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project.clj
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project.clj
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(defproject bcbio.variation "0.2.6"
:description "Toolkit to analyze genomic variation data, built on the GATK with Clojure"
:license {:name "MIT" :url "http://www.opensource.org/licenses/mit-license.html"}
:dependencies [[org.clojure/clojure "1.7.0"]
[org.clojure/math.combinatorics "0.1.1" :exclusions [org.clojure/clojure]]
[org.clojure/data.csv "0.1.2" :exclusions [org.clojure/clojure]]
[org.clojure/tools.cli "0.2.2"]
[clj-stacktrace "0.2.5"]
[bcbio.run "0.0.5"]
;; GATK requirements
[org.clojars.chapmanb/gatk-engine "3.2"]
[org.clojars.chapmanb/gatk-tools-public "3.2"]
[org.clojars.chapmanb/gatk-utils "3.2"]
[org.clojars.chapmanb/picard "1.112"]
[org.clojars.chapmanb/htsjdk "1.112"]
[colt/colt "1.2.0"]
[commons-lang "2.5"]
[log4j "1.2.17"]
[org.slf4j/slf4j-log4j12 "1.7.7"]
[org.apache.commons/commons-jexl "2.1.1"]
[org.reflections/reflections "0.9.9-RC1"]
[org.simpleframework/simple-xml "2.0.4"]
[org.apache.servicemix.bundles/org.apache.servicemix.bundles.jets3t "0.8.1_1"]
;;
[org.biojava/biojava-core "4.0.0"]
[org.biojava/biojava-alignment "4.0.0"]
[org.clojars.chapmanb/circdesigna "0.0.2" :exclusions [net.sf.beaver/beaver-ant]]
[nz.ac.waikato.cms.weka/weka-stable "3.6.6"]
[org.clojars.chapmanb/fast-random-forest "0.98"]
[com.leadtune/clj-ml "0.2.4" :exclusions [cs.waikato.ac.nz/weka
hr.irb/fastRandomForest
org.clojure/clojure
incanter/incanter-core
incanter/incanter-charts]]
[clj-yaml "0.4.0"]
[doric "0.8.0" :exclusions [org.clojure/clojure]]
[iota "1.1.1"]
[ordered "1.3.2" :exclusions [org.clojure/clojure]]
[de.kotka/lazymap "3.1.1"]
[lonocloud/synthread "1.0.4"]
[pallet-fsm "0.1.0"]
[criterium "0.4.1" :exclusions [org.clojure/clojure]]
[clj-time "0.5.1"]
[org.clojure/java.jdbc "0.2.2"]
[org.xerial/sqlite-jdbc "3.7.2"]
[c3p0/c3p0 "0.9.1.2"]
[hiccup "1.0.1"]
[enlive "1.0.1" :exclusions [org.clojure/clojure]]]
:min-lein-version "2.0.0"
:plugins [[lein-marginalia "0.7.1"]
[lein-midje "3.1.3"]]
:profiles {:dev {:dependencies
;; Testing dependencies
[[midje "1.7.0" :exclusions [org.clojure/clojure ordered]]
;; Non-uberjar dependencies we should extract into separate functionality
[incanter/incanter-core "1.5.1" :exclusions [org.clojure/clojure junit]]
[incanter/incanter-charts "1.5.1" :exclusions [org.clojure/clojure junit]]
[incanter/incanter-excel "1.5.1" :exclusions [org.clojure/clojure junit]]
[org.clojars.chapmanb/snpeff "3.1" :exclusions [com.googlecode.charts4j/charts4j
junit]]
[clj-genomespace "0.1.3"]
[clj-blend "0.1.1-SNAPSHOT"]
[clj-aws-s3 "0.3.10" :exclusions [org.codehaus.jackson/jackson-mapper-asl
org.codehaus.jackson/jackson-core-asl]]]}}
:repositories {"sonatype-snapshots" {:url "http://oss.sonatype.org/content/repositories/snapshots"
:snapshots true}}
:java-source-paths ["src/java"]
:javac-options ["-nowarn" "-target" "1.6" "-source" "1.6"]
;;:jvm-opts ["-Xms750m" "-Xmx2g"]
:omit-source false
:aot [bcbio.variation.vcfwalker bcbio.variation.core bcbio.variation.annotate.nbq
bcbio.variation.annotate.entropy bcbio.variation.annotate.mfe]
:main bcbio.variation.core
:aliases {"variant-compare" ["run" "-m" "bcbio.variation.compare"]
"variant-prep" ["run" "-m" "bcbio.variation.combine"]
"variant-evaluate" ["run" "-m" "bcbio.variation.evaluate"]
"variant-ensemble" ["run" "-m" "bcbio.variation.ensemble"]
"variant-haploid" ["run" "-m" "bcbio.variation.haploid"]
"variant-recall" ["run" "-m" "bcbio.variation.recall"]
"variant-reorder" ["run" "-m" "bcbio.align.reorder"]
"variant-utils" ["run" "-m" "bcbio.variation.utils.core"]
"variant-custom" ["run" "-m" "bcbio.variation.custom.core"]})