draft of file minus images

docs/user_guide/example_genomics/func_annots/blast.rst

@@ -133,7 +133,7 @@ The top section of this page provides multiple methods for providing results fil
 
 .. note::
 
-  For the **Server path** we need not give the full path.  Because we downloaded the files into the Drupal directory we can leave off any preceeding path and Tripal will resolve the path.  Otherwise we could provide the full path.
+  For the **Server path** we need not give the full path.  Because we downloaded the files into the Drupal directory we can leave off any preceding path and Tripal will resolve the path.  Otherwise we could provide the full path.
 
 .. note::
 

docs/user_guide/example_genomics/func_annots/interpro.rst

@@ -20,26 +20,24 @@ Create the Analysis Page
 
     It is always recommended to create an analysis page anytime you import data. The purpose of the analysis page is to describe how the data being added was derived or collected.
 
+Tripal defines the **InterPro Results** Bundle, which is a specific type of Chado analysis.  Create a new record by going to ``Content -> Tripal Content -> Add Tripal Content --> InterPro Results``.
 
-    Analysis Name: InterPro Annotations of C. sinensis v1.0
-Program: InterProScan
-Program Version: 4.8
-Algorithm: iprscan
-Source name: C. sinensis v1.0 mRNA
-Time Executed: (today's date)
-Materials & Methods: C. sinensis mRNA sequences were mapped to IPR domains and GO terms using a local installation of InterProScan executed on a computational cluster. InterProScan date files used were MATCH_DATA_v32, DATA_v32.0 and PTHR_DATA v31.0.
-InterPro Settings
-InterProScan XML File/Directory: /var/www/html/sites/default/files/Citrus_sinensis-orange1.1g015632m.g.iprscan.xml
+Fill out the fields as described in the table below.
 
 
+.. csv-table::
+  :header: "Field", "Value"
 
-Check the box 'Submit a job to parse the Interpro XML output'
-Check the box 'Load GO terms'
-Parameters: iprscan -cli -goterms -ipr -format xml
-Query Type: mRNA
-
-
+  "Name", "InterPro Annotations of C. sinensis v1.0"
+  "InterPro Program", "InterProScan"
+  "InterPro Version", 4.8
+  "Date Performed", "Current date"
+  "Data Source Name", "C. sinensis v1.0 mRNA"
+  "Data Source Version", "v1.0"
+  "Data Source URI", "n/a"
+  "Description", "Materials & Methods: C. sinensis mRNA sequences were mapped to IPR domains and GO terms using a local installation of InterProScan executed on a computational cluster. InterProScan date files used were MATCH_DATA_v32, DATA_v32.0 and PTHR_DATA v31.0."
 
+Press the **Save** button.
 
 Import the InterProScan XML results
 ------------------------------------
@@ -47,25 +45,28 @@ Import the InterProScan XML results
 
 Next, we will load InterProScan results for our citrus gene.  To do this, navigate to **Tripal > Data Loaders > Chado InterProScan XML results loader**.  The following page will be presented:
 
-.. image:: blast4.png
+.. image:: interpro1.png
 
-The top section of this page provides multiple methods for providing results file: via an upload interface, specifying a remote URL or a file path that is local to the server.  Most likely, you will always upload or provide a remote URL.  However, we download the file earlier, and stored them here: ```$DRUPAL_HOME/sites/default/files```.  So, in this case we can use the path on the local server.  Provide the following value for this form:
+The top section of this page provides multiple methods for providing results file: via an upload interface, specifying a remote URL or a file path that is local to the server.  Most likely, you will always upload or provide a remote URL.  However, we downloaded the files earlier, and stored them here: ```$DRUPAL_HOME/sites/default/files```.  So, in this case we can use the path on the local server.  Provide the following value for this form:
 
 .. csv-table::
   :header: "Field", "Value"
 
-  "Server path", "sites/default/files/Blastx_citrus_sinensis-orange1.1g015632m.g.fasta.0_vs_uniprot_sprot.fasta.out"
-  "Analysis", "blastx Citrus sinensis v1.0 genes vs ExPASy SwissProt (blastall 2.2.25, Citrus sinensis mRNA vs ExPASy SwissProt)"
-  "Database", "ExPASy SwissProt"
-  "BLAST XML File Extension", "out"
+  "Server path", "sites/default/files/Citrus_sinensis-orange1.1g015632m.g.iprscan.xml"
+  "Analysis", " InterPro Annotations of C. sinensis v1.0"
+  'Load GO terms to the database', 'checked'
+  "Query Name RE", ""
+  "Use Unique Name", "unchecked"
   "Query Type", "mRNA"
 
 .. note::
 
-  For the **Server path** we need not give the full path.  Because we downloaded the files into the Drupal directory we can leave off any preceeding path and Tripal will resolve the path.  Otherwise we could provide the full path.
+  For the **Server path** we need not give the full path.  Because we downloaded the files into the Drupal directory we can leave off any preceding path and Tripal will resolve the path.  Otherwise we could provide the full path.
 
-.. note::
 
-  Specifying **ExPASy SwissProt** as the database will allow the importer to use the database configuration settings we entered earlier.
 
-Clicking the **Import BLAST file** will add a job which we can manually execute with the following command:
+Clicking the **Import InterProScan file** will add a job which we can manually execute with the following command:
+
+::
+
+    drush trp-run-jobs --username=administrator --root=$DRUPAL_HOME