From d5374e266a3507fc69068b80a28f4d75ea5dbd19 Mon Sep 17 00:00:00 2001 From: Peter Amstutz Date: Mon, 25 Jan 2021 17:27:20 -0500 Subject: [PATCH] Remove vscode specific instructions. Arvados-DCO-1.1-Signed-off-by: Peter Amstutz --- dockerfile/Dockerfile | 2 -- lesson1/lesson1.md | 10 ++-------- lesson2/lesson2.md | 8 +------- lesson6/lesson6.md | 7 ++++++- 4 files changed, 9 insertions(+), 18 deletions(-) delete mode 100644 dockerfile/Dockerfile diff --git a/dockerfile/Dockerfile b/dockerfile/Dockerfile deleted file mode 100644 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 f394c90..cf10e40 100644 --- 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 c1107c2..d7fb5a9 100644 --- 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 cf75df4..c367a2b 100644 --- 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 -- 2.30.2