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01/02: Revert "gnu: Add freebayes."
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From: |
guix-commits |
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Subject: |
01/02: Revert "gnu: Add freebayes." |
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Date: |
Thu, 8 Aug 2019 08:35:27 -0400 (EDT) |
efraim pushed a commit to branch master
in repository guix.
commit 6bc63fd8a7a44a3b2bd1686be619237e7dd94ef1
Author: Efraim Flashner <address@hidden>
Date: Thu Aug 8 15:32:39 2019 +0300
Revert "gnu: Add freebayes."
This reverts commit 173e046950e153477a6aaa0f4860d8f080df6843.
---
gnu/packages/bioinformatics.scm | 123 ----------------------------------------
1 file changed, 123 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 311a83e..7808976 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -15100,126 +15100,3 @@ 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
- `(("zlib" ,zlib)
- ("htslib" ,htslib)))
- (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.
- ("bamtools" ,bamtools)
- ("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
- `(#:tests? #f ; TODO: Re-enable when we have grep with perl support.
- #:test-target "test"
- #:phases
- (modify-phases %standard-phases
- (delete 'configure)
- (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-makefile
- (lambda* (#:key inputs #:allow-other-keys)
- ;; We don't have the .git folder to get the version tag from.
- (substitute* '("vcflib/Makefile")
- (("^GIT_VERSION.*") (string-append "GIT_VERSION = v"
,version)))))
- (replace 'build
- (lambda* (#:key inputs make-flags #:allow-other-keys)
- (with-directory-excursion "vcflib"
- (with-directory-excursion "tabixpp"
- (pk "Compile tabixpp before compiling the main project.")
- (let ((htslib-ref (assoc-ref inputs "htslib")))
- (invoke "make" "HTS_HEADERS="
- (string-append "HTS_LIB=" htslib-ref
"/lib/libhts.a")
- (string-append "LIBPATH=-L. -L" htslib-ref
"/include"))))
- (pk "Compile vcflib before compiling the main project.")
- (invoke "make" "CC=gcc"
- (string-append "CFLAGS=\"" "-Itabixpp "
- "-I" (assoc-ref inputs "htslib")
"/include " "\"")
- "all"))
- (pk "Compile the main project.")
- (with-directory-excursion "src"
- (substitute* "Makefile"
- (("-I\\$\\(BAMTOOLS_ROOT\\)/src")
"-I$(BAMTOOLS_ROOT)/include/bamtools"))
- (invoke "make"
- (string-append "BAMTOOLS_ROOT="
- (assoc-ref inputs "bamtools"))))))
- (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))))