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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 4a97d14fadd86dda8abd088023c7f9f2dcab2a88
author bebatut
date Fri, 04 May 2018 05:40:24 -0400
parents 626cd6334dbc
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626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
bebatut
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1 CD_HIT memory usage
626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
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2 ====================
626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
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626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
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4 By default, maximum of 4Gb is attributed to CD_HIT.
626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
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626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
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6 To change the maximum memory usage, you can edit the CD_HIT_MEM_OPTIONS in the file:
626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
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626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
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8 <tool_dependency_dir>/cd-hit/4.6.4/bebatut/cdhit/<hash_string>/env.sh
626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
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626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
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10 For example to increase to 8Gb, you will write:
626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
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626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
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12 CD_HIT_MEM_OPTIONS='-M 8000'