gnu: pplacer: Remove the package, which is affected by a CVE on ocaml@4.01.
This makes progress towards fixing <https://bugs.gnu.org/27462>. * gnu/packages/bioinformatics.scm (pplacer, pplacer-scripts): Remove variables.
This commit is contained in:
Andreas Enge
parent
c12b234695
commit
2e125ece09
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@ -4365,130 +4365,6 @@ interrupted by stop codons. OrfM finds and prints these ORFs.")
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(home-page "https://github.com/wwood/OrfM")
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(license license:lgpl3+)))
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(define-public pplacer
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(let ((commit "807f6f3"))
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(package
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(name "pplacer")
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;; The commit should be updated with each version change.
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(version "1.1.alpha19")
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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/matsen/pplacer.git")
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(commit (string-append "v" version))))
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(file-name (git-file-name name version))
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(sha256
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(base32 "11ppbbbx20p2g9wj3ff64dhnarb12q79v7qh4rk0gj6lkbz4n7cn"))))
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(build-system ocaml-build-system)
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(arguments
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`(#:ocaml ,ocaml-4.01
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#:findlib ,ocaml4.01-findlib
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#:modules ((guix build ocaml-build-system)
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(guix build utils)
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(ice-9 ftw))
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#:phases
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(modify-phases %standard-phases
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(delete 'configure)
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(add-after 'unpack 'replace-bundled-cddlib
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(lambda* (#:key inputs #:allow-other-keys)
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(let* ((cddlib-src (assoc-ref inputs "cddlib-src"))
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(local-dir "cddlib_guix"))
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(mkdir local-dir)
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(with-directory-excursion local-dir
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(invoke "tar" "xvf" cddlib-src))
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(let ((cddlib-src-folder
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(string-append local-dir "/"
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(list-ref (scandir local-dir) 2)
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"/lib-src")))
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(for-each make-file-writable (find-files "cdd_src" ".*"))
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(for-each
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(lambda (file)
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(copy-file file
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(string-append "cdd_src/" (basename file))))
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(find-files cddlib-src-folder ".*[ch]$")))
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#t)))
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(add-after 'unpack 'fix-makefile
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(lambda _
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;; Remove system calls to 'git'.
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(substitute* "Makefile"
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(("^DESCRIPT:=pplacer-.*")
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(string-append
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"DESCRIPT:=pplacer-$(shell uname)-v" ,version "\n")))
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(substitute* "myocamlbuild.ml"
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(("git describe --tags --long .*\\\" with")
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(string-append
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"echo -n v" ,version "-" ,commit "\" with")))
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#t))
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(replace 'install
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(lambda* (#:key outputs #:allow-other-keys)
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(let* ((out (assoc-ref outputs "out"))
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(bin (string-append out "/bin")))
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(copy-recursively "bin" bin))
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#t)))))
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(native-inputs
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`(("zlib" ,zlib)
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("gsl" ,gsl)
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("ocaml-ounit" ,ocaml4.01-ounit)
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("ocaml-batteries" ,ocaml4.01-batteries)
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("ocaml-camlzip" ,ocaml4.01-camlzip)
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("ocaml-csv" ,ocaml4.01-csv)
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("ocaml-sqlite3" ,ocaml4.01-sqlite3)
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("ocaml-xmlm" ,ocaml4.01-xmlm)
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("ocaml-mcl" ,ocaml4.01-mcl)
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("ocaml-gsl" ,ocaml4.01-gsl)
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("cddlib-src" ,(package-source cddlib))))
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(propagated-inputs
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`(("pplacer-scripts" ,pplacer-scripts)))
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(synopsis "Phylogenetic placement of biological sequences")
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(description
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"Pplacer places query sequences on a fixed reference phylogenetic tree
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to maximize phylogenetic likelihood or posterior probability according to a
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reference alignment. Pplacer is designed to be fast, to give useful
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information about uncertainty, and to offer advanced visualization and
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downstream analysis.")
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(home-page "http://matsen.fhcrc.org/pplacer")
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(license license:gpl3))))
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;; This package is installed alongside 'pplacer'. It is a separate package so
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;; that it can use the python-build-system for the scripts that are
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;; distributed alongside the main OCaml binaries.
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(define pplacer-scripts
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(package
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(inherit pplacer)
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(name "pplacer-scripts")
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(build-system python-build-system)
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(arguments
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`(#:python ,python-2
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#:phases
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(modify-phases %standard-phases
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(add-after 'unpack 'enter-scripts-dir
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(lambda _ (chdir "scripts") #t))
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(replace 'check
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(lambda _ (invoke "python" "-m" "unittest" "discover" "-v") #t))
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(add-after 'install 'wrap-executables
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(lambda* (#:key inputs outputs #:allow-other-keys)
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(let* ((out (assoc-ref outputs "out"))
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(bin (string-append out "/bin")))
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(let ((path (string-append
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(assoc-ref inputs "hmmer") "/bin:"
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(assoc-ref inputs "infernal") "/bin")))
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(display path)
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(wrap-program (string-append bin "/refpkg_align.py")
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`("PATH" ":" prefix (,path))))
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(let ((path (string-append
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(assoc-ref inputs "hmmer") "/bin")))
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(wrap-program (string-append bin "/hrefpkg_query.py")
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`("PATH" ":" prefix (,path)))))
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#t)))))
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(inputs
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`(("infernal" ,infernal)
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("hmmer" ,hmmer)))
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(propagated-inputs
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`(("python-biopython" ,python2-biopython)
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("taxtastic" ,taxtastic)))
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(synopsis "Pplacer Python scripts")))
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(define-public python2-pbcore
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(package
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(name "python2-pbcore")
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