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/ > > >
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