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annotate readme.rst @ 3:82ced0e47b9d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1cd738ce63dc53cebf13439456e761ef63dc019c
author iuc
date Fri, 12 Apr 2024 20:19:26 +0000
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c05232655d00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce
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c05232655d00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce
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2 =================
c05232655d00 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
c05232655d00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce
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4 =================
c05232655d00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce
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c05232655d00 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.
c05232655d00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce
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c05232655d00 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/>`
c05232655d00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce
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c05232655d00 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:
c05232655d00 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"
c05232655d00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce
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c05232655d00 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:
c05232655d00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce
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14 1) _JAVA_OPTIONS
c05232655d00 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
c05232655d00 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
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17 4) 4 GB
c05232655d00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce
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