Items missing from installation guide

[swzCuroverse]

So, I am running on Ubuntu , so this is just my experience.

I need to install
wheel
node.js
graphviz

and remove all instances of emphasize from the markdown.

For others having similar issues - please note what else you needed to do.

[swzCuroverse]

Also, all pre-reqs listed in user guide.

[smyja]

So, I am running on Ubuntu , so this is just my experience.

I need to install wheel node.js graphviz

and remove all instances of emphasize from the markdown.

For others having similar issues - please note what else you needed to do.

I needed to install graphviz and upgrade my pip. You'd also need to do an apt update.

[swzCuroverse]

Also I needed to close this block in prereq --> #278

[mr-c]

The wheel install is fixed in bb948f0

[remigathoni]

I followed the instructions in the setup tutorial. which included installing graphviz. However, I did not need to remove all the emphasize instances. Only the one on line 40 in src/topics/troubleshooting.md following this error message.

[simplyrucha]

Hi. I am an Outreachy internship applicant. Perhaps a bit late to join the contribution phase.
I am absolutely new to CWL and started going through the three guides (contribution, user & style). I was wondering if this could be a relevant task for me to take up, as I will have to start the installation process from scratch and work on (hopefully successive) bugs/ errors/ warnings I get. Please advise. Thank You.

[MARVEBUKA]

Hello @swzCuroverse, when setting up the development environment on Ubuntu, I had similar issues as those mentioned here. I had to install:

• tree (that will fix the issue at Items missing from installation guide #279 (comment))
• node.js
• graphviz

Will it be alright if i added a prerequisite section for Ubuntu under the buiding section of the contributing docs

[simplyrucha]

I followed the setup tutorial too but for Windows (Windows 10).
Few things that were different from the document:
Step 2:

• upgrade of WSL from 1 to version 2 required Enabling "Virtual Machine Platform" from the Window Features (Turn on/off features) >> reboot.
• Windows subsystem for Linux was already checked.

Step 3: I did not understand this step as after rebooting Ubuntu did not ask to configure any username or password.
When prompted at Step 5, I first tried blank (did not work) and then the password same as username, which worked.

Step 4: Docker setup did not prompt or initiated reboot but asked to close and log out. Post-logout steps were performed as listed in the tutorial.

After that everything worked except at the time of STAR Gnome Index creation. Received error for file format:

raise ValidationException(
schema_salad.exceptions.ValidationException: File has an incompatible format: {
  "class": "File",
  "location": "file:///home/dell/novice-tutorial-exercises/rnaseq/dm6.fa",
  "format": "https://edamontology.org/format_1929",

I changed the file format from https://edamontology.org/format_1929 to http://edamontology.org/format_1929 which debugged the error.

[swzCuroverse]

I followed the setup tutorial too but for Windows (Windows 10). Few things that were different from the document: Step 2:

* upgrade of WSL from 1 to version 2 required Enabling "Virtual Machine Platform" from the Window Features (Turn on/off features) >> reboot.

* Windows subsystem for Linux was already checked.

Step 3: I did not understand this step as after rebooting Ubuntu did not ask to configure any username or password. When prompted at Step 5, I first tried blank (did not work) and then the password same as username, which worked.

Step 4: Docker setup did not prompt or initiated reboot but asked to close and log out. Post-logout steps were performed as listed in the tutorial.

After that everything worked except at the time of STAR Gnome Index creation. Received error for file format:

raise ValidationException(
schema_salad.exceptions.ValidationException: File has an incompatible format: {
  "class": "File",
  "location": "file:///home/dell/novice-tutorial-exercises/rnaseq/dm6.fa",
  "format": "https://edamontology.org/format_1929",

I changed the file format from https://edamontology.org/format_1929 to http://edamontology.org/format_1929 which debugged the error.

I followed the setup tutorial too but for Windows (Windows 10). Few things that were different from the document: Step 2:

* upgrade of WSL from 1 to version 2 required Enabling "Virtual Machine Platform" from the Window Features (Turn on/off features) >> reboot.

* Windows subsystem for Linux was already checked.

Step 3: I did not understand this step as after rebooting Ubuntu did not ask to configure any username or password. When prompted at Step 5, I first tried blank (did not work) and then the password same as username, which worked.

Step 4: Docker setup did not prompt or initiated reboot but asked to close and log out. Post-logout steps were performed as listed in the tutorial.

After that everything worked except at the time of STAR Gnome Index creation. Received error for file format:

raise ValidationException(
schema_salad.exceptions.ValidationException: File has an incompatible format: {
  "class": "File",
  "location": "file:///home/dell/novice-tutorial-exercises/rnaseq/dm6.fa",
  "format": "https://edamontology.org/format_1929",

I changed the file format from https://edamontology.org/format_1929 to http://edamontology.org/format_1929 which debugged the error.

@simplyrucha -- since you were using the instructions from the Novice guide - I would open issues there for these differences here
https://github.com/carpentries-incubator/cwl-novice-tutorial/issues -->
since this is the repo for the User Guide.

It looks like the http issues was already addressed in bio-cwl-tools which the User Guides users --> common-workflow-library/bio-cwl-tools#144

[swzCuroverse]

I would also re-try the installl if you have any issues with the install from the cwltool itself here --> https://github.com/common-workflow-language/cwltool --> if those have the same issues then I would also place an issue in that repo.