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googlegenomics / pipelines-api-examples

Examples for the Google Genomics Pipelines API.
BSD 3-Clause "New" or "Revised" License
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E: Package 'docker.io' has no installation candidate #72

Open wenweiliang opened 6 years ago

wenweiliang commented 6 years ago

I was running the example provided by cwl_runner. It seems like docker.io can't be installed. Here is the error:

Copying gs://genomics-public-data/cwl-examples/gdc-dnaseq-cwl/workflows/dnaseq/transform.cwl...
/ [0/1 files][    0.0 B/ 19.1 KiB]   0% Done                                    
/ [1/1 files][ 19.1 KiB/ 19.1 KiB] 100% Done                                    
Operation completed over 1 objects/19.1 KiB.                                     
Copying gs://genomics-public-data/cwl-examples/gdc-dnaseq-cwl/input/gdc-dnaseq-input.json...
/ [0/1 files][    0.0 B/  363.0 B]   0% Done                                    
/ [1/1 files][  363.0 B/  363.0 B] 100% Done                                    
Operation completed over 1 objects/363.0 B.                                      
E: Package 'docker.io' has no installation candidate
sudo: easy_install: command not found
Failed to start docker.service: Unit docker.service not found.
/startup-bmLh_c/tmpy1X4h2: line 120: virtualenv: command not found
/startup-bmLh_c/tmpy1X4h2: line 121: cwl/bin/activate: No such file or directory
/startup-bmLh_c/tmpy1X4h2: line 122: pip: command not found
/startup-bmLh_c/tmpy1X4h2: line 130: cwl-runner: command not found
/startup-bmLh_c/tmpy1X4h2: line 132: deactivate: command not found
Building synchronization state...
Starting synchronization...
Copying file:///tmp/status-20359.txt [Content-Type=text/plain]...
/ [0 files][    0.0 B/    7.0 B]                                                
/ [1 files][    7.0 B/    7.0 B]                                                
Operation completed over 1 objects/7.0 B.                                        
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100    41  100    41    0     0   4849      0 --:--:-- --:--:-- --:--:--  5125
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100    12  100    12    0     0   1423      0 --:--:-- --:--:-- --:--:--  1500
mbookman commented 6 years ago

I don't believe there is anyone maintaining the cwl_runner example. I think the right thing is to at least mark it as such in the README or take it down.

That said, I can make a few suggestions:

Docker installation has changed since this script was written. Instructions are on the docker web site, but the steps depend on the platform (Debian, Ubuntu, etc.) that you are using.

It might end up being a slippery slope of fixes to get it working. I'm just guessing since this file has not changed in a meaningful way since it was checked in over a year ago (Feb 2017).

Cromwell documentation indicates that by Cromwell 30 it will support both WDL and CWL, although I don't see this called out in the release notes for Cromwell 30 or 31, and I have not yet tested it.

wenweiliang commented 6 years ago

Hi @mbookman Thanks for the suggestions. I have fixed the docker installation issue by changing docker.io to docker , but here is another error:

debconf: unable to initialize frontend: Dialog
debconf: (Dialog frontend will not work on a dumb terminal, an emacs shell buffer, or without a controlling terminal.)
debconf: falling back to frontend: Readline
debconf: unable to initialize frontend: Readline
debconf: (Can't locate Term/ReadLine.pm in @INC (you may need to install the Term::ReadLine module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.24.1 /usr/local/share/perl/5.24.1 /usr/lib/x86_64-linux-gnu/perl5/5.24 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.24 /usr/share/perl/5.24 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at /usr/share/perl5/Debconf/FrontEnd/Readline.pm line 7, <> line 46.)
debconf: falling back to frontend: Teletype
dpkg-preconfigure: unable to re-open stdin: 
warning: no previously-included files matching '*' found under directory 'docs/_templates'
warning: no previously-included files matching '*' found under directory 'docs/_build'
Failed to start docker.service: Unit docker.service not found.
/cwl/bin/cwl-runner 1.0.20180403145700
Resolved '/mnt/data/input/gs/genomics-public-data/cwl-examples/gdc-dnaseq-cwl/workflows/dnaseq/transform.cwl' to 'file:///mnt/data/input/gs/genomics-public-data/cwl-examples/gdc-dnaseq-cwl/workflows/dnaseq/transform.cwl'
I'm sorry, I couldn't load this CWL file, try again with --debug for more information.
The error was: cwltool requires Node.js engine to evaluate and validate Javascript expressions, but couldn't find it.  Tried nodejs, node, docker run node:slim
Building synchronization state...
Starting synchronization...
Copying file:///tmp/status-7627.txt [Content-Type=text/plain]...
/ [0 files][    0.0 B/    7.0 B]                                                
/ [1 files][    7.0 B/    7.0 B]                                                
Operation completed over 1 objects/7.0 B.                                        
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100    41  100    41    0     0   5922      0 --:--:-- --:--:-- --:--:--  6833
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100    11  100    11    0     0   1549      0 --:--:-- --:--:-- --:--:--  1571

I don't see any CWL support in Cromwell documentation. In stead of waiting for Crowell updates, I am thinking to take a roundabout like installing rabix in VM to run cwl on google cloud. Anyways, please let me know if you have other thoughts.

smrgit commented 6 years ago

@wenweiliang I too was looking at whether or not Cromwell supports CWL and although it was advertised as coming with release 30 (which was released in December of last year), I don't see it mentioned in the release notes or elsewhere in the documentation. I did come across this Rabix tutorial which seems to illustrate running Rabix on GCP using Funnel and TES, which might worth looking at.