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Question: Installing new tools
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gravatar for jannetta.steyn
2.6 years ago by
jannetta.steyn • 10
jannetta.steyn • 10 wrote:

When installing tools from the toolshed, does it also install the binaries for the tool? For instance, on a local installation of Galaxy, if I go to Admin, Search Tool Shed, find bwa and then install it. Does this only install the wrappers into Galaxy or does it actually install bwa too? Do I have to install bwa binaries separately or not?

Thanks Jannetta
toolshed • 793 views
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modified 2.5 years ago by tuto345 • 20 • written 2.6 years ago by jannetta.steyn • 10
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gravatar for Jennifer Hillman Jackson
2.6 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

If you install with Managed Dependencies, then most tools will include the binaries. Check the Tool Shed repository to see which components are included. Exceptions are usually tools with special licencing (example: BLAT).

Thanks, Jen, Galaxy team
ADD COMMENT • link written 2.6 years ago by Jennifer Hillman Jackson ♦ 25k
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gravatar for jannetta.steyn
2.6 years ago by
jannetta.steyn • 10
jannetta.steyn • 10 wrote:

I installed bwa and it results in this error when I try to run it from Galaxy: Fatal error: Exit code 127 () /home/jannetta/galaxy/database/job_working_directory/000/12/tool_script.sh: 9: /home/jannetta/galaxy/database/job_working_directory/000/12/tool_script.sh: bwa: not found

What is causing this?
ADD COMMENT • link written 2.6 years ago by jannetta.steyn • 10
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gravatar for tuto345
2.5 years ago by
tuto345 • 20
France
tuto345 • 20 wrote:

Hello,

Is there any news on this subject? I have the same problem, installed bwa, the dependencies are all installed, but bwa is not found by galaxy. In the bwa-mem.xml file the macros are imported and the requirements are expanded but somehow the $GALAXY_HOME/dependency_dir/bwa/0.7.12/iuc/package_bwa_0_7_12/6af9b24ddeee/env.sh never gets sourced.

For now I circumvent the problem by creating a symbolic link in ~/bin to the bwa executable in $GALAXY_HOME/dependency_dir/bwa/0.7.12/iuc/package_bwa_0_7_12/6af9b24ddeee/bin/ as it is the only bwa on my system, but it would be nice to have a proper solution.

Any help appreciated! Thanks, Cristian
ADD COMMENT • link written 2.5 years ago by tuto345 • 20
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