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authorMarius Bakke <mbakke@fastmail.com>2019-08-13 20:42:06 +0200
committerMarius Bakke <mbakke@fastmail.com>2019-08-13 20:42:06 +0200
commit462ad9f56b9665b8d22960acee73ad91f1052c9c (patch)
tree814be463d6d0517e7db9b9e6f15dbc7516955674 /gnu/packages/bioinformatics.scm
parent7f5f61ae99321a7a6e08b0100cd428e11ce6a837 (diff)
parent1b1b006afd31c5526f34d157baef492c7dde2e9c (diff)
downloadpatches-462ad9f56b9665b8d22960acee73ad91f1052c9c.tar
patches-462ad9f56b9665b8d22960acee73ad91f1052c9c.tar.gz
Merge branch 'master' into core-updates
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
-rw-r--r--gnu/packages/bioinformatics.scm455
1 files changed, 433 insertions, 22 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b1cf294177..898b8d200e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13,6 +13,7 @@
;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com>
;;; Copyright © 2018 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
;;; Copyright © 2019 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2019 Brian Leung <bkleung89@gmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -4195,8 +4196,15 @@ command, or queried for specific k-mers with @code{jellyfish query}.")
(modify-phases %standard-phases
(add-after 'unpack 'set-cc
(lambda _ (setenv "CC" "gcc") #t))
- ;; FIXME: This fails with "permission denied".
- (delete 'reset-gzip-timestamps))))
+
+ (add-before 'reset-gzip-timestamps 'make-files-writable
+ (lambda* (#:key outputs #:allow-other-keys)
+ ;; Make sure .gz files are writable so that the
+ ;; 'reset-gzip-timestamps' phase can do its work.
+ (let ((out (assoc-ref outputs "out")))
+ (for-each make-file-writable
+ (find-files out "\\.gz$"))
+ #t))))))
(native-inputs
`(("python-cython" ,python-cython)
("python-pytest" ,python-pytest)
@@ -7439,13 +7447,13 @@ names in their natural, rather than lexicographic, order.")
(define-public r-edger
(package
(name "r-edger")
- (version "3.26.5")
+ (version "3.26.6")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "edgeR" version))
(sha256
(base32
- "0iba4krz30dx5b0s89n5cfkwn64867s7vmvvfqms9lbcr4kj439m"))))
+ "17vadhamjv4x0l4qqq2p2fi6j2bkllz5zd8dq761vgd5ic23zizm"))))
(properties `((upstream-name . "edgeR")))
(build-system r-build-system)
(propagated-inputs
@@ -7506,13 +7514,13 @@ coding changes and predict coding outcomes.")
(define-public r-limma
(package
(name "r-limma")
- (version "3.40.2")
+ (version "3.40.6")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "limma" version))
(sha256
(base32
- "1d4ig2b7fa9mwja52isxrwmprfdjdk1mlcf2skhdp51l24z6wbk7"))))
+ "166z8cdh6w90rldqqaar7hyaskwiy4smawjfbn4sn58clv6q3mp8"))))
(build-system r-build-system)
(home-page "http://bioinf.wehi.edu.au/limma")
(synopsis "Package for linear models for microarray and RNA-seq data")
@@ -7639,13 +7647,13 @@ annotation data packages using SQLite data storage.")
(define-public r-biomart
(package
(name "r-biomart")
- (version "2.40.1")
+ (version "2.40.3")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "biomaRt" version))
(sha256
(base32
- "1abl0c4qbhfqf9ixdp74183phm7s8rszrr5ldczm59b8vyng8rhx"))))
+ "022m1r44s00c5k9bmv0lr22lcn662nhc91aazvv0yyysxjamyf60"))))
(properties
`((upstream-name . "biomaRt")))
(build-system r-build-system)
@@ -7672,13 +7680,13 @@ powerful online queries from gene annotation to database mining.")
(define-public r-biocparallel
(package
(name "r-biocparallel")
- (version "1.18.0")
+ (version "1.18.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocParallel" version))
(sha256
(base32
- "0v8rhf3hbgb3v32h2pmsv1y6q2x4airmpp50fk7z6ardcn4aza7x"))))
+ "1j6wbls4qgvi5gj99c51r00jhxrzxk3x3258wg7dcjzbfqypvyw3"))))
(properties
`((upstream-name . "BiocParallel")))
(build-system r-build-system)
@@ -7800,13 +7808,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns),
(define-public r-summarizedexperiment
(package
(name "r-summarizedexperiment")
- (version "1.14.0")
+ (version "1.14.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "SummarizedExperiment" version))
(sha256
(base32
- "1ypk63pdml89y81pr41i2zq0fimsaxsa5lgpg6xs5cwikyaq0pci"))))
+ "0bhwgzrdipr0qjzc4j0qspqprx3v1rvshmx4j6506dv43pqlgp3f"))))
(properties
`((upstream-name . "SummarizedExperiment")))
(build-system r-build-system)
@@ -7864,13 +7872,13 @@ alignments.")
(define-public r-rtracklayer
(package
(name "r-rtracklayer")
- (version "1.44.0")
+ (version "1.44.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "rtracklayer" version))
(sha256
(base32
- "161gcks9b12993g9k27gf7wfh8lgd8m8rr7x2slgfqqssk0yrmpd"))))
+ "03b4rfsbzjjf5kxcsjv7kq8hrsgcvz9rfzcn2v7fx3nr818pbb8s"))))
(build-system r-build-system)
(arguments
`(#:phases
@@ -7911,13 +7919,13 @@ as well as query and modify the browser state, such as the current viewport.")
(define-public r-genomicfeatures
(package
(name "r-genomicfeatures")
- (version "1.36.3")
+ (version "1.36.4")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicFeatures" version))
(sha256
(base32
- "0zkd57i5qjxsravv0gbyckc0wrnqzgxd61ibh3jmhmrccrr9ihn3"))))
+ "0mzqv8pyxx5nwchyx3radym9ws2f9hb50xc9abjsjs4w4pv91j3k"))))
(properties
`((upstream-name . "GenomicFeatures")))
(build-system r-build-system)
@@ -8335,13 +8343,13 @@ paired-end data.")
(define-public r-rcas
(package
(name "r-rcas")
- (version "1.10.0")
+ (version "1.10.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "RCAS" version))
(sha256
(base32
- "1h4vf5gzilqbdrd8m9l3zc2m4sca8cir8366a7njgd558k7ld5kl"))))
+ "06z5zmdi34jblw37z6ff8hb6lvvi0chwr37acwqfn8d27ax9lakz"))))
(properties `((upstream-name . "RCAS")))
(build-system r-build-system)
(propagated-inputs
@@ -9399,14 +9407,14 @@ of mass spectrometry based proteomics data.")
(define-public r-msnid
(package
(name "r-msnid")
- (version "1.18.0")
+ (version "1.18.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MSnID" version))
(sha256
(base32
- "18mp8zacawhfapfwpq8czbswxix2ykvqhwjga54v0a99zg3k87h3"))))
+ "1n49l5mjdz7p4g2nwsbhm1jcj42sv6lsriq77n2imvacsvk0qfmb"))))
(properties `((upstream-name . "MSnID")))
(build-system r-build-system)
(propagated-inputs
@@ -10406,14 +10414,14 @@ provided.")
(define-public r-hdf5array
(package
(name "r-hdf5array")
- (version "1.12.1")
+ (version "1.12.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "HDF5Array" version))
(sha256
(base32
- "0n8zc1x582vwb0zfhrjmnqbnpqky9zbhjc2j836i0a4yisklwdcp"))))
+ "0afradisrr5gn0lf2kxjw55vdm3lm9mlgx53qlr9r40c1hrydpf5"))))
(properties `((upstream-name . "HDF5Array")))
(build-system r-build-system)
(inputs
@@ -14804,3 +14812,406 @@ trees by inserting random mutations. The tbsp package implements an
alternative method to detect significant, cell type specific sequence
mutations from scRNA-Seq data.")
(license license:expat))))
+
+(define-public tabixpp
+ (package
+ (name "tabixpp")
+ (version "1.0.0")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/ekg/tabixpp")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "08vx6nsipk971cyr8z53rnzwkvlld63kcn1fw0pwddynz91xfny8"))))
+ (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")))
+ (invoke "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))
+ #t)))))
+ (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)))
+
+(define tabixpp-freebayes
+ ;; 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.
+ (let ((commit "bbc63a49acc52212199f92e9e3b8fba0a593e3f7"))
+ (package
+ (inherit tabixpp)
+ (name "tabixpp-freebayes")
+ (version (git-version "0.0.0" "1" commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/ekg/tabixpp/")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "017qsmsc2kyiyzqr9nl8cc6pfldxf16dbn8flx5i59mbqr9ydi7g")))))))
+
+(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 git-fetch)
+ (uri (git-reference
+ (url "https://github.com/ekg/smithwaterman/")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0z9xsmsv452kgdfbbwydyc6nymg3fwyv8zswls8qjin3r4ia4415"))))
+ (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))
+ #t)))))
+ (home-page "https://github.com/ekg/smithwaterman")
+ (synopsis "Implementation of the Smith-Waterman algorithm")
+ (description "Implementation of the Smith-Waterman algorithm.")
+ ;; The licensing terms are unclear: https://github.com/ekg/smithwaterman/issues/9.
+ (license (list license:gpl2 license:expat)))))
+
+(define-public multichoose
+ (package
+ (name "multichoose")
+ (version "1.0.3")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/ekg/multichoose/")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0ci5fqvmpamwgxvmyd79ygj6n3bnbl3vc7b6h1sxz58186sm3pfs"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; Tests require node.
+ #: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))
+ #t)))))
+ (home-page "https://github.com/ekg/multichoose")
+ (synopsis "Efficient loopless multiset combination generation algorithm")
+ (description "This 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 (git-version "0.0.0" "1" commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/ekg/fsom/")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0gw1lpvr812pywg9y546x0h1hhj261xwls41r6kqhddjlrcjc0pi"))))
+ (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))
+ #t)))))
+ (home-page "https://github.com/ekg/fsom")
+ (synopsis "Manage SOM (Self-Organizing Maps) neural networks")
+ (description "A tiny C library for managing SOM (Self-Organizing Maps)
+neural networks.")
+ (license license:gpl3))))
+
+(define-public fastahack
+ (let ((commit "c68cebb4f2e5d5d2b70cf08fbdf1944e9ab2c2dd"))
+ (package
+ (name "fastahack")
+ (version (git-version "0.0.0" "1" commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/ekg/fastahack/")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0hfdv67l9g611i2ck4l92pd6ygmsp9g1ph4zx1ni7qkpsikf0l19"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; Unclear how to run tests: https://github.com/ekg/fastahack/issues/15
+ #: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))
+ #t)))))
+ (home-page "https://github.com/ekg/fastahack")
+ (synopsis "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 library
+provides a FASTA reader and indexer that can be embedded into applications
+which would benefit from directly reading subsequences from FASTA files. The
+library automatically handles index file generation and use.")
+ (license (list license:expat license:gpl2)))))
+
+(define-public vcflib
+ (let ((commit "5ac091365fdc716cc47cc5410bb97ee5dc2a2c92")
+ (revision "1"))
+ (package
+ (name "vcflib")
+ (version (git-version "0.0.0" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/vcflib/vcflib/")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1gijvcz1lcdn5kvgzb671l6iby0379qk00nqmcrszgk67hfwx6kq"))))
+ (build-system gnu-build-system)
+ (inputs
+ `(("zlib" ,zlib)))
+ (native-inputs
+ `(("perl" ,perl)
+ ("python" ,python-2)
+ ;; Submodules.
+ ;; This package builds against the .o files so we need to extract the source.
+ ("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 git-fetch)
+ (uri (git-reference
+ (url "https://github.com/ekg/intervaltree/")
+ (commit "dbb4c513d1ad3baac516fc1484c995daf9b42838")))
+ (file-name "intervaltree-src-checkout")
+ (sha256
+ (base32 "1fy5qbj4bg8d2bjysvaa9wfnqn2rj2sk5yra2h4l5pzvy53f23fj"))))))
+ (arguments
+ `(#:tests? #f ; no tests
+ #: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
+ (if (file-is-directory? (assoc-ref inputs source))
+ (copy-recursively (assoc-ref inputs source) ".")
+ (invoke "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")))))
+ (replace 'build
+ (lambda* (#:key inputs make-flags #:allow-other-keys)
+ (with-directory-excursion "tabixpp"
+ (invoke "make"))
+ (invoke "make" "CC=gcc"
+ (string-append "CFLAGS=\"" "-Itabixpp " "\"")
+ "all")))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
+ (lib (string-append (assoc-ref outputs "out") "/lib")))
+ (for-each (lambda (file)
+ (install-file file bin))
+ (find-files "bin" ".*"))
+ ;; The header files in src/ do not interface libvcflib,
+ ;; therefore they are left out.
+ (install-file "libvcflib.a" lib))
+ #t)))))
+ (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 freebayes
+ (let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb")
+ (revision "1")
+ (version "1.0.2"))
+ (package
+ (name "freebayes")
+ (version (git-version version revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/ekg/freebayes.git")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1sbzwmcbn78ybymjnhwk7qc5r912azy5vqz2y7y81616yc3ba2a2"))))
+ (build-system gnu-build-system)
+ (inputs
+ `(("bamtools" ,bamtools)
+ ("htslib" ,htslib)
+ ("zlib" ,zlib)))
+ (native-inputs
+ `(("bc" ,bc) ; Needed for running tests.
+ ("samtools" ,samtools) ; Needed for running tests.
+ ("parallel" ,parallel) ; Needed for running tests.
+ ("perl" ,perl) ; Needed for running tests.
+ ("procps" ,procps) ; Needed for running tests.
+ ("python" ,python-2) ; Needed for running tests.
+ ("vcflib-src" ,(package-source vcflib))
+ ;; These are submodules for the vcflib version used in freebayes.
+ ;; This package builds against the .o files so we need to extract the source.
+ ("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 git-fetch)
+ (uri (git-reference
+ (url "https://github.com/ekg/intervaltree/")
+ (commit "dbb4c513d1ad3baac516fc1484c995daf9b42838")))
+ (file-name "intervaltree-src-checkout")
+ (sha256
+ (base32 "1fy5qbj4bg8d2bjysvaa9wfnqn2rj2sk5yra2h4l5pzvy53f23fj"))))
+ ;; These submodules are needed to run the tests.
+ ("bash-tap-src" ,(package-source bash-tap))
+ ("test-simple-bash-src"
+ ,(origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/ingydotnet/test-simple-bash/")
+ (commit "124673ff204b01c8e96b7fc9f9b32ee35d898acc")))
+ (file-name "test-simple-bash-src-checkout")
+ (sha256
+ (base32 "043plp6z0x9yf7mdpky1fw7zcpwn1p47px95w9mh16603zqqqpga"))))))
+ (arguments
+ `(#:make-flags
+ (list "CC=gcc"
+ (string-append "BAMTOOLS_ROOT="
+ (assoc-ref %build-inputs "bamtools")))
+ #:test-target "test"
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (add-after 'unpack 'fix-tests
+ (lambda _
+ (substitute* "test/t/01_call_variants.t"
+ (("grep -P \"\\(\\\\t500\\$\\|\\\\t11000\\$\\|\\\\t1000\\$\\)\"")
+ "grep -E ' (500|11000|1000)$'"))
+ #t))
+ (add-after 'unpack 'unpack-submodule-sources
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((unpack (lambda (source target)
+ (with-directory-excursion target
+ (if (file-is-directory? (assoc-ref inputs source))
+ (copy-recursively (assoc-ref inputs source) ".")
+ (invoke "tar" "xvf"
+ (assoc-ref inputs source)
+ "--strip-components=1"))))))
+ (and
+ (unpack "vcflib-src" "vcflib")
+ (unpack "fastahack-src" "vcflib/fastahack")
+ (unpack "filevercmp-src" "vcflib/filevercmp")
+ (unpack "fsom-src" "vcflib/fsom")
+ (unpack "intervaltree-src" "vcflib/intervaltree")
+ (unpack "multichoose-src" "vcflib/multichoose")
+ (unpack "smithwaterman-src" "vcflib/smithwaterman")
+ (unpack "tabixpp-src" "vcflib/tabixpp")
+ (unpack "test-simple-bash-src" "test/test-simple-bash")
+ (unpack "bash-tap-src" "test/bash-tap")))))
+ (add-after 'unpack-submodule-sources 'fix-makefiles
+ (lambda _
+ ;; We don't have the .git folder to get the version tag from.
+ (substitute* "vcflib/Makefile"
+ (("^GIT_VERSION.*")
+ (string-append "GIT_VERSION = v" ,version)))
+ (substitute* "src/Makefile"
+ (("-I\\$\\(BAMTOOLS_ROOT\\)/src")
+ "-I$(BAMTOOLS_ROOT)/include/bamtools"))
+ #t))
+ (add-before 'build 'build-tabixpp-and-vcflib
+ (lambda* (#:key inputs make-flags #:allow-other-keys)
+ (with-directory-excursion "vcflib"
+ (with-directory-excursion "tabixpp"
+ (apply invoke "make"
+ (string-append "HTS_LIB="
+ (assoc-ref inputs "htslib")
+ "/lib/libhts.a")
+ make-flags))
+ (apply invoke "make"
+ (string-append "CFLAGS=-Itabixpp")
+ "all"
+ make-flags))))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+ (install-file "bin/freebayes" bin)
+ (install-file "bin/bamleftalign" bin))
+ #t)))))
+ (home-page "https://github.com/ekg/freebayes")
+ (synopsis "Haplotype-based variant detector")
+ (description "FreeBayes is a Bayesian genetic variant detector designed to
+find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms),
+indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and
+complex events (composite insertion and substitution events) smaller than the
+length of a short-read sequencing alignment.")
+ (license license:expat))))