Old tool not showing up properly in Tool Shed
Hi all, I've just uploaded an update to my (previously protein only) sequence analysis bundle on the ToolShed, which is stuck with the original name: tmhmm_and_signalp This now offers Galaxy wrappers for several standalone command line sequence analysis tools: * SignalP 3.0 predicts signal peptides, see: http://www.cbs.dtu.dk/services/SignalP/ * TMHMM 2.0 predicts transmembrane helices, see: http://www.cbs.dtu.dk/services/TMHMM/ * Promoter 2.0 predicts eukaryotic PolII promoters [NEW WRAPPER], see: http://www.cbs.dtu.dk/services/Promoter/ * WoLF PSORT predicts Eukaryote protein sub-cellular localization, see: http://wolfpsort.org/ * Oomycete RXLR motif prediction - a Python script implementing three published methods, which calls SignalP 3.0 and HMMER 2.3.2 internally. In this update I added the new Promoter 2.0 wrapper, and made some small changes to the SignalP and TMHMM wrappers. The other tools are unchanged. Looking at the tool bundle via the Tool Shed, for revision 7:9b45a8743100 it only shows four "valid" tools: * Promoter 2.0 - Find eukaryotic PolII promoters in DNA sequences * RXLR Motifs - Find RXLR Effectors of Plant Pathogenic Oomycetes * SignalP 3.0 - Find signal peptides in protein sequences * TMHMM 2.0 - Find transmembrane domains in protein sequences Why is this missing?: * WoLF PSORT - Eukaryote protein subcellular localization prediction The missing tool is NOT showing up under "Browse my invalid tools", and the wrapper XML seems to still be there if I browse the tip files. Thanks, Peter
Hi Peter, This issue is part of a larger known issue that I have not had time to resolve due to preparation for the 2 consecutive recent conferences I've been involved in. This is my next chunk of though, and I'll let you know when I get it finished. In the meantime, even though the WoLF PSORT tool is not being displayed as part of what will get installed, it should still be installed along with the tools that are being displayed. Greg Von Kuster On Jul 30, 2012, at 10:37 AM, Peter Cock wrote:
Why is this missing?:
* WoLF PSORT - Eukaryote protein subcellular localization prediction
The missing tool is NOT showing up under "Browse my invalid tools", and the wrapper XML seems to still be there if I browse the tip files.
Thanks,
Peter ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
On Mon, Jul 30, 2012 at 4:32 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Hi Peter,
This issue is part of a larger known issue that I have not had time to resolve due to preparation for the 2 consecutive recent conferences I've been involved in. This is my next chunk of though, and I'll let you know when I get it finished.
In the meantime, even though the WoLF PSORT tool is not being displayed as part of what will get installed, it should still be installed along with the tools that are being displayed.
Greg Von Kuster
Thanks Greg - good to know you've already got a handle on what is amiss here. Peter
Hi Peter (and others in the Galaxy community using the tool shed), This issue should now be resolved in the Galaxy tool shed. Determining tool validity and whether certain change sets in the tool shed are valid (downloadable) is very complex, so there may still be some scenarios where things are not quite right. I'll continue to keep a close watch on this area and provide fixes as necessary. Please don't hesitate to contact me if you come across anything that is questionable. Thanks! Greg Von Kuster On Jul 30, 2012, at 11:32 AM, Greg Von Kuster wrote:
Hi Peter,
This issue is part of a larger known issue that I have not had time to resolve due to preparation for the 2 consecutive recent conferences I've been involved in. This is my next chunk of though, and I'll let you know when I get it finished.
In the meantime, even though the WoLF PSORT tool is not being displayed as part of what will get installed, it should still be installed along with the tools that are being displayed.
Greg Von Kuster
On Jul 30, 2012, at 10:37 AM, Peter Cock wrote:
Why is this missing?:
* WoLF PSORT - Eukaryote protein subcellular localization prediction
The missing tool is NOT showing up under "Browse my invalid tools", and the wrapper XML seems to still be there if I browse the tip files.
Thanks,
Peter ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
participants (2)
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Greg Von Kuster -
Peter Cock