User:James Estevez/Notebook/Spring 2011: Bdellovibrio Independent Study/2011/01/22
Bdellovibrio Independent Study | Main project page Next entry |
Friday night. Proposal draft is up the food chain for review. Lab notebook set-up. Need to prep the analysis pipeline: CloVR
Running the first 16s pipeline
<source lang="text">
[input] GROUP_COUNT=1 FASTA_FILES=/mnt/AMP_Lung.small.fasta MAPPING_FILE=/mnt/IGS.qmap PIPELINE_NAME=clovr_16S_pipeline FASTA_TAG=16S_FASTA MAPPING_TAG=MAPPING DB_TAG=clovr-core-set-aligned-imputed-fasta
[cluster] CLUSTER_NAME=local EXEC_NODES=1 CLOVR_CONF=clovr.conf CLUSTER_CREDENTIAL=local
[output] OUTPUT_DIRECTORY=/mnt/output log_file=/mnt/clovr_16S_run.log
debug_level=3 [pipeline] PIPELINE_TEMPLATE=clovr_16S PIPELINE_ARGS=--FASTA_FILES=${input.FASTA_TAG} --MAPPING_FILE=${input.MAPPING_TAG} --DB_PATH=${input.DB_TAG} --GROUP_COUNT=${input.GROUP_COUNT}
PRESTART_TEMPLATE_XML=/opt/clovr_pipelines/workflow/project_saved_templates/clovr_16S/clovr_16S.prestart.xml
PRERUN_TEMPLATE_XML=/opt/clovr_pipelines/workflow/project_saved_templates/clovr_16S/clovr_16S.prerun.xml
POSTRUN_TEMPLATE_XML=/opt/clovr_pipelines/workflow/project_saved_templates/clovr_16S/clovr_16S.postrun.xml </source>
<source lang="text"> [cluster] ami=ami-0c7b8d65 key=vappio_00 master_type=c1.xlarge master_groups=vappio,web
master_bid_price=0.68 exec_type=c1.xlarge exec_groups=vappio,web
exec_bid_price=0.68
exec_max_instances=5
[] -include /mnt/vappio-conf/clovr_base.conf </source> The first pass errored out. The mailing list says there needs to be a Vappio script to handle the cluster config. This set-up only started the local cluster. There'll be upstream problems modifying the pipeline, too, I expect. |