[Fix Bug] multiqc cannot work properly.

resources/renv.lock

@@ -48,15 +48,15 @@
     },
     "ProtQC": {
       "Package": "ProtQC",
-      "Version": "0.1.3",
+      "Version": "0.1.4",
       "Source": "GitHub",
       "RemoteType": "github",
       "RemoteHost": "api.github.com",
       "RemoteRepo": "ProtQC",
       "RemoteUsername": "chinese-quartet",
-      "RemoteRef": "v0.1.3",
-      "RemoteSha": "01edb13db10e24e38aa06299bfe7b69e009cd134",
-      "Hash": "c5ae657d64a2afd72770effa4767a049"
+      "RemoteRef": "v0.1.4",
+      "RemoteSha": "412e0040e713af756ee1c5381f352b2c04df96f5",
+      "Hash": "7251a9d21c0c5d39f251d4e1a488a203"
     },
     "R6": {
       "Package": "R6",

resources/tservice-plugin.yaml

@@ -19,7 +19,7 @@ init:
   # Unpack environment file to the directory, repository/envs/quartet-protqc-report
   - step: unpack-env
     envname: quartet-protqc-report
-    postunpack: chmod a+x {{ENV_DEST_DIR}}/quartet-protqc-report/bin/protqc.sh
+    postunpack: chmod a+x {{ENV_DEST_DIR}}/bin/protqc.sh
   - step: load-namespace
     namespace: tservice.plugins.quartet-protqc-report
   - step: register-plugin

src/tservice/plugins/quartet_protqc_report.clj

@@ -4,7 +4,7 @@
             [spec-tools.core :as st]
             [clojure.tools.logging :as log]
             [tservice.lib.files :as ff]
-            [clojure.string :as clj-str]
+            [tservice.api.config :refer [add-env-to-path]]
             [tservice.lib.fs :as fs-lib]
             [tservice.vendor.multiqc :as mq]
             [tservice.plugins.quartet-protqc-report.protqc :as protqc]
@@ -62,7 +62,7 @@
                      metadata-file (protqc/correct-filepath metadata_file)
                      workdir (protqc/dirname data-file)
                      log-path (fs-lib/join-paths workdir "log")
-                     response {:report (format "%s/multireport.html" workdir)
+                     response {:report (format "%s/multiqc_report.html" workdir)
                                :log log-path
                                :response-type :data2report}
                      task-id (create-task! {:name           name
@@ -123,7 +123,10 @@
                                      {:status "Success" :msg ""})
                                    (fn []
                                      (update-process! task-id 80)
-                                     (mq/multiqc result-dir dest-dir {:template "default" :title "Quartet Report for Proteomics"}))]
+                                     (mq/multiqc result-dir dest-dir
+                                                 {:template "quartet_proteome_report"
+                                                  :title "Quartet Report for Proteomics"
+                                                  :env {:PATH (add-env-to-path "quartet-protqc-report")}}))]
                                   (fn [result] (= (:status result) "Success")))
         status (:status (last results))
         msg (apply str (map :msg results))

src/tservice/plugins/quartet_protqc_report/protqc.clj

@@ -1,8 +1,9 @@
 (ns tservice.plugins.quartet-protqc-report.protqc
   "A wrapper for protqc tool."
   (:require [tservice.api.config :refer [add-env-to-path]]
-            [tservice.lib.files :refer [is-localpath?]]
+            [tservice.lib.files :refer [is-localpath? get-plugin-jar-env-dir]]
             [clojure.string :as clj-str]
+            [tservice.lib.fs :as fs-lib]
             [clojure.java.shell :as shell :refer [sh]]
             [clojure.java.io :refer [file]]))
 
@@ -14,6 +15,7 @@
   "
   [exp-file meta-file result-dir]
   (shell/with-sh-env {:PATH   (add-env-to-path "quartet-protqc-report")
+                      :R_PROFILE_USER (fs-lib/join-paths (get-plugin-jar-env-dir "quartet-protqc-report") "Rprofile")
                       :LC_ALL "en_US.utf-8"
                       :LANG   "en_US.utf-8"}
     (let [command ["bash" "-c"