solved the first problem

.gitignore

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/target
/lib
/classes
/checkouts
pom.xml
*.jar
*.class
.lein-deps-sum
.lein-failures
.lein-plugins

README.md

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# rosalind

A Clojure library designed to ... well, that part is up to you.

## Usage

FIXME

## License

Copyright © 2013 FIXME

Distributed under the Eclipse Public License, the same as Clojure.

data/rosalind_dna.txt

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ATATTCTAAGTTCCCGCACTATCTTCTAACCCGACTACGGGACCGGCATACGACCACACCCTCTCTTATACATGGCGGTTCTGACCATTGTTGATGCCTCTCTTGATACCGCAGAACGGAATCTAAGCCCGCGACAACTTATGTCGGCCCCAAGGGCATGGCCAGGCTTTTTATCAGTTACATTACATTGGAATAGGCATCTGCGGCGAGTCACTCTCGTGTCTACGGTCCGCTTCGACGAGGTTTGCCTTTGCCGGTCTCGGACGAATATCTATCGAGAATCATGCTGGACTTAACTCTATGAGTGGTCGTTAACACGCAACTTAAAACCAAAGACTAAAGGAATTGCCGTTGCATACTCGGAGATACTAACCACGACAAGATTTAGGATCGCTCCTGTCGGGTCATTACTGATTGGTTAGTGAGATTTCGACTCTTTGAGAAGAGCACTTTACTTAAGTCGCCGGTGACGTCATCACCTCAGCCATATAATAGGTACATTTTTCCGATCTCGGTGCTGGACGTCACACGCGGTTGTAGTGAGACGACGAGAATGGACTCAGTCAGAAGCTATTAACTGCTTGACACGCCCTCGACCTGGTGCCGAAAAAGTGAACTCTGTTTTGATTTTTATAAAGGGATCACGGTTTCAAAGATCCTGCTCTCTGCCTATGAACGTCATTCTTAATGCAGAGATTTACAGATGAGACGATGTAGCGGCGGCACCTAATACTGTATAGCATACCGGTGGCAGCAAATCTGTATGCGATGCCATCTGGGCCAGCTATATATCACGATGTTCTAGATAGGAGTTGCAACACGGACTCGACATCACTACGAATACAAAACCATATTATAGTCTAGCATTGAATGCTTGGAATTACTCCTAGAACTAGCCCGCACGGTATGTGGCAAAGG

doc/intro.md

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# Introduction to rosalind

TODO: write [great documentation](http://jacobian.org/writing/great-documentation/what-to-write/)

project.clj

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(defproject rosalind "0.1.0"
  :description "FIXME: write description"
  :url "http://example.com/FIXME"
  :license {:name "Eclipse Public License"
            :url "http://www.eclipse.org/legal/epl-v10.html"}
  :dependencies [[org.clojure/clojure "1.4.0"]]
  :main rosalind.core)

src/rosalind/basics.clj

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(ns rosalind.basics)

(defn dna-counter-fn
  "This actually does the counting"
  [dna cnt]
  (loop [d dna
         c cnt]
    (let [l (first d)
          r (rest d)]
      (case l
          \A (def h (assoc c :A (+ 1 (:A c))))
          \G (def h (assoc c :G (+ 1 (:G c))))
          \C (def h (assoc c :C (+ 1 (:C c))))
          \T (def h (assoc c :T (+ 1 (:T c))))
          nil)
      (if (empty? r)
        h
        (recur r h)))))

(defn dna-count
  "Counts DNA Neucleotides"
  [dna]
  (let [h (dna-counter-fn dna {:A 0 :C 0 :T 0 :G 0})]
    [(:A h) (:C h) (:G h) (:T h)]))

src/rosalind/core.clj

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(ns rosalind.core)

(defn foo
  "I don't do a whole lot."
  [x]
  (println x "Hello, World!"))

(defn -main
  "Main entry point"
  []
  (foo "oh bother..."))

test/rosalind/basics_test.clj

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(ns rosalind.basics-test
  (:use clojure.test
        rosalind.basics))

(deftest a-test
  (testing "DNA counting stuff"
    (is (=
      [20 12 17 21]
      (dna-count "AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC")))))

test/rosalind/core_test.clj

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(ns rosalind.core-test
  (:use clojure.test
        rosalind.core))

(deftest a-test
  (testing "FIXME, I fail."
    (is (= 0 0))))