Hello Sheldon, What is the configuration setting you are using for the location to install repositories? This is defined by the tool_path attribute of the <toolbox> tag in your shed_tools_conf.xml file. The default is:
<toolbox tool_path="../shed_tools"> On Feb 28, 2014, at 3:47 PM, "Briand, Sheldon" <sheldon.bri...@ssc-spc.gc.ca> wrote: > Hi, > > No joy on the migration strategy. Deseq is example of a tool that I > installed successfully yesterday. Do you mean that you installed the deseq repository from the main tool shed: http://toolshed.g2.bx.psu.edu/view/nikhil-joshi/deseq_and_sam2counts and that its contained deseq tool "DE Seq (version 1.0.0)" was properly displayed in your Galaxy tool panel? If so, what is now happening? > Bowtie2 is an example of a tool that isn’t showing up even though the web > interface indicates that it is successfully installed. Can you uninstall the repsository and reinstall it? If so, what happens? > > Here is my directory structure relating to bowtie2: > > $ find . -name "*bowtie2*" > ./shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/bowtie2 > ./shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/package_bowtie2_2_1_0 > ./shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/package_bowtie2_2_1_0/017a00c265f1/package_bowtie2_2_1_0 > ./shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/tophat2/ffa30bedbee3/tophat2/.hg/store/data/tool-data/bowtie2__indices.loc.sample.i > ./shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/tophat2/ffa30bedbee3/tophat2/tool-data/bowtie2_indices.loc.sample > ./galaxy-dist/.hg/store/data/tool-data/bowtie2__indices.loc.sample.i > ./galaxy-dist/.hg/store/data/tools/sr__mapping/bowtie2__wrapper.xml.i > ./galaxy-dist/.hg/store/data/tools/sr__mapping/bowtie2__wrapper.py.i > ./galaxy-dist/.hg/store/data/test-data/bowtie2 > ./galaxy-dist/tool-data/bowtie2_indices.loc.sample > ./galaxy-dist/tool-data/bowtie2_indices.loc > ./galaxy-dist/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/tophat2/ffa30bedbee3/bowtie2_indices.loc > ./galaxy-dist/dependancies/samtools/0.1.18/devteam/bowtie2 > ./galaxy-dist/dependancies/samtools/0.1.19/iuc/package_samtools_0_1_19/00e17a794a2e/bin/bowtie2sam.pl > ./galaxy-dist/dependancies/bowtie2 > ./galaxy-dist/dependancies/bowtie2/2.1.0/devteam/bowtie2 > ./galaxy-dist/dependancies/bowtie2/2.1.0/devteam/package_bowtie2_2_1_0 > ./galaxy-dist/dependancies/bowtie2/2.1.0/devteam/package_bowtie2_2_1_0/017a00c265f1/bowtie2-align > ./galaxy-dist/dependancies/bowtie2/2.1.0/devteam/package_bowtie2_2_1_0/017a00c265f1/bowtie2-build-debug > ./galaxy-dist/dependancies/bowtie2/2.1.0/devteam/package_bowtie2_2_1_0/017a00c265f1/bowtie2-inspect-debug > ./galaxy-dist/dependancies/bowtie2/2.1.0/devteam/package_bowtie2_2_1_0/017a00c265f1/bowtie2 > ./galaxy-dist/dependancies/bowtie2/2.1.0/devteam/package_bowtie2_2_1_0/017a00c265f1/bowtie2-inspect > ./galaxy-dist/dependancies/bowtie2/2.1.0/devteam/package_bowtie2_2_1_0/017a00c265f1/bowtie2-align-debug > ./galaxy-dist/dependancies/bowtie2/2.1.0/devteam/package_bowtie2_2_1_0/017a00c265f1/bowtie2-build > [galaxy@eugene galaxy]$ cd > shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/ > > I seem to be missing the .py and .xml files in the shed_tools directory. > > -Sheldon > > > From: Briand, Sheldon > Sent: Friday, February 28, 2014 2:11 PM > To: 'Greg Von Kuster' > Subject: RE: [galaxy-dev] tool trouble > > Hi, > > Thanks for getting back to me. > > I didn’t get your first reply (email trouble here) when I sent my second > email. I have not played with the sql tables. > > I think my problem is that I need to run tool migration scripts. The > reinstall log I sent was for tophat 2. It didn’t show up in > shed_tool_conf.xml after the update so I thought it had once again failed. > After I sent the email I noticed that tophat2 had shown up in the tool menu > (not where I wanted it but it was there). So I looked around and there was > an entry in migrated_tools_conf.xml. > > I think the tools I am missing are because I likely missed the migration > step. I’ll try that first and report back. > > Cheers, > -Sheldon > > From: Greg Von Kuster [mailto:g...@bx.psu.edu] > Sent: Friday, February 28, 2014 11:04 AM > To: Briand, Sheldon > Cc: galaxy-dev@lists.bx.psu.edu > Subject: Re: [galaxy-dev] tool trouble > > Hello Briand, > > This may take some back-and-forth with you to understand the steps you have > taken so far. Successfully installing a repository that contains tools > usually results in the tools being displayed in the Galaxy tool panel. > However, there may be issues that result in the tools not properly loading. > This often occurs when you stop and restart your Galaxy instance. Your > Galaxy pasxter log will include information about any tool that does not > properly load. Uninstalling and reinstalling the repository will usually not > have any affect on this. > > On Feb 28, 2014, at 9:17 AM, "Briand, Sheldon" <sheldon.bri...@ssc-spc.gc.ca> > wrote: > > > Hi, > > I’ve been poking around a bit more. It looks as though galaxy isn’t actually > downloading and installing the tools. The tool status changes to installed > in the web interface and postgres but the tool is not present on disk. > > What is present on disk? If you install a repository with tools, the > repository revision's contents should be on disk. However, if the repository > is uninstalled, disk files are deleted. Do you have repositories that are > installed but do not have any files on disk? > > > > The log below shows no download and make of the tool and dependancies. > Hopefully the log gives a bit more information. Sorry for the second email. > > tool_shed.util.shed_util_common DEBUG 2014-02-28 09:58:48,567 Updating an > existing row for repository 'tophat2' in the tool_shed_repository table, > status set to 'New'. > tool_shed.util.repository_dependency_util DEBUG 2014-02-28 09:58:48,714 > Creating repository dependency objects... > > > The log looks ok at first inspection, but it's not useful without more > information. > > > > > From: galaxy-dev-boun...@lists.bx.psu.edu > [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Briand, Sheldon > Sent: Thursday, February 27, 2014 8:18 PM > To: galaxy-dev@lists.bx.psu.edu > Subject: [galaxy-dev] tool trouble > > Hi, > > I’m having trouble with some of my tools not appearing in the Analyze Data > menu. I’ve successfully installed the tools via the manage installed tool > shed repositories(so they are installed to disk). I have tried uninstalling > and installing again. > > The above should not be necessary. When you install, are you checking the > optional checkboxes to install repository dependencies and tool dependencies? > If so, are they installing as well? > > > The tool installs but does not appear in the menu. > > Do you have an example of a repository that contains tools that installls > corruptly, but the tools do not load into the tool panel? > > > Other tools install the menu updates just fine. > > Do you have an example of a repsoitory that contains tools that do show up in > the tool panel after successfule repository installation? > > > > This is probably due to me corrupting the misbehaving tools installation > somehow. I’m guessing that I need to uninstall the tool and wipe some > postgres entries. > > I strongly advise not manually changing inaything in your database suing sql > commands. If you have done this, it could be the cause of the behavor you > are describing. The Galaxy UI or API should be used. > > Greg Von Kuster > > > > My shed tool path: > <toolbox tool_path="../shed_tools"> > > My current version: > parent: 12441:dc067a95261d > Added tag release_2014.02.10 for changeset 5e605ed6069f > branch: stable > > Could someone point me in the right direction? > > Thanks, > -Sheldon > > Sheldon Briand > NRC Research Computing Support Analyst > Research Computing Support / Soutien Informartique a la Recherche > Operations, Science Portfolio / Operations, Portefeuil des sciences > SSC-NRC / SPC-CNRC > Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford > Halifax, NS B3H 3Z1 > 902 426-1677 > sheldon.bri...@ssc-spc.gc.ca > > ___________________________________________________________ > 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/
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