[Fix Bug] Cannot find exp2qcdt command.

project.clj

@@ -17,7 +17,7 @@
   {:provided
    {:dependencies
     [[org.clojure/clojure "1.10.1"]
-     [org.clojars.yjcyxky/tservice "0.5.6"]]}
+     [org.clojars.yjcyxky/tservice "0.5.8"]]}
 
    :uberjar
    {:auto-clean    true

src/tservice/plugins/quartet_rnaseq_report.clj

@@ -135,6 +135,12 @@
     (fs-lib/create-directories! files-keep-dir)
     (fs-api/copy-files! files-keep files-keep-dir {:replace-existing true})))
 
+(defn update-log-process!
+  "Update message into log file and process into database."
+  [log-path coll task-id process]
+  (spit log-path (json/write-str coll))
+  (update-process! task-id process))
+
 (defn date
   []
   (.format (java.text.SimpleDateFormat. "yyyy-MM-dd")
@@ -181,24 +187,33 @@
         (decompression-tar files-qualimap-RNA-tar))
       (update-process! task-id 50)
       (gen-multiqc-config config-path)
-      (spit parameters-file (json/write-str {"Report Name" (:name parameters)
-                                             "Description" (:description parameters)
-                                             "Report Tool" (format "%s-%s"
-                                                                   (:plugin-name parameters)
-                                                                   (:plugin-version parameters))
-                                             "Team" "Quartet Team"
-                                             "Date" (date)}))
-      (let [exp2qcdt-result (exp2qcdt/call-exp2qcdt! exp-fpkm-filepath exp-count-filepath metadata-file result-dir)
-            multiqc-result (if (= (:status exp2qcdt-result) "Success")
-                             (mq/multiqc result-dir dest-dir {:config config-path :template "default" :title "Quartet RNA report"})
-                             ;;(mq/multiqc result-dir)
-                             exp2qcdt-result)
-            result {:status (:status multiqc-result)
-                    :msg (:msg multiqc-result)}
-            log (json/write-str result)]
-        (log/info "Status: " result)
-        (spit log-path log))
-      (update-process! task-id 100)
+      (let [results (ff/chain-fn-coll [(fn []
+                                         (update-process! task-id 60)
+                                         (exp2qcdt/call-exp2qcdt! exp-fpkm-filepath exp-count-filepath metadata-file result-dir))
+                                       (fn []
+                                         (update-process! task-id 70)
+                                         (spit parameters-file (json/write-str {"Report Name" (:name parameters)
+                                                                                "Description" (:description parameters)
+                                                                                "Report Tool" (format "%s-%s"
+                                                                                                      (:plugin-name parameters)
+                                                                                                      (:plugin-version parameters))
+                                                                                "Team" "Quartet Team"
+                                                                                "Date" (date)}))
+                                         {:status "Success" :msg ""})
+                                       (fn []
+                                         (update-process! task-id 80)
+                                         (mq/multiqc result-dir dest-dir {:config config-path
+                                                                          :template "default"
+                                                                          :title "Quartet RNA report"
+                                                                          :env {:PATH (add-env-to-path "quartet-metqc-report")}}))]
+                                      (fn [result] (= (:status result) "Success")))
+            status (:status (last results))
+            msg (apply str (map :msg results))
+            process (if (= status "Success") 100 -1)]
+        (log/info (format "Running batch command: %s" (pr-str results)))
+        (update-log-process! log-path {:status status
+                                       :msg msg}
+                             task-id process))
       (catch Exception e
         (update-process! task-id -1)
         (let [log (json/write-str {:status "Error" :msg (.toString e)})]

src/tservice/plugins/quartet_rnaseq_report/exp2qcdt.clj

@@ -1,6 +1,8 @@
 (ns tservice.plugins.quartet-rnaseq-report.exp2qcdt
   "A wrapper for exp2qcdt tool."
   (:require [tservice.api.config :refer [add-env-to-path]]
+            [tservice.lib.files :refer [get-plugin-jar-env-dir]]
+            [tservice.lib.fs :as fs-lib]
             [clojure.java.shell :as shell :refer [sh]]))
 
 (defn call-exp2qcdt!
@@ -12,10 +14,11 @@
   "
   [exp-file cnt-file meta-file result-dir]
   (shell/with-sh-env {:PATH   (add-env-to-path "quartet-rnaseq-report")
+                      :R_PROFILE_USER (fs-lib/join-paths (get-plugin-jar-env-dir "quartet-rnaseq-report") "Rprofile")
                       :LC_ALL "en_US.utf-8"
                       :LANG   "en_US.utf-8"}
     (let [command ["bash" "-c"
-                   (format "exp2qcdt -e %s -c %s -m %s -o %s" exp-file cnt-file meta-file result-dir)]
+                   (format "exp2qcdt.sh -e %s -c %s -m %s -o %s" exp-file cnt-file meta-file result-dir)]
           result  (apply sh command)
           status (if (= (:exit result) 0) "Success" "Error")
           msg (str (:out result) "\n" (:err result))]