(package-source fastahack))
("intervaltree-src"
,(origin
(method url-fetch)
@@ -162,55 +503,15 @@ mappability data (files created by GEM). ")
(file-name "intervaltree-src.tar.gz")
(sha256
(base32 "19prwpn2wxsrijp5svfqvfcxl5nj7zdhm3jycd5kqhl9nifpmcks"))))
- ("smithwaterman-src"
- ,(origin
- (method url-fetch)
- (uri (string-append "https://github.com/ekg/smithwaterman/archive/"
- "203218b47d45ac56ef234716f1bd4c741b289be1" ".tar.gz"))
- (file-name "smithwaterman-src.tar.gz")
- (sha256
- (base32 "1lkxy4xkjn96l70jdbsrlm687jhisgw4il0xr2dm33qwcclzzm3b"))))
- ("multichoose-src"
- ,(origin
- (method url-fetch)
- (uri (string-append "https://github.com/ekg/multichoose/archive/"
- "73d35daa18bf35729b9ba758041a9247a72484a5" ".tar.gz"))
- (file-name "multichoose-src.tar.gz")
- (sha256
- (base32 "07aizwdabmlnjaq4p3v0vsasgz1xzxid8xcxcw3paq8kh9c1099i"))))
- ("fsom-src"
- ,(origin
- (method url-fetch)
- (uri (string-append "https://github.com/ekg/fsom/archive/"
- "a6ef318fbd347c53189384aef7f670c0e6ce89a3" ".tar.gz"))
- (file-name "fsom-src.tar.gz")
- (sha256
- (base32 "0q6b57ppxfvsm5cqmmbfmjpn5qvx2zi5pamvp3yh8gpmmz8cfbl3"))))
- ("filevercmp-src"
- ,(origin
- (method url-fetch)
- (uri (string-append "https://github.com/ekg/filevercmp/archive/"
- "1a9b779b93d0b244040274794d402106907b71b7" ".tar.gz"))
- (file-name "filevercmp-src.tar.gz")
- (sha256
- (base32 "0yp5jswf5j2pqc6517x277s4s6h1ss99v57kxw9gy0jkfl3yh450"))))
- ("fastahack-src"
- ,(origin
- (method url-fetch)
- (uri (string-append "https://github.com/ekg/fastahack/archive/"
- "c68cebb4f2e5d5d2b70cf08fbdf1944e9ab2c2dd" ".tar.gz"))
- (file-name "fastahack-src.tar.gz")
- (sha256
- (base32 "0j25lcl3jk1kls66zzxjfyq5ir6sfcvqrdwfcva61y3ajc9ssay2"))))
;; These submodules are needed to run the tests.
- ("bash-tap-src"
- ,(origin
- (method url-fetch)
- (uri (string-append "https://github.com/illusori/bash-tap/archive/"
- "c38fbfa401600cc81ccda66bfc0da3ea56288d03" ".tar.gz"))
- (file-name "bash-tap-src.tar.gz")
- (sha256
- (base32 "07ijb1p0aa65ajpg9nkghc183iha6lwiydkckay8pghapa01j6nz"))))
+ ("bash-tap-src" ,(package-source bash-tap))
+ ;; ,(origin
+ ;; (method url-fetch)
+ ;; (uri (string-append "https://github.com/illusori/bash-tap/archive/"
+ ;; "c38fbfa401600cc81ccda66bfc0da3ea56288d03" ".tar.gz"))
+ ;; (file-name "bash-tap-src.tar.gz")
+ ;; (sha256
+ ;; (base32 "07ijb1p0aa65ajpg9nkghc183iha6lwiydkckay8pghapa01j6nz"))))
("test-simple-bash-src"
,(origin
(method url-fetch)
@@ -233,7 +534,7 @@ mappability data (files created by GEM). ")
(and
(unpack "bamtools-src" "bamtools")
(unpack "vcflib-src" "vcflib")
- (unpack "intervaltree-src" "intervaltree")
+ ;;(unpack "intervaltree-src" "intervaltree")
(unpack "fastahack-src" "vcflib/fastahack")
(unpack "filevercmp-src" "vcflib/filevercmp")
(unpack "fsom-src" "vcflib/fsom")
@@ -261,7 +562,11 @@ mappability data (files created by GEM). ")
;; Compile vcflib before we compiling the main project.
(with-directory-excursion "vcflib"
(with-directory-excursion "tabixpp"
- (zero? (system* "make")))
+ (let ((htslib-ref (assoc-ref inputs "htslib")))
+ (zero?
+ (system* "make" "HTS_HEADERS="
+ (string-append "HTS_LIB=" htslib-ref "/lib/libhts.a")
+ (string-append "LIBPATH=-L. -L" htslib-ref "/include")))))
(zero? (system* "make" "CC=gcc"
(string-append "CFLAGS=\"" "-Itabixpp "
"-I" (assoc-ref inputs "htslib") "/include " "\"") "all")))
diff --git a/gn/packages/llvm.scm b/gn/packages/llvm.scm
index 83ea5d1..607f7c2 100644
--- a/gn/packages/llvm.scm
+++ b/gn/packages/llvm.scm
@@ -19,7 +19,7 @@
;;; 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 (gnu packages llvm)
+(define-module (gn packages llvm)
#:use-module (guix packages)
#:use-module (guix licenses)
#:use-module (guix download)
@@ -62,4 +62,4 @@ languages. It currently supports compilation of C and C++ programs, using
front-ends derived from GCC 4.0.1. A new front-end for the C family of
languages is in development. The compiler infrastructure includes mirror sets
of programming tools as well as libraries with equivalent functionality.")
- (license license:ncsa)))
+ (license ncsa)))