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1 standard {
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2 process.executor = 'local'
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3 process.cpus = 1
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4 params.enable_conda = false
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5 params.enable_module = true
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6 singularity.enabled = false
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7 docker.enabled = false
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8 }
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9
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10 stdkondagac {
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11 process.executor = 'local'
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12 process.cpus = 4
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13 params.enable_conda = true
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14 conda.enabled = true
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15 conda.useMicromamba = true
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16 params.enable_module = false
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17 singularity.enabled = false
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18 docker.enabled = false
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19 }
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20
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21 stdcingularitygac {
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22 process.executor = 'local'
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23 process.cpus = 4
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24 params.enable_conda = false
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25 params.enable_module = false
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26 singularity.enabled = true
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27 singularity.autoMounts = true
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28 singularity.runOptions = "-B ${params.input} -B ${params.bcs_root_dbdir}"
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29 docker.enabled = false
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30 }
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31
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32 raven {
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33 process.executor = 'slurm'
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34 process.queue = 'prod'
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35 process.memory = '10GB'
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36 process.cpus = 4
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37 params.enable_conda = false
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38 params.enable_module = true
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39 singularity.enabled = false
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40 docker.enabled = false
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41 clusterOptions = '--signal B:USR2'
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42 }
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43
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44 eprod {
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45 process.executor = 'slurm'
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46 process.queue = 'lowmem,midmem,bigmem'
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47 process.memory = '10GB'
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48 process.cpus = 4
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49 params.enable_conda = false
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50 params.enable_module = true
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51 singularity.enabled = false
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52 docker.enabled = false
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53 clusterOptions = '--signal B:USR2'
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54 }
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55
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56 eprodkonda {
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57 process.executor = 'slurm'
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58 process.queue = 'lowmem,midmem,bigmem'
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59 process.memory = '10GB'
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60 process.cpus = 4
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61 params.enable_conda = true
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62 conda.enabled = true
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63 conda.useMicromamba = true
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64 params.enable_module = false
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65 singularity.enabled = false
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66 singularity.autoMounts = true
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67 singularity.runOptions = "-B ${params.input} -B ${params.bcs_root_dbdir}"
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68 docker.enabled = false
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69 clusterOptions = '--signal B:USR2'
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70 }
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71
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72 eprodcingularity {
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73 process.executor = 'slurm'
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74 process.queue = 'lowmem,midmem,bigmem'
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75 process.memory = '10GB'
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76 process.cpus = 4
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77 params.enable_conda = false
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78 params.enable_module = false
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79 singularity.enabled = true
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80 singularity.autoMounts = true
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81 singularity.runOptions = "-B ${params.input} -B ${params.bcs_root_dbdir}"
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82 docker.enabled = false
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83 clusterOptions = '--signal B:USR2'
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84 }
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85
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86 cingularity {
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87 process.executor = 'slurm'
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88 process.queue = 'prod'
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89 process.memory = '10GB'
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90 process.cpus = 4
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91 singularity.enabled = true
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92 singularity.autoMounts = true
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93 singularity.runOptions = "-B ${params.input} -B ${params.bcs_root_dbdir}"
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94 docker.enabled = false
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95 params.enable_conda = false
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96 params.enable_module = false
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97 clusterOptions = '--signal B:USR2'
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98 }
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99
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100 cingularitygac {
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101 process.executor = 'slurm'
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102 executor.$slurm.exitReadTimeout = 120000
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103 process.queue = 'centriflaken'
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104 process.cpus = 4
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105 singularity.enabled = true
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106 singularity.autoMounts = true
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107 singularity.runOptions = "-B ${params.input} -B ${params.bcs_root_dbdir}"
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108 docker.enabled = false
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109 params.enable_conda = false
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110 params.enable_module = false
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111 clusterOptions = '-n 1 --signal B:USR2'
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112 }
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113
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114 konda {
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115 process.executor = 'slurm'
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116 process.queue = 'prod'
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117 process.memory = '10GB'
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118 process.cpus = 4
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119 singularity.enabled = false
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120 docker.enabled = false
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121 params.enable_conda = true
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122 conda.enabled = true
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123 conda.useMicromamba = true
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124 params.enable_module = false
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125 clusterOptions = '--signal B:USR2'
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126 }
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127
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128 kondagac {
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129 process.executor = 'slurm'
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130 executor.$slurm.exitReadTimeout = 120000
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131 process.queue = 'centriflaken'
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132 process.cpus = 4
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133 singularity.enabled = false
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134 docker.enabled = false
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135 params.enable_conda = true
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136 conda.enabled = true
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137 conda.useMicromamba = true
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138 params.enable_module = false
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139 clusterOptions = '-n 1 --signal B:USR2'
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140 }
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141
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142 cfsanawsbatch {
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143 process.executor = 'awsbatch'
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144 process.queue = 'cfsan-nf-batch-job-queue'
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145 aws.batch.cliPath = '/home/ec2-user/miniconda/bin/aws'
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146 aws.batch.region = 'us-east-1'
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147 aws.batch.volumes = ['/hpc/db:/hpc/db:ro', '/hpc/scratch:/hpc/scratch:rw']
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148 singularity.enabled = false
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149 singularity.autoMounts = true
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150 docker.enabled = true
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151 params.enable_conda = false
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152 conda.enabled = false
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153 conda.useMicromamba = false
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154 params.enable_module = false
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155 }
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156
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157 gxkubernetes {
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158 process.executor = 'k8s'
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159 k8s.namespace = 'galaxy'
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160 k8s.serviceAccount = 'default'
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161 k8s.pod = [
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162 [volumeClaim: 's3-centriflaken-claim', mountPath: '/galaxy/cfsan-centriflaken-db'],
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163 [volumeClaim: 's3-nextflow-claim', mountPath: '/galaxy/nf-work-dirs'],
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164 [volumeClaim: 'galaxy-galaxy-pvc', mountPath: '/galaxy/server/database'],
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165 [priorityClassName: 'galaxy-job-priority']
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166 ]
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167 singularity.enabled = false
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168 docker.enabled = true
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169 params.enable_conda = false
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170 params.enable_module = false
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171 }
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