Re: [galaxy-user] remove versions of tool
Hi Bjoern, This is a tool I am developing. In Galaxy admin, I could not find any option to manage tools and versions. In my tools directory, there is just one tool xml file for this tool. Thanks, Ketan On Sat, Feb 1, 2014 at 6:40 PM, Björn Grüning wrote: > Hi Ketan, > > have you installed your tool via the Tool Shed? > If so, than you need to delete the old revision of your tool. > > Cheers, > Bjoern > > > Hi, > > > > > > I renamed my tool name in but when I restart Galaxy > > server, I see a dropdown in front of the tool title with two versions > > with same value. When I select one it gives current name and when > > selecting other it gives the older name of the tool. > > > > > > My intention here was to rename the tool and I did not do anything > > that would tell Galaxy to preserve versions. After looking into the > > past mailing list posts, I tried to : > > > > > > 1. Restart Galaxy server. > > 2. Deleted integrated_tool_panel.xml > > 3. cleared my browser cache and cookies > > > > > > None of the above worked though. Any suggestions? > > > > > > Attached is a snapshot of what I am seeing. > > > > > > Best, > > -- > > Ketan > > > > > > ___ > > The Galaxy User list should be used for the discussion of > > Galaxy analysis and other features on the public server > > at usegalaxy.org. Please keep all replies on the list by > > using "reply all" in your mail client. For discussion of > > local Galaxy instances and the Galaxy source code, please > > use the Galaxy Development list: > > > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > > > To manage your subscriptions to this and other Galaxy lists, > > please use the interface at: > > > > http://lists.bx.psu.edu/ > > > > To search Galaxy mailing lists use the unified search at: > > > > http://galaxyproject.org/search/mailinglists/ > > > -- Ketan ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-user] remove versions of tool
Hi, I renamed my tool name in but when I restart Galaxy server, I see a dropdown in front of the tool title with two versions with same value. When I select one it gives current name and when selecting other it gives the older name of the tool. My intention here was to rename the tool and I did not do anything that would tell Galaxy to preserve versions. After looking into the past mailing list posts, I tried to : 1. Restart Galaxy server. 2. Deleted integrated_tool_panel.xml 3. cleared my browser cache and cookies None of the above worked though. Any suggestions? Attached is a snapshot of what I am seeing. Best, -- Ketan <>___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] special character $ gets converted to X in tool
Thank you. It worked and the sanitizer tag sounds very useful. On Sat, Feb 1, 2014 at 4:14 AM, Björn Grüning wrote: > Hi Ketan! > > it sounds like your input is sanitized. You can disable it for your > whole wrapper or you can write a special sanitizer for your input field: > > > https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Csanitizer.3E_tag_set > > Cheers, > Bjoern > > > Hi, > > > > > > In a test tool that I am working on, I need to enter text preceded by > > a $ sign to be interpreted as an environment variable by the > > underlying running script. However, it seems that the $ sign gets > > converted to X when it gets passed to the tool executable. > > > > > > Is there a way to work around this or should I be doing something else > > to pass environment variables via Galaxy tool UI. > > > > > > Thanks, > > Ketan > > > > > > > > > > ___ > > The Galaxy User list should be used for the discussion of > > Galaxy analysis and other features on the public server > > at usegalaxy.org. Please keep all replies on the list by > > using "reply all" in your mail client. For discussion of > > local Galaxy instances and the Galaxy source code, please > > use the Galaxy Development list: > > > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > > > To manage your subscriptions to this and other Galaxy lists, > > please use the interface at: > > > > http://lists.bx.psu.edu/ > > > > To search Galaxy mailing lists use the unified search at: > > > > http://galaxyproject.org/search/mailinglists/ > > > -- Ketan ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] special character $ gets converted to X in tool
Thanks! Just wanted to report that \$ does not work; \ adds one more X. On Fri, Jan 31, 2014 at 11:29 AM, Peter Cock wrote: > On Fri, Jan 31, 2014 at 5:13 PM, Ketan Maheshwari > wrote: > > Hi, > > > > In a test tool that I am working on, I need to enter text preceded by a $ > > sign to be interpreted as an environment variable by the underlying > running > > script. However, it seems that the $ sign gets converted to X when it > gets > > passed to the tool executable. > > > > Is there a way to work around this or should I be doing something else to > > pass environment variables via Galaxy tool UI. > > > > Thanks, > > Ketan > > This is a security feature I think - or it may just need escaping as \$ > > Since you are writing the script, why not pass in the environment > variable name without the dollar? > > Peter > -- Ketan ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-user] special character $ gets converted to X in tool
Hi, In a test tool that I am working on, I need to enter text preceded by a $ sign to be interpreted as an environment variable by the underlying running script. However, it seems that the $ sign gets converted to X when it gets passed to the tool executable. Is there a way to work around this or should I be doing something else to pass environment variables via Galaxy tool UI. Thanks, Ketan ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-user] tool within a tool
Hi, I am wondering if it is possible in Galaxy to design a tool whose sole purpose is to run other tools. This is motivated by our desire to enhance execution capabilities of existing tools via a generic tool which acts as a wrapper. Thanks, -- Ketan ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-user] viewing data live while tool is running
Hi, I am a relatively new Galaxy user. I am wondering if there is an example of a tool which allows users to view at the stdout/err of a tool live while it is still running to get a sense of progress it is making. The tools I have had experience with so far will save the stdout/err or an elaborate report as they are running and those results would be available for users only after the tool has completed running. Admittedly I have not searched through the toolshed exhaustively. Best, -- Ketan ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
