[med-svn] [trinityrnaseq] 02/02: manpage; mark scripts +x
Michael Crusoe
misterc-guest at moszumanska.debian.org
Thu Feb 12 18:11:56 UTC 2015
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch master
in repository trinityrnaseq.
commit 0be291ddbe454eba219bdc0bf774adf84b7a6c6c
Author: Michael R. Crusoe <mcrusoe at 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
--
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