Hi Geert, thanks for the information. Are you running GATK-2.4 or GATK-Lite-2.4. As far I know the lite version is deprecated. JJ are your wrappers in bitbucket/github? If you agree I would try to migrate to a recent GATK version and implement GALAXY_SLOTS. Not sure about the installation recipe ... Ciao, Bjoern
Hi,
I have GATK 2.4 running in our local galaxy, next to the default galaxy 1.x version. Both are in the tool menu, but only users that have provided a licence or proof that they are from an academic site have access to the 2.4 version. This is based on a usergroup check in a dynamic job runner configuration.
I used & modified the GATK 2 tool configuration from the test toolshed (by jjohnson). Modifications to the xmls included: --max_jvm_heap "xG" instead of --max_jvm_heap_fraction "1" : we use shared nodes, so it's not allowed to use all ram. --num_threads : some hard coded thread settings were changed made sure the '--et 'NO_ET' is commented out, as we don't have a key.
relevant dynamic_runner part:
from galaxy.jobs.mapper import JobMappingException if 'gatk2' in tool_id >= 0: user_group_assocs = user.groups or [] user_has_license = 'gatk2_license' in [user_group_assoc.group.name for user_group_assoc in user_group_assocs] if not user_has_license: raise JobMappingException("GATKv2 is only available to non-profit, academic users. Please send a mail to geert.vandeweyer2@uantwerpen.be to confirm this.")
Best,
Geert
On 11/19/2013 12:26 PM, Bjoern Gruening wrote:
Hi,
I found that the GATK tools do not have the same requirement tag. For example indel-realigner has version 1.4, realigner_target_creator has version 1.3. Is that correct? What is the recent version that is required for GATK?
Also realigner_target_creator uses the "gatk_picard_indexes" location file, but under tool-data is only a gatk_sorted_picard_indexes.loc file.
Are there any concrete plans for the GATK wrappers. Especially to update to a newer version. Or is that not feasible because of this complicated license policy and the phone-home option ...
I found the following trello card, but its a little bit outdated: https://trello.com/c/IPkT2spd
Is anyone running a recent GATK version in Galaxy?
Thanks! Bjoern
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