Question: Tools appearing/disappearing from tool panel (FreeBayes and BamLeftAlign)
1
gravatar for flwu
2.7 years ago by
flwu10
United States
flwu10 wrote:

Hi All,

I am seeing a problem where the tools FreeBayes and BamLeftAlign (under the NGS: Variant Analysis group) appear/disappear from the the left-hand tool panel when usegalaxy.org is refreshed. That is, upon refreshing the usegalaxy.org page FreeBayes and BamLeftAlign are missing from the tool panel when previously they were present. A few minutes later, refreshing will cause FreeBayes and BamLeftAlign to reappear. And so on and so forth.

I am fairly certain this is a server-side (not client-side) issue. I have replicated this issue on Firefox and Chrome. Moreover, when loading a personal workflow that uses FreeBayes during a "down" period, Galaxy fails to load the FreeBayes step properly and returns the error "Unrecognized Tool: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/0.4". (Tools other than FreeBayes and BamLeftAlign may also be affected; these two are the only ones I noticed).

Is this a known issue? Is the disappearance of the FreeBayes and BamLeftAlign tool due to the fact that they fall under the NGS Toolbox Beta umbrella?

Many thanks,

-F

bug software error • 648 views
ADD COMMENTlink modified 2.7 years ago by Martin Čech ♦♦ 4.3k • written 2.7 years ago by flwu10
0
gravatar for Martin Čech
2.7 years ago by
Martin Čech ♦♦ 4.3k
United States
Martin Čech ♦♦ 4.3k wrote:

It is certainly a backend issue and we are working on resolving it. Thank you very much for the precise report.

ADD COMMENTlink written 2.7 years ago by Martin Čech ♦♦ 4.3k

No problem. Thank you for looking into it.

ADD REPLYlink written 2.7 years ago by flwu10

I think we should be in a better shape now. Please let me know if this behavior persists for you.

ADD REPLYlink written 2.7 years ago by Martin Čech ♦♦ 4.3k

Will do. Things seem to be working well right now. Out of curiosity, can users assume that tools under the NGS Toolbox Beta umbrella are stable? Or should we avoid building workflows out of them because they are likely to change? Thanks again.

ADD REPLYlink written 2.7 years ago by flwu10

If they change it will result in a new version of the tool and the former version will still remain accessible. Some of them are out of beta now, like SAMtools section or RNA-Seq section with cufflinks, tophat etc.

ADD REPLYlink written 2.7 years ago by Martin Čech ♦♦ 4.3k
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