add shakefile to build read simulators and test them

Makefile

@@ -0,0 +1,40 @@
+include gmsl
+
+ILLUMINA_URL := http://www.niehs.nih.gov/research/resources/assets/docs/artbinchocolatecherrycake031915linux64tgz.tgz
+PBSIM_URL := https://pbsim.googlecode.com/files/pbsim-1.0.3-Linux-amd64.tar.gz
+DIR_FROM_URL := $(basename $(call last, $(call split, "/", $(1))))
+#ILLUMINA_DIR := $(call DIR_FROM_URL, ILLUMINA_URL)
+#PBSIM_DIR := $(call DIR_FROM_URL, PBSIM_URL)
+
+pbsim-1.0.3-Linux-amd64.tar.gz:
+	wget $(PBSIM_URL)
+
+pbsim-1.0.3-Linux-amd64: pbsim-1.0.3-Linux-amd64.tar.gz
+	tar -xf $<
+artbinchocolatecherrycake031915linux64tgz.tgz: 
+	wget $(ILLUMINA_URL)
+
+
+artbinchocolatecherrycake031915linux64tgz:
+define wget_and_untar
+
+$(basename $(call last, $(call split,/, $(1)))):  $(call last, $(call split,/, $(1))) 
+	tar -xf $(call last, $(call split,/, $(1)))
+
+$(call last, $(call split,/, $(1))):
+	wget $(1)
+	tar -xf $(call last, $(call split,/, $(1)))
+endef
+s := /
+#define wget_and_untar
+#$(basename 2): 
+#	wget $(1)$(2)
+#	tar xf $(2) 
+#endef
+
+bin/art_illumina: 
+	echo $(call wget_and_untar, $(ILLUMINA_URL))
+
+#bin/pbsim:
+#	$(call wget_and_untar, PBSIM_URL)
+

Shakefile.hs

@@ -0,0 +1,43 @@
+import System.Directory(getCurrentDirectory)
+import Control.Monad.IO.Class(liftIO)
+import Development.Shake.Command(cmd) 
+import Development.Shake
+import Development.Shake.FilePath
+
+bin = "bin" 
+illuminaUrl = Url "http://www.niehs.nih.gov/research/resources/assets/docs/artbinchocolatecherrycake031915linux64tgz.tgz"
+pbsimUrl = Url "https://pbsim.googlecode.com/files/pbsim-1.0.3-Linux-amd64.tar.gz"
+
+illuminaTestOut = ["paired_end_com1.aln" , "paired_end_com1.fq" , "paired_end_com2.aln" , "paired_end_com2.fq" , "paired_end_com.sam"]
+
+newtype Url = Url String
+
+wgetAndUnTar :: Url -> Action () 
+wgetAndUnTar (Url url) = do 
+  () <- cmd "wget" url
+  let tar = reverse $ takeWhile (/= '/') $ reverse url
+  cmd "tar" "-xf" tar
+
+downloadAndLink :: Url -> FilePath -> FilePath -> Action ()
+downloadAndLink url binPath linkPath = do 
+   _ <- wgetAndUnTar url
+   pwd <- liftIO getCurrentDirectory
+   cmd "ln" "-s" (pwd </> binPath) linkPath
+
+main :: IO ()
+main = shakeArgs shakeOptions{shakeFiles="_build"} $ do
+  want illuminaTestOut
+  bin </> "art_illumina" %> \out -> do
+    downloadAndLink illuminaUrl "art_bin_ChocolateCherryCake/art_illumina" out
+
+  bin </> "pbsim" %> \out -> do
+     downloadAndLink pbsimUrl "pbsim-1.0.3-Linux-amd64/Linux-amd64/bin/pbsim" out
+
+  illuminaTestOut &%> \_  -> do 
+    need [bin </> "art_illumina"]
+    cmd (bin </> "art_illumina") ["-i", "art_bin_ChocolateCherryCake/examples/testSeq.fa", "-o", "./paired_end_com", "-ss", "HS25", "-l", "150", "-f", "10", "-p", "-m", "500", "-s", "10", "-sam"]
+
+  ["sd_0001.fastq", "sd_0001.maf", "sd_0001.ref"] &%> \_ -> do
+
+    need [bin </> "pbsim"]
+    cmd "pbsim" ["--data-type", "CLR", "--depth", "20", "--model_qc", "data/model_qc_clr", "sample/sample.fasta"]