Tutorial fixes (#940)

Tutorial fixes

Author: nsoranzo

docs/_writing_testing.rst

@@ -10,7 +10,7 @@ install BWA - but however you obtain it should be fine.
 
 ::
 
-    $ conda install --force -c bioconda bwa
+    $ conda install --force -c conda-forge -c bioconda bwa
         ... bwa installation ...
     $ bwa
     Program: bwa (alignment via Burrows-Wheeler transformation)

docs/_writing_using_seqtk.rst

@@ -7,7 +7,7 @@ install Seqtk - but however you obtain it should be fine.
 
 ::
 
-    $ conda install --force --yes -c bioconda seqtk=1.2
+    $ conda install --force --yes -c conda-forge -c bioconda seqtk=1.2
         ... seqtk installation ...
     $ seqtk seq
             Usage:   seqtk seq [options] <in.fq>|<in.fa>

docs/appliance.rst

@@ -78,6 +78,15 @@ and the machine should become available.
 .. image:: images/ova_importing.png
    :alt: Screenshot OVA Import
 
+When the import is finished (and before starting the VM), right-click on the new appliance and select "Settings":
+
+1. in the "General" -> "Advanced" tab, select "Bidirectional" for "Shared Clipboard"
+2. in the "Display" -> "Screen" tab, tick "Enable 3D Acceleration"
+3. in the "Network" -> "Adapter 1" tab, select "PCnet-FAST III (Am79c973)" as "Adapter Type"
+4. Click the "OK" button
+
+Now start the appliance by clicking the "Start" button.
+
 The Firefox browser, Komodo_ and Atom_ editors, Galaxy, Planemo and everything else is
 available right away on the desktop along with useful links.
 

docs/tests/tests_building.sh

@@ -15,7 +15,7 @@ rm -rf tool_init_exercise
 
 # Tests
 
-conda install --force --yes -c bioconda seqtk=1.2
+conda install --force --yes -c conda-forge -c bioconda seqtk=1.2
 
 cat <(seqtk seq)
 

docs/tests/tests_building_cwl.sh

@@ -13,7 +13,7 @@ cd
 rm -rf tool_init_exercise
 
 # Tests
-conda install --force --yes -c bioconda seqtk=1.2
+conda install --force --yes -c conda-forge -c bioconda seqtk=1.2
 
 cat <(seqtk seq)
 

docs/tests/tests_tdd.sh

@@ -9,7 +9,7 @@ cd
 rm -rf bwa
 
 # Tests
-conda install --force --yes -c bioconda bwa
+conda install --force --yes -c conda-forge -c bioconda bwa
 
 echo "Executing bwa to see help - should see output, but it has a non-zero exit code."
 bwa | true

docs/writing/gc_content.xml

@@ -1,11 +1,11 @@
 <tool id="gc_content" name="Compute GC content">
   <description>for each sequence in a file</description>
-  <command>perl $__tool_directory__/gc_content.pl $input output.tsv</command>
+  <command>perl '$__tool_directory__/gc_content.pl' '$input' output.tsv</command>
   <inputs>
-    <param format="fasta" name="input" type="data" label="Source file"/>
+    <param name="input" type="data" format="fasta" label="Source file"/>
   </inputs>
   <outputs>
-    <data format="tabular" name="output" from_work_dir="output.tsv" />
+    <data name="output" format="tabular" from_work_dir="output.tsv" />
   </outputs>
   <help>
 This tool computes GC content from a FASTA file.