diff 0.7.0/conf/computeinfra.config @ 17:0e7a0053e4a6

planemo upload
author kkonganti
date Mon, 15 Jul 2024 10:42:02 -0400
parents
children 133571bf891f
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.7.0/conf/computeinfra.config	Mon Jul 15 10:42:02 2024 -0400
@@ -0,0 +1,171 @@
+standard {
+    process.executor = 'local'
+    process.cpus = 1
+    params.enable_conda = false
+    params.enable_module = true
+    singularity.enabled = false
+    docker.enabled = false
+}
+
+stdkondagac {
+    process.executor = 'local'
+    process.cpus = 4
+    params.enable_conda = true
+    conda.enabled = true
+    conda.useMicromamba = true
+    params.enable_module = false
+    singularity.enabled = false
+    docker.enabled = false
+}
+
+stdcingularitygac {
+    process.executor = 'local'
+    process.cpus = 4
+    params.enable_conda = false
+    params.enable_module = false
+    singularity.enabled = true
+    singularity.autoMounts = true
+    singularity.runOptions = "-B ${params.input} -B ${params.bcs_root_dbdir}"
+    docker.enabled = false
+}
+
+raven {
+    process.executor = 'slurm'
+    process.queue = 'prod'
+    process.memory = '10GB'
+    process.cpus = 4
+    params.enable_conda = false
+    params.enable_module = true
+    singularity.enabled = false
+    docker.enabled = false
+    clusterOptions = '--signal B:USR2'
+}
+
+eprod {
+    process.executor = 'slurm'
+    process.queue = 'combined'
+    process.memory = '10GB'
+    process.cpus = 4
+    params.enable_conda = false
+    params.enable_module = true
+    singularity.enabled = false
+    docker.enabled = false
+    clusterOptions = '--signal B:USR2'
+}
+
+eprodkonda {
+    process.executor = 'slurm'
+    process.queue = 'lowmem,midmem,bigmem'
+    process.memory = '10GB'
+    process.cpus = 4
+    params.enable_conda = true
+    conda.enabled = true
+    conda.useMicromamba = true
+    params.enable_module = false
+    singularity.enabled = false
+    singularity.autoMounts = true
+    singularity.runOptions = "-B ${params.input} -B ${params.bcs_root_dbdir}"
+    docker.enabled = false
+    clusterOptions = '--signal B:USR2'
+}
+
+eprodcingularity {
+    process.executor = 'slurm'
+    process.queue = 'lowmem,midmem,bigmem'
+    process.memory = '10GB'
+    process.cpus = 4
+    params.enable_conda = false
+    params.enable_module = false
+    singularity.enabled = true
+    singularity.autoMounts = true
+    singularity.runOptions = "-B ${params.input} -B ${params.bcs_root_dbdir}"
+    docker.enabled = false
+    clusterOptions = '--signal B:USR2'
+}
+
+cingularity {
+    process.executor = 'slurm'
+    process.queue = 'prod'
+    process.memory = '10GB'
+    process.cpus = 4
+    singularity.enabled = true
+    singularity.autoMounts = true
+    singularity.runOptions = "-B ${params.input} -B ${params.bcs_root_dbdir}"
+    docker.enabled = false
+    params.enable_conda = false
+    params.enable_module = false
+    clusterOptions = '--signal B:USR2'
+}
+
+cingularitygac {
+    process.executor = 'slurm'
+    executor.$slurm.exitReadTimeout = 120000
+    process.queue = 'centriflaken'
+    process.cpus = 4
+    singularity.enabled = true
+    singularity.autoMounts = true
+    singularity.runOptions = "-B ${params.input} -B ${params.bcs_root_dbdir}"
+    docker.enabled = false
+    params.enable_conda = false
+    params.enable_module = false
+    clusterOptions = '-n 1 --signal B:USR2'
+}
+
+konda {
+    process.executor = 'slurm'
+    process.queue = 'prod'
+    process.memory = '10GB'
+    process.cpus = 4
+    singularity.enabled = false
+    docker.enabled = false
+    params.enable_conda = true
+    conda.enabled = true
+    conda.useMicromamba = true
+    params.enable_module = false
+    clusterOptions = '--signal B:USR2'
+}
+
+kondagac {
+    process.executor = 'slurm'
+    executor.$slurm.exitReadTimeout = 120000
+    process.queue = 'centriflaken'
+    process.cpus = 4
+    singularity.enabled = false
+    docker.enabled = false
+    params.enable_conda = true
+    conda.enabled = true
+    conda.useMicromamba = true
+    params.enable_module = false
+    clusterOptions = '-n 1 --signal B:USR2'
+}
+
+cfsanawsbatch {
+    process.executor = 'awsbatch'
+    process.queue = 'cfsan-nf-batch-job-queue'
+    aws.batch.cliPath = '/home/ec2-user/miniconda/bin/aws'
+    aws.batch.region = 'us-east-1'
+    aws.batch.volumes = ['/hpc/db:/hpc/db:ro', '/hpc/scratch:/hpc/scratch:rw']
+    singularity.enabled = false
+    singularity.autoMounts = true
+    docker.enabled = true
+    params.enable_conda = false
+    conda.enabled = false
+    conda.useMicromamba = false
+    params.enable_module = false
+}
+
+gxkubernetes {
+        process.executor = 'k8s'
+        k8s.namespace = 'galaxy'
+        k8s.serviceAccount = 'default'
+        k8s.pod = [
+            [volumeClaim: 's3-centriflaken-claim', mountPath: '/galaxy/cfsan-centriflaken-db'],
+            [volumeClaim: 's3-nextflow-claim', mountPath: '/galaxy/nf-work-dirs'],
+            [volumeClaim: 'galaxy-galaxy-pvc', mountPath: '/galaxy/server/database'],
+            [priorityClassName: 'galaxy-job-priority']
+        ]
+        singularity.enabled = false
+        docker.enabled = true
+        params.enable_conda = false
+        params.enable_module = false
+    }