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commit 0be291ddbe454eba219bdc0bf774adf84b7a6c6c Author: Michael R. Crusoe <mcru...@msu.edu> Date: Thu Feb 12 12:00:43 2015 -0500 manpage; mark scripts +x --- debian/Trinity.1 | 110 ++++++++++++++++++++++++++++++++++++++++++ debian/rules | 10 +++- debian/trinityrnaseq.manpages | 1 + 3 files changed, 120 insertions(+), 1 deletion(-) diff --git a/debian/Trinity.1 b/debian/Trinity.1 new file mode 100644 index 0000000..2358fbc --- /dev/null +++ b/debian/Trinity.1 @@ -0,0 +1,110 @@ +.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.44.1. +.TH TRINITY "1" "February 2015" "Trinity version: Trinity_v2.0.2" "User Commands" +.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 +# +############################################################################### +.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. diff --git a/debian/rules b/debian/rules index 50d104d..adaa918 100755 --- a/debian/rules +++ b/debian/rules @@ -17,6 +17,9 @@ BUTTERFLY_LIBDIR := ${ROOT_DIR}/../Butterfly/src/lib export CLASSPATH=/usr/share/java/collections15.jar:/usr/share/java/gnu-getopt.jar:${BUTTERFLY_LIBDIR}/jung-algorithms-2.0.1.jar:${BUTTERFLY_LIBDIR}/jung-api-2.0.1.jar:${BUTTERFLY_LIBDIR}/jung-api-2.0.1.jar:${BUTTERFLY_LIBDIR}/jung-graph-impl-2.0.1.jar SOURCE_DIRECTORIES = Inchworm Chrysalis trinity-plugins/fastool trinity-plugins/parafly + +BASEDIR=debian/trinityrnaseq/usr/lib/trinityrnaseq + %: dh $@ --parallel @@ -44,4 +47,9 @@ override_dh_install: dh_install find debian/trinityrnaseq -name '*.p?' | xargs sed -i \ 's=^#!/usr/local/bin/perl=#!/usr/bin/perl=' - + chmod u+x \ + ${BASEDIR}/Analysis/DifferentialExpression/pairwise_summaries/class_to_separate_fpkm_matrices.pl \ + ${BASEDIR}/Analysis/FL_reconstruction_analysis/count_by_expression_quintile.pl \ + ${BASEDIR}/util/misc/capture_orig_n_unmapped_reads.pl \ + ${BASEDIR}/util/support_scripts/plugin_install_tests.sh \ + ${BASEDIR}/util/support_scripts/trinity_install_tests.sh diff --git a/debian/trinityrnaseq.manpages b/debian/trinityrnaseq.manpages new file mode 100644 index 0000000..eb2bcfa --- /dev/null +++ b/debian/trinityrnaseq.manpages @@ -0,0 +1 @@ +debian/Trinity.1 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/trinityrnaseq.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit