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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 4aa44523d9df9bf1773ed724735120476d773a19
author iuc
date Thu, 06 Mar 2025 11:48:56 +0000
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03646ca53c91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce
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03646ca53c91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce
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2 =================
03646ca53c91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce
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3 IMPORTANT NOTE REGARDING SYSTEM CONFIGURATION
03646ca53c91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce
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4 =================
03646ca53c91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce
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03646ca53c91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce
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6 All of the Galaxy wrappers contained herein call the respective bbtools' shell wrapper, which calls the underlying java-based tool. Unlike a C-based program, java will grab a pre-determined amount of memory at the very beginning of the execution.
03646ca53c91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce
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03646ca53c91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce
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8 Some of the algorithms (e.g. bbnorm) utilise a hash table, and potential collusions can decrease the numeric accuracy of the output. This problem is expected to become more pronounced if the fraction of the memory occupied w.r.t. allocated memory becomes high, i.e. when the available memory is low and/or the input file is big. If the tool generates a warning to stderr, and will be caught by the Galaxy wrapper resulting in a failed job. However, `count min sketch <https://en.wikipedia.org/wiki/Count%E2%80%93min_sketch>` does not run out of memory, this is a gradual effect, and will NOT trigger a fatal error unless the load reaches this critically high level. You can read more about the implications of this at the `BBtools manual <https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbnorm-guide/>`
03646ca53c91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce
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03646ca53c91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce
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10 If you are administering a heteregenous computing environment with multiple nodes of very different quantities of physically available RAM, it is recommended to define a global cap on the RAM to be used to avoid introducing run-to-run bias by exporting an environmental variable, by something like:
03646ca53c91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce
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11 export _JAVA_OPTIONS="-Xmx2048m -Xms256m"
03646ca53c91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce
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03646ca53c91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce
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13 The tool currently considers the following limits, in the given priority order:
03646ca53c91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce
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14 1) _JAVA_OPTIONS
03646ca53c91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce
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15 2) JAVA_TOOL_OPTIONS
03646ca53c91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce
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16 3) GALAXY_MEMORY_MB
03646ca53c91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce
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17 4) 4 GB
03646ca53c91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce
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