The migrated BWA installed but missing dependencies
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
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:
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 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:
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 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:
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 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:
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 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:
Okay, I found the button for installing the dependencies. The files are installed: galaxy-dist/tool_dependency_dir/bwa/0.5.9/devteam/bwa_wrappers/ffa8aaa14f7c Quite different from what the wiki states.. http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies Derrick On Wed, Oct 10, 2012 at 2:43 PM, Derrick Lin <klin938@gmail.com> wrote:
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 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:
Hi Derrick, The wiki page to which you refer describes the manual way that the Galaxy admin can install tool dependencies (using a manual process). The tool shed automatically does everything to install repositories, tools, tool dependencies, datatypes, and other repository contents. If you have not yet read the tool shed wiki, you should become familiar with all of the features it provides if you plan to continue using it. The link to the entire tool shed wiki is: http://wiki.g2.bx.psu.edu/Tool%20Shed For automatic installation of tool dependencies, see this specific section of the tool shed wiki: http://wiki.g2.bx.psu.edu/ToolShedToolFeatures#Automatic_third-party_tool_de... Sorry for the confusion the Admin wiki you were using caused. Greg Von Kuster On Oct 10, 2012, at 12:07 AM, Derrick Lin wrote:
Okay,
I found the button for installing the dependencies. The files are installed:
galaxy-dist/tool_dependency_dir/bwa/0.5.9/devteam/bwa_wrappers/ffa8aaa14f7c
Quite different from what the wiki states..
http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies
Derrick
On Wed, Oct 10, 2012 at 2:43 PM, Derrick Lin <klin938@gmail.com> wrote: 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 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:
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 <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 ___________________________________________________________ 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:
___________________________________________________________ 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:
participants (3)
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Derrick LIN -
Derrick Lin -
Greg Von Kuster