Remove vscode specific instructions.

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

diff --git a/dockerfile/Dockerfile b/dockerfile/Dockerfile
deleted file mode 100644 (file)
index c73bcf2..0000000
--- a/dockerfile/Dockerfile
+++ /dev/null
@@ -1,2 +0,0 @@
-FROM debian:10
-RUN apt-get update && apt-get -y --no-install-recommends install subread
\ No newline at end of file

diff --git a/lesson1/lesson1.md b/lesson1/lesson1.md
index f394c901f82c5583152839a31975ddfcf1eae3ac..cf10e406d17fc7f87136a0857577ac2487f5e822 100644 (file)
--- a/lesson1/lesson1.md
+++ b/lesson1/lesson1.md
@@ -7,9 +7,7 @@ In this lesson we will turn `rnaseq_analysis_on_input_file.sh` into a workflow.
 We will create a new git repository and import a library of existing
 tool definitions that will help us build our workflow.
 
-1. Select "Terminal->New terminal"
-
-2. Create a new git repository to hold our workflow with this command:
+Create a new git repository to hold our workflow with this command:
 
 ```
 git init rnaseq-cwl-training-exercises
@@ -21,11 +19,7 @@ On Arvados use this:
 git clone https://github.com/arvados/arvados-vscode-cwl-template.git rnaseq-cwl-training-exercises
 ```
 
-3. Go to File->Open Folder and select rnaseq-cwl-training-exercises
-
-4. Go to the terminal window
-
-5. Import bio-cwl-tools with this command:
+Next, import bio-cwl-tools with this command:
 
 ```
 git submodule add https://github.com/common-workflow-library/bio-cwl-tools.git

diff --git a/lesson2/lesson2.md b/lesson2/lesson2.md
index c1107c27d98072526312d567527245a22ff772b9..d7fb5a98b3b96d06e3d5bb84bf789dfb832075b6 100644 (file)
--- a/lesson2/lesson2.md
+++ b/lesson2/lesson2.md
@@ -52,8 +52,6 @@ Type this into the terminal:
 cwl-runner main.cwl main-input.yaml
 ```
 
-On Arvados with vscode, select "main.cwl" and then choose "Terminal -> Run task -> Run CWL workflow on Arvados"
-
 ### 3. Debugging the workflow
 
 A workflow can fail for many reasons: some possible reasons include
@@ -163,8 +161,6 @@ This is a rather large download (4 GB).  Depending on your bandwidth, it may be
 
 ### Downloading
 
-Go to the "Terminal" tab in the lower vscode panel.  If necessary, select `bash` from the dropdown list in the upper right corner.
-
 ```
 mkdir hg19-chr1-STAR-index
 cd hg19-chr1-STAR-index
@@ -187,9 +183,7 @@ Gtf:
 Overhang: 99
 ```
 
-Next, go to the "Terminal" tab in the lower vscode panel.  If
-necessary, select `bash` from the dropdown list in the upper right
-corner.  Generate the index with your local cwl-runner.
+Generate the index with your local cwl-runner.
 
 ```
 cwl-runner bio-cwl-tools/STAR/STAR-Index.cwl chr1-star-index.yaml

diff --git a/lesson6/lesson6.md b/lesson6/lesson6.md
index cf75df4b646acef87d0252492077cee116fa28f6..c367a2b58e9815e3c6f59ba3ca823f5d8b7ebbfe 100644 (file)
--- a/lesson6/lesson6.md
+++ b/lesson6/lesson6.md
@@ -23,8 +23,13 @@ Gitter (chat) https://gitter.im/common-workflow-language/common-workflow-languag
 
 Weekly video calls https://cwl.discourse.group/t/eu-us-timezone-cwl-video-chat/260
 
+## Software resources
+
 Github organization for repositories of CWL tool and workflow
-descriptions https://github.com/common-workflow-library/
+descriptions, including bio-cwl-tools
+https://github.com/common-workflow-library/
+
+BioContainers https://biocontainers.pro/
 
 Search for CWL files on github, try adding the name of a tool you are
 interested in to the search