Hi Derrick, This behavior is likely the result of your not having any entries for the bwa tools defined in your tool_conf.xml file. Your tool_conf.xml file is parsed as a part of the process of installing the migrated tools in order to load your tool panel in the same way it was defined before the migration. If there are no entries for the tools in the tool_conf.xml file the repository will not be installed, and the tools will not be loaded.
This information is discussed in the following section of the tool shed wiki. http://wiki.g2.bx.psu.edu/MigratingToolsFromGalaxyDistribution Greg Von Kuster On Oct 8, 2012, at 8:49 PM, Derrick Lin wrote: > Hi Greg, > > I did another test on a fresh installed galaxy Oct 5 release, I simply cloned > from the galaxy-dist, start the server once so everything's populated, then > here was how I ran the migration script and output: > > pwbcad@gamma00:galaxy-dist$ sh ./scripts/migrate_tools/0005_tools.sh > No handlers could be found for logger "galaxy.tools.data" > /home/pwbcad/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/pysam/__init__.py:1: > RuntimeWarning: __builtin__.file size changed, may indicate binary > incompatibility > from csamtools import * > Repositories will be installed into configured tool_path location > ../shed_tools > Adding new row (or updating an existing row) for repository 'bwa_wrappers' in > the tool_shed_repository table. > > The installation process is finished. You should now remove entries for the > installed tools from your file named > ./tool_conf.xml and start your Galaxy server. > > I then checked the migrated_tools_conf.xml but no entries for BWA still. > Note that I haven't run the previous migration scripts because I don't need > those tools. Will that be the issue? > > Cheers, > D > > On Tue, Oct 9, 2012 at 2:17 AM, Greg Von Kuster <g...@bx.psu.edu> wrote: > Hi Derrick, > > I am not able to reproduce this behavior, so it's difficult to tell what > problem may have occurred that resulted in the entries for the bwa tools to > not be added to you migrated_tools_conf.xml file. Choosing to install or not > install tool dependences makes no difference in whether the repository is > installed and the tools are properly configured in the > migrated_tools_conf.xml file and subsequently loaded into the Galaxy tool > panel. > > Can you try manually adding the following sections to your > migrated_tools_conf.xml file and see if that solves your problem (of course, > you can change the section id and name attributes if you want or eliminate > the section altogether). > > <section id="solexa_tools" name="NGS: Mapping" version=""> > <tool > file="../shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/ffa8aaa14f7c/bwa_wrappers/bwa_wrapper.xml" > guid="toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3"> > <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> > <repository_name>bwa_wrappers</repository_name> > <repository_owner>devteam</repository_owner> > > <installed_changeset_revision>ffa8aaa14f7c</installed_changeset_revision> > > <id>toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3</id> > <version>1.2.3</version> > </tool> > <tool > file="../shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/ffa8aaa14f7c/bwa_wrappers/bwa_color_wrapper.xml" > > guid="toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_color_wrapper/1.0.2"> > <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> > <repository_name>bwa_wrappers</repository_name> > <repository_owner>devteam</repository_owner> > > <installed_changeset_revision>ffa8aaa14f7c</installed_changeset_revision> > > <id>toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_color_wrapper/1.0.2</id> > <version>1.0.2</version> > </tool> > </section> > > Greg Von Kuster > > > On Oct 8, 2012, at 1:55 AM, Derrick LIN wrote: > >> Hi guys, >> >> I have updated the galaxy to Oct 5 dist, and BWA has been reinstalled via >> the migration script. However, I couldn't find any entry has been added in >> migrated_tools_conf.xml (thus the BWA tools are not display in the tool >> panel). >> >> I check in the admin "Installed tool shed repositories" section and BWA >> repos status is "Installed, missing dependencies", is that why it didn't get >> added into the migrated_tools_conf.xml? >> >> I have had BWA 0.5.9-r16 in path, and been used by the old BWA wrapper >> without an issue before. How can I fix this dependencies issue for a Shed >> Tool? Should I add something like: >> >> <tool_dependency_dir>/bowtie/0.12.7/env.sh >> >> thanks, >> Derrick >> ___________________________________________________________ >> 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/ > > > ___________________________________________________________ > 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/
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