diff --git a/docs/_writing_testing.rst b/docs/_writing_testing.rst index f00b5c755..2e2ab784a 100644 --- a/docs/_writing_testing.rst +++ b/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) diff --git a/docs/_writing_using_seqtk.rst b/docs/_writing_using_seqtk.rst index 874240147..7aa458d46 100644 --- a/docs/_writing_using_seqtk.rst +++ b/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] | diff --git a/docs/appliance.rst b/docs/appliance.rst index 2a406de65..467a711ae 100644 --- a/docs/appliance.rst +++ b/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. diff --git a/docs/tests/tests_building.sh b/docs/tests/tests_building.sh index 789b453c3..408e6a491 100644 --- a/docs/tests/tests_building.sh +++ b/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) diff --git a/docs/tests/tests_building_cwl.sh b/docs/tests/tests_building_cwl.sh index 4609ae18c..f37e9cacc 100644 --- a/docs/tests/tests_building_cwl.sh +++ b/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) diff --git a/docs/tests/tests_tdd.sh b/docs/tests/tests_tdd.sh index 8b8ff0742..b4c13c08d 100644 --- a/docs/tests/tests_tdd.sh +++ b/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 diff --git a/docs/writing/gc_content.xml b/docs/writing/gc_content.xml index dd2cd5805..eec57ee3d 100644 --- a/docs/writing/gc_content.xml +++ b/docs/writing/gc_content.xml @@ -1,11 +1,11 @@ for each sequence in a file - perl $__tool_directory__/gc_content.pl $input output.tsv + perl '$__tool_directory__/gc_content.pl' '$input' output.tsv - + - + This tool computes GC content from a FASTA file.