Add troubleshooting page in doc (issue #24 and #25.

docs/index.rst

@@ -37,6 +37,7 @@ Documentation of M2M
     suppinformation
     api
     m2m_analysis
+    troubleshooting
 
 
 Additional features

docs/troubleshooting.rst

@@ -0,0 +1,71 @@
+===============
+Troubleshooting
+===============
+
+Several potential fix for issues we encounter.
+
+`m2m_analysis`: "Can't connect to X11 window server using..."
+-------------------------------------------------------------
+
+Issue encountered when using `m2m_analysis` on a HPC:
+
+::
+    
+    <II> Create SVG ... Exception in thread "main" java.awt.AWTError: Can't connect to X11 window server using ':0' as the value of the DISPLAY variable.
+        at sun.awt.X11GraphicsEnvironment.initDisplay(Native Method)
+        at sun.awt.X11GraphicsEnvironment.access$200(X11GraphicsEnvironment.java:65)
+        at sun.awt.X11GraphicsEnvironment$1.run(X11GraphicsEnvironment.java:115)
+        at java.security.AccessController.doPrivileged(Native Method)
+        at sun.awt.X11GraphicsEnvironment.<clinit>(X11GraphicsEnvironment.java:74)
+        at java.lang.Class.forName0(Native Method)
+        at java.lang.Class.forName(Class.java:264)
+        at java.awt.GraphicsEnvironment.createGE(GraphicsEnvironment.java:103)
+        at java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment(GraphicsEnvironment.java:82)
+        at java.awt.image.BufferedImage.createGraphics(BufferedImage.java:1181)
+        at org.apache.batik.svggen.SVGGraphics2D.<init>(Unknown Source)
+        at org.apache.batik.svggen.SVGGraphics2D.<init>(Unknown Source)
+        at org.mattlab.eaglevista.ui.GraphImageFactory.getSVGGraphicsOfGraph(GraphImageFactory.java:157)
+        at org.mattlab.eaglevista.ui.GraphImageFactory.createImage(GraphImageFactory.java:80)
+        at org.mattlab.eaglevista.ui.EvCommandLineInterpreter.runImpl(EvCommandLineInterpreter.java:466)
+        at org.mattlab.eaglevista.ui.EvCommandLineInterpreter.main(EvCommandLineInterpreter.java:81)
+
+
+One potential fix is to unset DISPLAY before launching m2m:
+
+::
+
+    unset DISPLAY
+    m2m_analysys workflow...
+
+
+UnicodeDecodeError when running m2m_analysis with Singularity
+-------------------------------------------------------------
+
+Error encountered when using `m2m_analysis` in a Singularity:
+
+::
+
+    ######### Creation of the powergraph website accessible at results_m2m_analysis_scfa/html/metabolic_targets_scfa #########
+    Traceback (most recent call last):
+    File "/usr/local/bin/m2m_analysis", line 8, in <module>
+        sys.exit(main())
+    File "/usr/local/lib/python3.6/dist-packages/metage2metabo/__main_analysis__.py", line 289, in main
+        args.oog, new_arg_modelhost, args.level)
+    File "/usr/local/lib/python3.6/dist-packages/metage2metabo/__main_analysis__.py", line 303, in main_analysis_workflow
+        run_analysis_workflow(*allargs)
+    File "/usr/local/lib/python3.6/dist-packages/metage2metabo/m2m_analysis/m2m_analysis_workflow.py", line 48, in run_analysis_workflow
+        powergraph_analysis(gml_output, output_dir, oog_jar, taxon_file, taxonomy_level)
+    File "/usr/local/lib/python3.6/dist-packages/metage2metabo/m2m_analysis/graph_compression.py", line 174, in powergraph_analysis
+        merge_html_css_js(html_target +'_taxon', output_html_merged)
+    File "/usr/local/lib/python3.6/dist-packages/metage2metabo/m2m_analysis/graph_compression.py", line 473, in merge_html_css_js
+        cytoscape_min_js_str =  input_cytoscape_min_js.read()
+    File "/usr/lib/python3.6/encodings/ascii.py", line 26, in decode
+        return codecs.ascii_decode(input, self.errors)[0]
+    UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 234868: ordinal not in range(128)
+
+This is an issue with the encodign standard used. A solution is to set the local codec to `LC_ALL=C.UTF-8`:
+
+::
+
+    LC_ALL=C.UTF-8 && srun singularity exec -B....
+