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,

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 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
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