Re: [galaxy-dev] hmmer install
Thank you, Peter and Greg, for your feedback. Unfortunately, I am still hitting a wall with the hmmer install - even after creating a dummy hmmer.loc file and a hmmer.loc.sample file in my tool-data dir. All of my paths seem to be ok. Has anyone gotten hmmer to work on galaxy? Do I need to restart my cloud instance? Should I get instant feedback with the invalid hmmer.xml is valid, do I need to reinstall? Karen On Mon, Dec 2, 2013 at 3:51 AM, Peter Cock p.j.a.c...@googlemail.comwrote: On Mon, Dec 2, 2013 at 4:50 AM, Karen Miga khm...@soe.ucsc.edu wrote: Hi Greg, Thanks for the feedback. I cannot seem to find information for hmmdb.loc. When I look in the associated xml file it looks like it could be removed completely (does one need a precompiled HMM Database? I do not remember using anything like this when I run hmmer on the commandline). I have less experience with changing wrappers, etc. Have you tried just commenting this part out? And do I need to start the instance over to test it? Thanks in advance! - Karen conditional name=hmmdb param name=select type=select label=HMM Db option value=db selected=TruePrecompiled HMM Database/option option value=userHMM Database in your History/option /param when value=db param name=file type=select label=Precompiled HMM database options from_file=hmmdb.loc column name=name index=1/ column name=value index=2/ /options /param /when when value=user param name=file type=data format=hmmer label=HMM database / /when /conditional This lets the Galaxy HMMER wrapper either be used with system level HMM databases (listed in hmmer.loc, e.g. PFAM) or with the user's own HMM databases in their current history. [This is very similar to how the BLAST+ wrappers work.] If you don't have or need any standard HMM databases (e.g. PFAM) then an empty hmmer.loc file should work fine. Try that first. However, the tool author ought to provide an example named hmmer.loc.sample which explains how to set this up - it looks like two columns, description and filename. Peter -- Karen H. Miga, PhD Postdoctoral Scholar University of California, Santa Cruz (831)459-5232 ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] hmmer install
On Mon, Dec 2, 2013 at 4:50 AM, Karen Miga khm...@soe.ucsc.edu wrote: Hi Greg, Thanks for the feedback. I cannot seem to find information for hmmdb.loc. When I look in the associated xml file it looks like it could be removed completely (does one need a precompiled HMM Database? I do not remember using anything like this when I run hmmer on the commandline). I have less experience with changing wrappers, etc. Have you tried just commenting this part out? And do I need to start the instance over to test it? Thanks in advance! - Karen conditional name=hmmdb param name=select type=select label=HMM Db option value=db selected=TruePrecompiled HMM Database/option option value=userHMM Database in your History/option /param when value=db param name=file type=select label=Precompiled HMM database options from_file=hmmdb.loc column name=name index=1/ column name=value index=2/ /options /param /when when value=user param name=file type=data format=hmmer label=HMM database / /when /conditional This lets the Galaxy HMMER wrapper either be used with system level HMM databases (listed in hmmer.loc, e.g. PFAM) or with the user's own HMM databases in their current history. [This is very similar to how the BLAST+ wrappers work.] If you don't have or need any standard HMM databases (e.g. PFAM) then an empty hmmer.loc file should work fine. Try that first. However, the tool author ought to provide an example named hmmer.loc.sample which explains how to set this up - it looks like two columns, description and filename. 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] hmmer install
Hello Karen, You are undoubtedly seeing only the hmmpress tool because the other tool in that repository is not valid: Contents of this repository Valid tools - click the name to preview the tool and use the pop-up menu to inspect all metadata NameDescription Version hmmpressCompress profile db 1.0.0 Invalid tools - click the tool config file name to see why the tool is invalid hmmer.xml If you click on the invalid tool in the tool shed, you'll see the reason that it is invalid: hmmer.xml - This file refers to a file named hmmdb.loc. Upload a file named hmmdb.loc.sample to the repository to correct this error. You should also see an exception thrown in your paster when you start your Galaxy instance telling you why the tool is not being loaded into Galaxy. It look like this repository is missing a file named hmmdb.loc.sample that should provide sample entries for the Galaxy data tables that this tool must use. I'm not sure of the layout of this table for this particular tool, but if you discover what it should be, you can manually add them into a file named hmmdb.loc in the ~/tool-data directory in your Galaxy environment. Greg Von Kuster On Dec 1, 2013, at 4:44 PM, Karen Miga khm...@soe.ucsc.edu wrote: Hello, I would like to use hmmer on our cloudman instance. However, when I install I am only finding a wrapper for hmmpress. There was some conversation about this back in 2012 (http://gmod.827538.n3.nabble.com/Missing-tool-previews-in-tool-shed-e-g-hmmer-xml-td3838635.html). I installed the hmmer package 3.0 and 3.1 from the toolshed as well, however, I am not seeing a wrapper for these tools - perhaps I am missing something? Best wishes, Karen ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] hmmer install
Hi Greg, Thanks for the feedback. I cannot seem to find information for hmmdb.loc. When I look in the associated xml file it looks like it could be removed completely (does one need a precompiled HMM Database? I do not remember using anything like this when I run hmmer on the commandline). I have less experience with changing wrappers, etc. Have you tried just commenting this part out? And do I need to start the instance over to test it? Thanks in advance! - Karen conditional name=hmmdb param name=select type=select label=HMM Db option value=db selected=TruePrecompiled HMM Database/option option value=userHMM Database in your History/option /param when value=db param name=file type=select label=Precompiled HMM database options from_file=hmmdb.loc column name=name index=1/ column name=value index=2/ /options /param /when when value=user param name=file type=data format=hmmer label=HMM database / /when /conditional On Sun, Dec 1, 2013 at 5:32 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hello Karen, You are undoubtedly seeing only the hmmpress tool because the other tool in that repository is not valid: Contents of this repository Valid tools* - click the name to preview the tool and use the pop-up menu to inspect all metadata*http://toolshed.g2.bx.psu.edu/repository/manage_repository?sort=nameoperation=view_or_manage_repositoryid=e7e502574a48abf0async=falseshow_item_checkboxes=falsef-free-text-search=hmmerpage=1 NameDescriptionVersion hmmpresshttp://toolshed.g2.bx.psu.edu/repository/display_tool?repository_id=e7e502574a48abf0render_repository_actions_for=tool_shedtool_config=database%2Fcommunity_files%2F000%2Frepo_148%2Fhmmpress.xmlchangeset_revision=c0fb858f44a2 Compress profile db1.0.0 Invalid tools* - click the tool config file name to see why the tool is invalid*http://toolshed.g2.bx.psu.edu/repository/manage_repository?sort=nameoperation=view_or_manage_repositoryid=e7e502574a48abf0async=falseshow_item_checkboxes=falsef-free-text-search=hmmerpage=1 hmmer.xmlhttp://toolshed.g2.bx.psu.edu/repository/load_invalid_tool?repository_id=e7e502574a48abf0render_repository_actions_for=tool_shedtool_config=hmmer.xmlchangeset_revision=c0fb858f44a2 If you click on the invalid tool in the tool shed, you'll see the reason that it is invalid: *hmmer.xml* - This file refers to a file named *hmmdb.loc*. Upload a file named *hmmdb.loc.sample* to the repository to correct this error. You should also see an exception thrown in your paster when you start your Galaxy instance telling you why the tool is not being loaded into Galaxy. It look like this repository is missing a file named hmmdb.loc.sample that should provide sample entries for the Galaxy data tables that this tool must use. I'm not sure of the layout of this table for this particular tool, but if you discover what it should be, you can manually add them into a file named hmmdb.loc in the ~/tool-data directory in your Galaxy environment. Greg Von Kuster On Dec 1, 2013, at 4:44 PM, Karen Miga khm...@soe.ucsc.edu wrote: Hello, I would like to use hmmer on our cloudman instance. However, when I install I am only finding a wrapper for hmmpress. There was some conversation about this back in 2012 ( http://gmod.827538.n3.nabble.com/Missing-tool-previews-in-tool-shed-e-g-hmmer-xml-td3838635.html). I installed the hmmer package 3.0 and 3.1 from the toolshed as well, however, I am not seeing a wrapper for these tools - perhaps I am missing something? Best wishes, Karen ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Karen H. Miga, PhD Postdoctoral Scholar University of California, Santa Cruz (831)459-5232 ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
