Merge pull request #1 from NatPRoach/clustering

Add draft of clustering functionality; restructure directory layout to be inline with nimble recommendations; add .nimble file

.gitignore

@@ -5,19 +5,22 @@
 !*/
 
 # Whitelist gitignore, scripts, and figures
+!.gitmodules
 !.gitignore
 !CONDUIT.png
 !**.py
 !**.R
 !**.bsh
 !**.nim
+!**.nims
+!**.nimble
 !**.md
 !**.c
 !**.h
 !**.rst
 !**.html
 !Makefile
-!poaV2/Makefile
 !LICENSE
+!poaV2/Makefile
 !poaV2/LICENSE
 !poaV2/myNUC3.4.4.mat

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "threadpools"]
+	path = src/threadpools
+	url = https://github.com/yglukhov/threadpools.git

Makefile

@@ -1,7 +1,8 @@
 NIM = nim c
 
 conduit:
-	cd poaV2 && make
-	$(NIM) -d:release --threads:on --passL:poaV2/liblpo.a --passL:poaV2/align_score.o conduit.nim
-	$(NIM) -d:release conduitUtils.nim
+	cd src/poaV2 && make
+	mkdir bin/
+	cd src/ && $(NIM) -d:release --threads:on --passL:poaV2/liblpo.a --passL:poaV2/align_score.o conduit.nim && mv src/conduit bin/
+	cd src/ && $(NIM) -d:release conduitUtils.nim && mv src/conduitUtils bin/
 

conduit.nimble

@@ -0,0 +1,19 @@
+# Package
+
+version       = "0.1.0"
+author        = "Nathan Roach"
+description   = "De novo transcriptome assembler"
+license       = "GPLv2"
+
+# Dependencies
+
+requires "hts >= 0.3.1", "nim >= 1.0.0"
+
+srcDir = "src/"
+
+before install:
+  echo "Building poaV2"
+  withDir "src/poaV2":
+    exec "make"
+
+bin = @["conduit", "conduitUtils", "conduit_clustering"]

src/conduit.nims

@@ -0,0 +1,3 @@
+switch("threads", "on")
+switch("passL","src/poaV2/liblpo.a")
+switch("passL","src/poaV2/align_score.o")