Revert "gnu: Add vcflib."
This reverts commit 194e45f90a.
This commit does not have a good commit message, and it breaks master
This commit is contained in:
Efraim Flashner
parent
6bc63fd8a7
commit
1a069a170c
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@ -14868,24 +14868,6 @@ mutations from scRNA-Seq data.")
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some of the details of opening and jumping in tabix-indexed files.")
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some of the details of opening and jumping in tabix-indexed files.")
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(license license:expat)))
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(license license:expat)))
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(define tabixpp-freebayes
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;; This version works with FreeBayes while the released
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;; version doesn't. The released creates a variable with the name \"vcf\"
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;; somewhere, which is also the name of a namespace in vcflib.
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(let ((commit "bbc63a49acc52212199f92e9e3b8fba0a593e3f7"))
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(package
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(inherit tabixpp)
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(name "tabixpp-freebayes")
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(version (git-version "0.0.0" "1" commit))
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(source (origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/ekg/tabixpp/")
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(commit commit)))
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(file-name (git-file-name name version))
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(sha256
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(base32 "017qsmsc2kyiyzqr9nl8cc6pfldxf16dbn8flx5i59mbqr9ydi7g")))))))
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(define-public smithwaterman
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(define-public smithwaterman
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;; TODO: Upgrading smithwaterman breaks FreeBayes.
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;; TODO: Upgrading smithwaterman breaks FreeBayes.
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(let ((commit "203218b47d45ac56ef234716f1bd4c741b289be1"))
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(let ((commit "203218b47d45ac56ef234716f1bd4c741b289be1"))
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@ -15013,90 +14995,3 @@ provides a FASTA reader and indexer that can be embedded into applications
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which would benefit from directly reading subsequences from FASTA files. The
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which would benefit from directly reading subsequences from FASTA files. The
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library automatically handles index file generation and use.")
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library automatically handles index file generation and use.")
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(license (list license:expat license:gpl2)))))
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(license (list license:expat license:gpl2)))))
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(define-public vcflib
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(let ((commit "5ac091365fdc716cc47cc5410bb97ee5dc2a2c92")
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(revision "1"))
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(name "vcflib")
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(version (git-version "0.0.0" revision commit))
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(source
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(origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/vcflib/vcflib/")
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(commit commit)))
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(file-name (git-file-name name version))
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(sha256
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(base32 "1gijvcz1lcdn5kvgzb671l6iby0379qk00nqmcrszgk67hfwx6kq"))))
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(build-system gnu-build-system)
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(inputs
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`(("zlib" ,zlib)))
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(native-inputs
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`(("perl" ,perl)
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("python" ,python-2)
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;; Submodules.
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;; This package builds against the .o files so we need to extract the source.
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("tabixpp-src" ,(package-source tabixpp-freebayes))
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("smithwaterman-src" ,(package-source smithwaterman))
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("multichoose-src" ,(package-source multichoose))
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("fsom-src" ,(package-source fsom))
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("filevercmp-src" ,(package-source filevercmp))
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("fastahack-src" ,(package-source fastahack))
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("intervaltree-src"
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,(origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/ekg/intervaltree/")
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(commit "dbb4c513d1ad3baac516fc1484c995daf9b42838")))
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(file-name "intervaltree-src-checkout")
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(sha256
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(base32 "1fy5qbj4bg8d2bjysvaa9wfnqn2rj2sk5yra2h4l5pzvy53f23fj"))))))
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(arguments
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`(#:tests? #f ; no tests
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#:phases
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(modify-phases %standard-phases
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(delete 'configure)
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(delete 'check)
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(add-after 'unpack 'unpack-submodule-sources
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(lambda* (#:key inputs #:allow-other-keys)
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(let ((unpack (lambda (source target)
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(with-directory-excursion target
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(if (file-is-directory? (assoc-ref inputs source))
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(copy-recursively (assoc-ref inputs source) ".")
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(invoke "tar" "xvf"
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(assoc-ref inputs source)
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"--strip-components=1"))))))
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(and
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(unpack "intervaltree-src" "intervaltree")
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(unpack "fastahack-src" "fastahack")
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(unpack "filevercmp-src" "filevercmp")
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(unpack "fsom-src" "fsom")
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(unpack "multichoose-src" "multichoose")
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(unpack "smithwaterman-src" "smithwaterman")
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(unpack "tabixpp-src" "tabixpp")))))
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(replace 'build
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(lambda* (#:key inputs make-flags #:allow-other-keys)
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(with-directory-excursion "tabixpp"
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(invoke "make"))
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(invoke "make" "CC=gcc"
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(string-append "CFLAGS=\"" "-Itabixpp " "\"")
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"all")))
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(replace 'install
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(lambda* (#:key outputs #:allow-other-keys)
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(let ((bin (string-append (assoc-ref outputs "out") "/bin"))
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(lib (string-append (assoc-ref outputs "out") "/lib")))
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(for-each (lambda (file)
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(install-file file bin))
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(find-files "bin" ".*"))
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;; The header files in src/ do not interface libvcflib,
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;; therefore they are left out.
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(install-file "libvcflib.a" lib))
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#t)))))
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(home-page "https://github.com/vcflib/vcflib/")
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(synopsis "Library for parsing and manipulating VCF files")
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(description "Vcflib provides methods to manipulate and interpret
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sequence variation as it can be described by VCF. It is both an API for parsing
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and operating on records of genomic variation as it can be described by the VCF
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format, and a collection of command-line utilities for executing complex
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manipulations on VCF files.")
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(license license:expat))))
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