Thanks Greg,

Indeed, I tried to be smart and removed the entries from tool conf xml before running the script. :)

About the missing dependencies, I still couldn't make it happy. I have added:

$GALAXY_ROOT/tool_dependency_dir/bwa/0.5.9/env.sh

and add appropriate export PATH inside the env.sh, restart the galaxy but it still complains about the missing dependencies.

Is there an official way to  setup the files to meet the dependencies requirement defined in shed tool's xml?

Cheers,
Derrick

On Tue, Oct 9, 2012 at 9:26 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Hi Derrick,

Yes, this approach will work fine.

Greg Von Kuster

On Oct 8, 2012, at 11:44 PM, Derrick Lin wrote:

Can I actually just skip executing the migration script, and just install BWA from the tool shed like I did for other shed tools?? Should be fine I guess?

Derrick

On Tue, Oct 9, 2012 at 11:49 AM, Derrick Lin <klin938@gmail.com> 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 <greg@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_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>
            <version>1.2.3</version>
            </tool>
            <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>
            <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
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