From e405e5af0c726f8bf9cd4475de079983fc8afa90 Mon Sep 17 00:00:00 2001
From: roryk <rory.kirchner@gmail.com>
Date: Thu, 30 Jan 2014 19:53:52 -0500
Subject: [PATCH] Add ability to run SEQC comparisons from the JAR file.

---
 src/bcbio/rnaseq/compare.clj |  4 +++-
 src/bcbio/rnaseq/core.clj    | 13 ++++++++++++-
 src/bcbio/rnaseq/util.clj    | 17 +++++++++++++----
 3 files changed, 28 insertions(+), 6 deletions(-)

diff --git a/src/bcbio/rnaseq/compare.clj b/src/bcbio/rnaseq/compare.clj
index c07e1c9..852b179 100644
--- a/src/bcbio/rnaseq/compare.clj
+++ b/src/bcbio/rnaseq/compare.clj
@@ -1,4 +1,5 @@
 (ns bcbio.rnaseq.compare
+  (:require [clojure.java.io :as io])
   (:use [bcbio.rnaseq.util]
         [bcbio.rnaseq.config]
         [clostache.parser :only [render-resource]]
@@ -15,7 +16,8 @@
   "create a fold change plot comparing to the seqc qPCR data"
   (let [template-file "comparisons/qPCR_foldchange.template"
         out-file (swap-directory "fc-plot.pdf" (analysis-dir))
-        qpcr-file (get-resource "seqc/qPCR/qpcr_HBRR_vs_UHRR.tidy")
+        qpcr-file (copy-resource
+                   "seqc/qPCR/qpcr_HBRR_vs_UHRR.tidy" (analysis-dir))
         template-config {:out-file (escape-quote out-file)
                          :qpcr-file (escape-quote qpcr-file)
                          :in-files (seq-to-rlist in-files)}]
diff --git a/src/bcbio/rnaseq/core.clj b/src/bcbio/rnaseq/core.clj
index 4c0ac25..b359a7e 100644
--- a/src/bcbio/rnaseq/core.clj
+++ b/src/bcbio/rnaseq/core.clj
@@ -58,6 +58,10 @@
   (setup-config project-file)
   (compare-callers (run-callers key cores)))
 
+(defn compare-seqc-run [project-file key cores]
+  (setup-config project-file)
+  (run-comparisons (keyword key) cores))
+
 (def compare-bcbio-run-options
   [["-h" "--help"]
    ["-n" "--cores CORES" "Number of cores"
@@ -71,11 +75,18 @@
         cores (get-in cli-options [:options :cores])]
     (compare-bcbio-run project-file (keyword key) cores)))
 
+(defn compare-seqc-cl-entry [& args]
+  (let [cli-options (parse-opts args compare-bcbio-run-options)
+        [project-file key] (:arguments cli-options)
+        cores (get-in cli-options [:options :cores])]
+    (compare-seqc-run project-file (keyword key) cores)))
+
+
 (defn -main [cur-type & args]
   (apply sh ["Rscript" (get-resource "scripts/install_libraries.R")])
   (apply (case (keyword cur-type)
            :compare-bcbio-run compare-bcbio-cl-entry
            :combine-counts combine-counts/cl-entry
-           :seqc-comparisons run-comparisons
+           :seqc-comparisons compare-seqc-cl-entry
            :compare-callers compare-callers)
          args))
diff --git a/src/bcbio/rnaseq/util.clj b/src/bcbio/rnaseq/util.clj
index db6cab9..fe94d8e 100644
--- a/src/bcbio/rnaseq/util.clj
+++ b/src/bcbio/rnaseq/util.clj
@@ -2,6 +2,19 @@
   (:require [clojure.java.io :as io]
             [me.raynes.fs :as fs]))
 
+(defn get-resource [filename]
+  "return a path to an included resource"
+  (try
+    (.getFile (io/resource filename))
+    (catch Exception e (println (format "Resource %s not found." filename)))))
+
+(defn copy-resource [resource dir]
+  "copy a resource from the .jar file to an external directory so
+   outside programs can use it"
+  (let [out-file (io/file dir (str (fs/base-name resource)))]
+    (spit out-file (slurp (io/resource resource)))
+    (str out-file)))
+
 (defn swap-directory [file dir]
   "/path/to/file -> /dir/file"
   (str (io/file dir (fs/base-name file))))
@@ -9,10 +22,6 @@
 (defn escape-quote [string]
   (str "\"" string "\""))
 
-(defn get-resource [filename]
-  (try
-    (.getFile (io/resource filename))
-    (catch Exception e (println (format "Resource %s not found." filename)))))
 
 (defn base-filename [filename]
   (fs/split-ext (fs/base-name filename)))