[med-svn] [trinityrnaseq] 01/01: In some cases help2man has poor results - here it was the case. So I did some (boring) manual editing
Andreas Tille
tille at debian.org
Thu Feb 12 22:28:12 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository trinityrnaseq.
commit 8e8f11d75f692fb769204e8423f775ec8944ab8c
Author: Andreas Tille <tille at debian.org>
Date: Thu Feb 12 23:28:37 2015 +0100
In some cases help2man has poor results - here it was the case. So I did some (boring) manual editing
---
debian/Trinity.1 | 206 +++++++++++++++++++++++++++----------------------------
1 file changed, 102 insertions(+), 104 deletions(-)
diff --git a/debian/Trinity.1 b/debian/Trinity.1
index 2358fbc..5cae151 100644
--- a/debian/Trinity.1
+++ b/debian/Trinity.1
@@ -3,108 +3,106 @@
.SH NAME
Trinity \- RNA-Seq De novo Assembly
.SH DESCRIPTION
-###############################################################################
-#
-# ______ ____ ____ ____ ____ ______ __ __
-# | || \e | || \e | || || | |
-# | || D ) | | | _ | | | | || | |
-# |_| |_|| / | | | | | | | |_| |_|| ~ |
-# | | | \e | | | | | | | | | |___, |
-# | | | . \e | | | | | | | | | | |
-# |__| |__|\e_||____||__|__||____| |__| |____/
-#
-###############################################################################
-#
-# Required:
-#
-# \fB\-\-seqType\fR <string> :type of reads: ( fa, or fq )
-#
-# \fB\-\-max_memory\fR <string> :suggested max memory to use by Trinity where limiting can be enabled. (jellyfish, sorting, etc)
-# provied in Gb of RAM, ie. '\-\-max_memory 10G'
-#
-# If paired reads:
-# \fB\-\-left\fR <string> :left reads, one or more (separated by space)
-# \fB\-\-right\fR <string> :right reads, one or more (separated by space)
-#
-# Or, if unpaired reads:
-# \fB\-\-single\fR <string> :single reads, one or more (note, if single file contains pairs, can use flag: \fB\-\-run_as_paired\fR )
-#
-####################################
-## Misc: #########################
-#
-# \fB\-\-SS_lib_type\fR <string> :Strand\-specific RNA\-Seq read orientation.
-# if paired: RF or FR,
-# if single: F or R. (dUTP method = RF)
-# See web documentation.
-#
-# \fB\-\-CPU\fR <int> :number of CPUs to use, default: 2
-# \fB\-\-min_contig_length\fR <int> :minimum assembled contig length to report
-# (def=200)
-#
-# \fB\-\-long_reads\fR <string> :fasta file containing error\-corrected or circular consensus (CCS) pac bio reads
-#
-# \fB\-\-genome_guided_bam\fR <string> :genome guided mode, provide path to coordinate\-sorted bam file.
-# (see genome\-guided param section under \fB\-\-show_full_usage_info\fR)
-#
-# \fB\-\-jaccard_clip\fR :option, set if you have paired reads and
-# you expect high gene density with UTR
-# overlap (use FASTQ input file format
-# for reads).
-# (note: jaccard_clip is an expensive
-# operation, so avoid using it unless
-# necessary due to finding excessive fusion
-# transcripts w/o it.)
-#
-# \fB\-\-trimmomatic\fR :run Trimmomatic to quality trim reads
-# see '\-\-quality_trimming_params' under full usage info for tailored settings.
-#
-#
-# \fB\-\-normalize_reads\fR :run in silico normalization of reads. Defaults to max. read coverage of 50.
-# see '\-\-normalize_max_read_cov' under full usage info for tailored settings.
-#
-# \fB\-\-no_distributed_trinity_exec\fR :do not run Trinity phase 2 (assembly of partitioned reads), and stop after generating command list.
-#
-#
-# \fB\-\-output\fR <string> :name of directory for output (will be
-# created if it doesn't already exist)
-# default( your current working directory: "/home/mcrusoe/debian/trinityrnaseq/trinity_out_dir"
-# note: must include 'trinity' in the name as a safety precaution! )
-#
-# \fB\-\-full_cleanup\fR :only retain the Trinity fasta file, rename as ${output_dir}.Trinity.fasta
-#
-# \fB\-\-cite\fR :show the Trinity literature citation
-#
-# \fB\-\-version\fR :reports Trinity version (Trinity_v2.0.2) and exits.
-#
-# \fB\-\-show_full_usage_info\fR :show the many many more options available for running Trinity (expert usage).
-.PP
-###############################################################################
-#
-# *Note, a typical Trinity command might be:
-#
-# Trinity \fB\-\-seqType\fR fq \fB\-\-max_memory\fR 50G \fB\-\-left\fR reads_1.fq \fB\-\-right\fR reads_2.fq \fB\-\-CPU\fR 6
-#
-#
-# and for Genome\-guided Trinity:
-#
-# Trinity \fB\-\-genome_guided_bam\fR rnaseq_alignments.csorted.bam \fB\-\-max_memory\fR 50G
-# \fB\-\-genome_guided_max_intron\fR 10000 \fB\-\-CPU\fR 6
-#
-# see: /usr/lib/trinityrnaseq/sample_data/test_Trinity_Assembly/
-# for sample data and 'runMe.sh' for example Trinity execution
-#
-# For more details, visit: http://trinityrnaseq.github.io
-#
-###############################################################################
+Trinity 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.
+.SH OPTIONS
+Required:
+.IP
+\fB\-\-seqType\fR <string>
+type of reads: ( fa, or fq )
+.IP
+\fB\-\-max_memory\fR <string>
+suggested max memory to use by Trinity where limiting can be enabled. (jellyfish, sorting, etc)
+provied in Gb of RAM, ie. '\-\-max_memory 10G'
+.P
+If paired reads:
+.IP
+\fB\-\-left\fR <string>
+left reads, one or more (separated by space)
+.IP
+\fB\-\-right\fR <string>
+right reads, one or more (separated by space)
+.P
+Or, if unpaired reads:
+.IP
+\fB\-\-single\fR <string>
+single reads, one or more (note, if single file contains pairs, can use flag: \fB\-\-run_as_paired\fR )
+.P
+Misc:
+.IP
+\fB\-\-SS_lib_type\fR <string>
+Strand\-specific RNA\-Seq read orientation.
+if paired: RF or FR,
+if single: F or R. (dUTP method = RF)
+See web documentation.
+.IP
+\fB\-\-CPU\fR <int>
+number of CPUs to use, default: 2
+.IP
+\fB\-\-min_contig_length\fR <int>
+minimum assembled contig length to report (def=200)
+.IP
+\fB\-\-long_reads\fR <string>
+fasta file containing error\-corrected or circular consensus (CCS) pac bio reads
+.IP
+\fB\-\-genome_guided_bam\fR <string>
+genome guided mode, provide path to coordinate\-sorted bam file.
+(see genome\-guided param section under \fB\-\-show_full_usage_info\fR)
+.IP
+\fB\-\-jaccard_clip\fR
+option, set if you have paired reads and
+you expect high gene density with UTR
+overlap (use FASTQ input file format
+for reads).
+(note: jaccard_clip is an expensive
+operation, so avoid using it unless
+necessary due to finding excessive fusion
+transcripts w/o it.)
+.IP
+\fB\-\-trimmomatic\fR
+run Trimmomatic to quality trim reads
+see '\-\-quality_trimming_params' under full usage info for tailored settings.
+.IP
+\fB\-\-normalize_reads\fR
+run in silico normalization of reads. Defaults to max. read coverage of 50.
+see '\-\-normalize_max_read_cov' under full usage info for tailored settings.
+.IP
+\fB\-\-no_distributed_trinity_exec\fR
+do not run Trinity phase 2 (assembly of partitioned reads), and stop after generating command list.
+.IP
+\fB\-\-output\fR <string>
+name of directory for output (will be
+created if it doesn't already exist)
+default(your current working directory)
+.IP
+\fB\-\-full_cleanup\fR
+only retain the Trinity fasta file, rename as ${output_dir}.Trinity.fasta
+.IP
+\fB\-\-cite\fR
+show the Trinity literature citation
+.IP
+\fB\-\-version\fR
+reports Trinity version (Trinity_v2.0.2) and exits.
+.IP
+\fB\-\-show_full_usage_info\fR
+show the many many more options available for running Trinity (expert usage).
+.SH EXAMPLES
+A typical Trinity command might be:
+.IP
+Trinity \fB\-\-seqType\fR fq \fB\-\-max_memory\fR 50G \fB\-\-left\fR reads_1.fq \fB\-\-right\fR reads_2.fq \fB\-\-CPU\fR 6
+.P
+and for Genome\-guided Trinity:
+.IP
+Trinity \fB\-\-genome_guided_bam\fR rnaseq_alignments.csorted.bam \fB\-\-max_memory\fR 50G
+ \fB\-\-genome_guided_max_intron\fR 10000 \fB\-\-CPU\fR 6
.SH "SEE ALSO"
-The full documentation for
-.B Trinity
-is maintained as a Texinfo manual. If the
-.B info
-and
-.B Trinity
-programs are properly installed at your site, the command
-.IP
-.B info Trinity
-.PP
-should give you access to the complete manual.
+see: /usr/lib/trinityrnaseq/sample_data/test_Trinity_Assembly/
+for sample data and 'runMe.sh' for example Trinity execution
+.P
+For more details, visit: http://trinityrnaseq.github.io
--
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