Hi Ross,

I was indeed expecting something like that and when I tried what you suggestyed, it worked :) you need to use the complete path to the tool (including version number??!?!) in the tool-runner definition to make it be able to be set in the universe_wsgi.ini...

So indeed the toolshed move of BWA breaks the individual tool_runner settings and makes for one ugly config file now... But at least we found a workaround...

Thanks

Thon

On Dec 05, 2012, at 01:52 PM, Ross ross.lazarus@gmail.com wrote:

Hi, Thon  I'm guessing here: but now that bwa is kept in the toolshed, the tool name appears to be toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3 according to your job runner entry - so I wonder if that whole ugly string now needs to be in the tool_runners section to over-ride the default rather thant "bwa_wrapper" ?

This might be an unforseen consequence of the way the toolshed adapts tool names to keep versions under control. Fixing this might be a little tricky since one goal is to keep multiple tool versions separate - but we will all want all versions of bwa_wrapper to use the same runner flags?

On Thu, Dec 6, 2012 at 8:40 AM, Anthonius deBoer thondeboer@me.com wrote: Hi,

In my fresh copy of galaxy-dist I am having a problem with tools being run only with the default tool runner and not with the assigned tool runner I created in the [galaxy:tool_runners] section...

This is the setting for bwa_wrapper in my universe_wsgi.ini:

bwa_wrapper = drmaa://-V -q long.q -pe smp 4/

and this is what the job admin page shows:

It's in a different queue and does not use the smp setting I ask for...(It's the default setting)

any ideas?

7 X 26 minutes ago toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3 running python /mnt/ngs/analysis/svcgalaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/ffa8aaa14f7c/bwa_wrappers/bwa_wrapper.py --threads="4" --fileSource=indexed --ref="/mnt/ngs/analysis/svcgalaxy/DATA/galaxy-indexes/bwa-indexes/human_g1k_v37_decoy.fasta" --do_not_build_index --input1=/home/tdeboer/P/MUT190-MAIN/fastq-2_205/2_205_1_AAACAT_R1.fastq --input2=/home/tdeboer/P/MUT190-MAIN/fastq-2_205/2_205_1_AAACAT_R2.fastq --output=/mnt/ngs/analysis/svcgalaxy/DATA/files/000/dataset_776.dat --genAlignType=paired --params=pre_set --suppressHeader=false drmaa://-V -q all.q -pe smp 1/ 4440144

On Dec 5, 2012, at 5:10 PM, Anthonius deBoer wrote:

I confirmed that you have to include the version numbers for these toolshed tools:

This works: toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3 = drmaa://-V -q long.q -pe smp 4/

this does not: toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper = drmaa://-V -q long.q -pe smp 4/

Thon

Hi Thon,

I just committed a fix for this in 75a97c971d36 that will be available in our next distribution release. It will also match from most to least specific so you can define all of:

toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3 = foo:// toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper = bar:// bwa_wrapper = baz://

In this example:

- version 1.2.3 of the bwa wrapper installed from the toolshed would use foo:// - all other versions installed from the toolshed would use bar:// - any tool with <tool id="bwa_wrapper">, regardless of how it's installed (from the toolshed or directly added to tool_conf.xml) would use baz://

Only the most specific match will be used if there are multiple matches (as in the example).

--nate

On Dec 05, 2012, at 02:00 PM, Anthonius deBoer thondeboer@me.com wrote:

...

Hi Ross,

I was indeed expecting something like that and when I tried what you suggestyed, it worked :) you need to use the complete path to the tool (including version number??!?!) in the tool-runner definition to make it be able to be set in the universe_wsgi.ini...

So indeed the toolshed move of BWA breaks the individual tool_runner settings and makes for one ugly config file now... But at least we found a workaround...

Thanks

Thon

On Dec 05, 2012, at 01:52 PM, Ross ross.lazarus@gmail.com wrote:

...

Hi, Thon I'm guessing here: but now that bwa is kept in the toolshed, the tool name appears to be toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3 according to your job runner entry - so I wonder if that whole ugly string now needs to be in the tool_runners section to over-ride the default rather thant "bwa_wrapper" ?

This might be an unforseen consequence of the way the toolshed adapts tool names to keep versions under control. Fixing this might be a little tricky since one goal is to keep multiple tool versions separate - but we will all want all versions of bwa_wrapper to use the same runner flags?

On Thu, Dec 6, 2012 at 8:40 AM, Anthonius deBoer thondeboer@me.com wrote: Hi,

In my fresh copy of galaxy-dist I am having a problem with tools being run only with the default tool runner and not with the assigned tool runner I created in the [galaxy:tool_runners] section...

This is the setting for bwa_wrapper in my universe_wsgi.ini:

bwa_wrapper = drmaa://-V -q long.q -pe smp 4/

and this is what the job admin page shows:

It's in a different queue and does not use the smp setting I ask for...(It's the default setting)

any ideas?

7 X 26 minutes ago toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3 running python /mnt/ngs/analysis/svcgalaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/ffa8aaa14f7c/bwa_wrappers/bwa_wrapper.py --threads="4" --fileSource=indexed --ref="/mnt/ngs/analysis/svcgalaxy/DATA/galaxy-indexes/bwa-indexes/human_g1k_v37_decoy.fasta" --do_not_build_index --input1=/home/tdeboer/P/MUT190-MAIN/fastq-2_205/2_205_1_AAACAT_R1.fastq --input2=/home/tdeboer/P/MUT190-MAIN/fastq-2_205/2_205_1_AAACAT_R2.fastq --output=/mnt/ngs/analysis/svcgalaxy/DATA/files/000/dataset_776.dat --genAlignType=paired --params=pre_set --suppressHeader=false drmaa://-V -q all.q -pe smp 1/ 4440144

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Great solution... Glad I could help!

On Dec 05, 2012, at 02:56 PM, Nate Coraor nate@bx.psu.edu wrote:

On Dec 5, 2012, at 5:10 PM, Anthonius deBoer wrote:

I confirmed that you have to include the version numbers for these toolshed tools:

This works: toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3 = drmaa://-V -q long.q -pe smp 4/

this does not: toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper = drmaa://-V -q long.q -pe smp 4/

Thon

Hi Thon,

I just committed a fix for this in 75a97c971d36 that will be available in our next distribution release. It will also match from most to least specific so you can define all of:

toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3 = foo:// toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper = bar:// bwa_wrapper = baz://

In this example:

- version 1.2.3 of the bwa wrapper installed from the toolshed would use foo:// - all other versions installed from the toolshed would use bar:// - any tool with <tool id="bwa_wrapper">, regardless of how it's installed (from the toolshed or directly added to tool_conf.xml) would use baz://

Only the most specific match will be used if there are multiple matches (as in the example).

--nate

On Dec 05, 2012, at 02:00 PM, Anthonius deBoer thondeboer@me.com wrote:

...

Hi Ross,

I was indeed expecting something like that and when I tried what you suggestyed, it worked :) you need to use the complete path to the tool (including version number??!?!) in the tool-runner definition to make it be able to be set in the universe_wsgi.ini...

So indeed the toolshed move of BWA breaks the individual tool_runner settings and makes for one ugly config file now... But at least we found a workaround...

Thanks

Thon

On Dec 05, 2012, at 01:52 PM, Ross ross.lazarus@gmail.com wrote:

...

Hi, Thon I'm guessing here: but now that bwa is kept in the toolshed, the tool name appears to be toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3 according to your job runner entry - so I wonder if that whole ugly string now needs to be in the tool_runners section to over-ride the default rather thant "bwa_wrapper" ?

This might be an unforseen consequence of the way the toolshed adapts tool names to keep versions under control. Fixing this might be a little tricky since one goal is to keep multiple tool versions separate - but we will all want all versions of bwa_wrapper to use the same runner flags?

On Thu, Dec 6, 2012 at 8:40 AM, Anthonius deBoer thondeboer@me.com wrote: Hi,

In my fresh copy of galaxy-dist I am having a problem with tools being run only with the default tool runner and not with the assigned tool runner I created in the [galaxy:tool_runners] section...

This is the setting for bwa_wrapper in my universe_wsgi.ini:

bwa_wrapper = drmaa://-V -q long.q -pe smp 4/

and this is what the job admin page shows:

It's in a different queue and does not use the smp setting I ask for...(It's the default setting)

any ideas?

7 X 26 minutes ago toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3 running python /mnt/ngs/analysis/svcgalaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/ffa8aaa14f7c/bwa_wrappers/bwa_wrapper.py --threads="4" --fileSource=indexed --ref="/mnt/ngs/analysis/svcgalaxy/DATA/galaxy-indexes/bwa-indexes/human_g1k_v37_decoy.fasta" --do_not_build_index --input1=/home/tdeboer/P/MUT190-MAIN/fastq-2_205/2_205_1_AAACAT_R1.fastq --input2=/home/tdeboer/P/MUT190-MAIN/fastq-2_205/2_205_1_AAACAT_R2.fastq --output=/mnt/ngs/analysis/svcgalaxy/DATA/files/000/dataset_776.dat --genAlignType=paired --params=pre_set --suppressHeader=false drmaa://-V -q all.q -pe smp 1/ 4440144

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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:

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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:

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