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Question: How to know the tool id name in job_conf.xml?
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gravatar for vebaev
3.3 years ago by
vebaev • 130
vebaev • 130 wrote:

 Hi, I have added some tools in my jobs_conf file so they can use more than one cpu, however I probably have mistaken some tool id, as bowtie is working properly on 16 cores but samtools and htseq-count not (only 1 core as before)? So probably I'm doing something not wright?

 

  <tool id="bowtie2" destination="multicore16" />
  <tool id="bowtie"  destination="multicore16" />
  <tool id="tophat2" destination="multicore16" />

  <tool id="htseq-count" destination="multicore16" />
  <tool id="samtools" destination="multicore16" />
cpu job conf samtools multicore • 771 views
ADD COMMENT • link •
modified 3.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.3 years ago by vebaev • 130
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gravatar for Jennifer Hillman Jackson
3.3 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

One simple way to look up this information is to go to the Tool Shed and examine the repository. Tools will be listed under dependencies by their "tool id". For example, you have "tophat2" listed in your example, when this almost certainly should be just "tophat" (if you are using the most recent Tophat2 repository).

Best, Jen, Galaxy team
ADD COMMENT • link written 3.3 years ago by Jennifer Hillman Jackson ♦ 25k

I have found also that the tool name string on the end of the location:

Location:
/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/a430da4f04cd/samtools_sort

but even there it is run with option for multi thread (samtools sort -@ 16), it was running on one cpu, do you know where is the problem?


 

ADD REPLY • link modified 3.3 years ago • written 3.3 years ago by vebaev • 130
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