Question: How to know the tool id name in job_conf.xml?
gravatar for vebaev
3.3 years ago by
vebaev130 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 COMMENTlink modified 3.3 years ago by Jennifer Hillman Jackson25k • written 3.3 years ago by vebaev130
gravatar for Jennifer Hillman Jackson
3.3 years ago by
United States
Jennifer Hillman Jackson25k wrote:


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 COMMENTlink written 3.3 years ago by Jennifer Hillman Jackson25k

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


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 REPLYlink modified 3.3 years ago • written 3.3 years ago by vebaev130
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