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cl-genomic.asd
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cl-genomic.asd
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;;;
;;; Copyright (c) 2007-2013 Keith James. All rights reserved.
;;;
;;; This file is part of cl-genomic.
;;;
;;; This program is free software: you can redistribute it and/or modify
;;; it under the terms of the GNU General Public License as published by
;;; the Free Software Foundation, either version 3 of the License, or
;;; (at your option) any later version.
;;;
;;; This program is distributed in the hope that it will be useful,
;;; but WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with this program. If not, see <http://www.gnu.org/licenses/>.
;;;
(in-package :cl-user)
(asdf:load-system :deoxybyte-systems)
(in-package :uk.co.deoxybyte-systems)
(defsystem cl-genomic
:name "Common Lisp Genomics"
:version "0.9.0"
:author "Keith James"
:licence "GPL v3"
:depends-on ((:version :deoxybyte-systems "1.0.0")
(:version :cffi "0.10.3")
(:version :cl-ppcre "2.0.0")
(:version :cl-base64 "3.1") ; Actually 3.3.1, but
; cl-base64's ASDF file
; is out of sync with its
; professed version
(:version :ironclad "0.27")
(:version :deoxybyte-io "0.8.0")
(:version :deoxybyte-unix "0.6.5")
(:version :deoxybyte-utilities "0.9.0")
:puri)
:in-order-to ((test-op (load-op :cl-genomic :cl-genomic-test))
(doc-op (load-op :cl-genomic :cldoc)))
:components ((:module :core
:pathname "src/"
:components
((:file "package")
(:file "generics"
:depends-on ("package"))
(:file "conditions"
:depends-on ("package"))
(:file "bio-sequence-encoding"
:depends-on ("package"))
(:file "bio-alphabets"
:depends-on ("package"
"generics"
"bio-sequence-encoding"))
(:file "bio-sequence-classes"
:depends-on ("package"
"bio-alphabets"
"bio-sequence-encoding"))
(:file "checksum"
:depends-on ("package"
"bio-alphabets"
"bio-sequence-encoding"
"bio-sequence-classes"))
(:file "bio-sequence-interval"
:depends-on ("package"
"generics"
"bio-sequence-classes"))
(:file "genetic-codes"
:depends-on ("package"
"bio-alphabets"
"bio-sequence-encoding"))
(:file "bio-sequence"
:depends-on ("package"
"generics"
"bio-alphabets"
"bio-sequence-encoding"
"bio-sequence-classes"
"genetic-codes"))
(:file "fjoin"
:depends-on ("package"
"bio-sequence-interval"))))
(:module :io
:pathname "src/io/"
:components
((:file "bio-sequence-io-classes")
(:file "bio-sequence-io"
:depends-on ("bio-sequence-io-classes"))
(:file "pure"
:depends-on ("bio-sequence-io"))
(:file "raw"
:depends-on ("bio-sequence-io"))
(:file "fasta"
:depends-on ("bio-sequence-io"))
(:file "fastq"
:depends-on ("bio-sequence-io"))
(:file "format-conversion"
:depends-on ("bio-sequence-io"
"pure"
"raw"
"fasta"
"fastq"))
(:file "obo-io-classes")
(:file "obo"
:depends-on ("obo-io-classes"))
(:file "obo-powerloom"
:depends-on ("obo-io-classes"
"obo"))
(:file "gff3"))
:depends-on (:core))
(:module :align
:pathname "src/alignment/"
:components
((:file "bio-sequence-alignment")
(:file "hamming")
(:file "matrices")
(:file "pairwise"
:depends-on ("matrices"
"bio-sequence-alignment")))
:depends-on (:core)))
:perform (test-op :after (op c)
(maybe-run-lift-tests :cl-genomic
"cl-genomic-test.config"))
:perform (doc-op :after (op c)
(maybe-build-cldoc-docs :cl-genomic "doc/html")))