update version of Rabix in cwl_runner; also Rabix option does not work

[smrgit]

the current version of Rabix baked into cwl_runner is v1.0.0-rc2 (released Dec 2016) -- Rabix is now up to v1.0.0-rc5

[smrgit]

also, btw, as far as I can tell, the option to use rabix (rather than cwltool) does not work -- neither with the "rc2" version, nor when I tried to use the newer "rc5" release

[jbingham]

Did you modify the startup script to change the Rabix version to rc2/5? What's the error message?

As I recall, it didn't work with Rabix even when cwl_runner was first created; that's why cwltool is the default. The Seven Bridges folks said that the dev branch did work, but it was not tested with cwl_runner.

[smrgit]

Ah, I was actually surprised to see that rabix was an option and assumed that it must have worked at least at some point in time.

Here is some of what I see in stdout when it gets to the Rabix installation part:

Sun Apr 30 20:31:08 UTC 2017
Installing Docker and CWL runner rabix
Reading package lists...
Building dependency tree...
Reading state information...
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
 openjdk-8-jre : Depends: openjdk-8-jre-headless (= 8u121-b13-1~bpo8+1) but it is not going to be installed
Hit http://packages.cloud.google.com cloud-sdk-jessie InRelease
Get:1 http://packages.cloud.google.com google-cloud-compute-jessie InRelease [3,771 B]
Hit http://packages.cloud.google.com google-cloud-packages-archive-keyring-jessie InRelease
Get:2 http://security.debian.org jessie/updates InRelease [63.1 kB]
Hit http://packages.cloud.google.com cloud-sdk-jessie/main amd64 Packages
Get:3 http://packages.cloud.google.com google-cloud-compute-jessie/main amd64 Packages [722 B]
Hit http://packages.cloud.google.com google-cloud-packages-archive-keyring-jessie/main amd64 Packages
<etc>

... although the installation may have eventually succeeded since it does eventually try to run the CWL workflow. In stderr, here is what I see:

mke2fs 1.42.12 (29-Aug-2014)
dirname: missing operand
Try 'dirname --help' for more information.
CommandException: Wrong number of arguments for "cp" command.
Building synchronization state...
Starting synchronization
Copying gs://genomics-public-data/cwl-examples/gdc-dnaseq-cwl/README.md...
Copying gs://genomics-public-data/cwl-examples/gdc-dnaseq-cwl/input/GRCh38.d1.vd1.fa.sa...

and then later:

E: Unable to correct problems, you have held broken packages.
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

<etc>

2017-04-30 20:32:13 (10.3 MB/s) - ârabix-1.0.0-rc2.tar.gzâ saved [31675917/31675917]

/mnt/data/input/rabix-1.0.0-rc2/rabix: 29: /mnt/data/input/rabix-1.0.0-rc2/rabix: java: not found
Building synchronization state...
Starting synchronization
Copying file:///tmp/status-9712.txt [Content-Type=text/plain]...

and that seems to be where it finally fails completely.

(All of the above is with the "rc2" version, but the stdout/stderr from the "rc5" test look pretty similar.)

[smrgit]

suggest removing this line from the README, pending a fix