NGS Tools missing for Knime 4.7

[mwiegand]

Hi,

It seems the KNIME NGS tools – KNIME Community Hub is nowhere to be found in the repositories. Anyone got an idea about a possible fix?

Best
Mike

[Martyna]

Hi @mwiegand

yes, you are right. They don’t work with 4.7 anymore. As the development team (which is coming from the community and not in our hands) isn’t active here anymore but code adjustment was needed, we had to take them out. In older KNIME versions you can still find it.

Is there any particular node or functionality you are missing? Maybe there is an alternative?

Best regards,
Martyna

[mwiegand]

Hi @Martyna,

thanks a lot for your reply. I was desperately searching for a statement about NGS and find it sad to hear, by the way it’s the first time ever in many years, that development for some great extensions came to a halt.

The Bash – KNIME Community Hub node in particular, albeit having it’s limitations covered in other posts, I found to have great potential. Possible replacements are KNIME External Tool Support – KNIME Community Hub

But, frankly speaking, these are quite inconvenient to use. They require a bash script which is significantly more complex than executing a bash command. That bash script might also be required to get saved manually as a real external script and made executable. The Permissions node fails to set 755 for POSIX I noticed lately. Writing and reading files to pass data into the bash script is complex to say the least and adds, because of enclosing quotes being added, a ton of complexity. Not to speak about parallelization.

Despite spending hours in an attempt to just do a simple ping -c 1 google.com I had zero success. Enough of the whining … I was quite perplexed to see well working workflows breaking all of a sudden w/o a statement / notice.

The example workflows for the external tools are either not working or not explanatory. So it feels like a humongous regression. Hope this could explain the “situation”.

Best
Mike

[mwiegand]

Just as a follow up as I have noticed there a a few other community members which got caught by surprise. I have tried my very best to summarize the struggle about the external nodes in this post:

External Tool "issues" and high difficulty to use

Hi, Preamble I apologize for the lengthly post but have been working on it, reading through many Knime community posts, working through Hub examples, try & erroring over quite some time, in order to provide a comprehensive picture. Actual Post I am trying to replace the Bash Node from NGS, which got removed entirely with Knime 4.7 (Corresponding posts here and here) , by any of the external tools nodes like External Tool (Labs) – KNIME Community Hub However, the input and output files as we…

I hope this sheds some light on the issue since I believe how the decommissioning was carried out is a great opportunity to improve.

Best
Mike