Mercurial > repos > trinity_ctat > testing_how_to_do_this

comparison trinity.xml @ 7:f7e70316b7ca draft default tip

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author trinity_ctat
date Thu, 31 Aug 2017 15:50:15 -0400
parents 4c1d32673942
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6:4c1d32673942 7:f7e70316b7ca
127 </test> 127 </test>
128 </tests> 128 </tests>
129 <help> 129 <help>
130 This instance is running Trinity version 2.4.0 and uses the following command: 130 This instance is running Trinity version 2.4.0 and uses the following command:
131 131
132 Trinity --max_memory \${TRINITY_MAX_MEMORY:-31G} --CPU \${GALAXY_SLOTS:-4} --seqType seq_type --single singlefile or --left left_file --right right_file 132 Trinity --max_memory 31G --CPU 4 --seqType seq_type --single singlefile or --left left_file --right right_file
133 Define TRINITY_MAX_MEMORY and GALAXY_SLOTS to change the default values for --max_memory and --CPU. 133
134 Define TRINITY_MAX_MEMORY and GALAXY_SLOTS to change the default values for --max_memory and --CPU, respectively.
134 135
135 .. class:: infomark 136 .. class:: infomark
136 137
137 Trinity_, developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-seq reads. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived from paralogous genes. For more information, visit Trinity's wiki page here_. 138 Trinity_, developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-seq reads. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived from paralogous genes. For more information, visit Trinity's wiki page here_.
138 139