[med-svn] [art-nextgen-simulation-tools] 02/03: Add manpages
Andreas Tille
tille at debian.org
Wed Feb 17 09:48:32 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository art-nextgen-simulation-tools.
commit f8cfb0ef19b170690ea14c45fde1329ae35d9154
Author: Andreas Tille <tille at debian.org>
Date: Wed Feb 17 10:01:24 2016 +0100
Add manpages
---
debian/art-nextgen-simulation-tools.manpages | 1 +
debian/mans/art_454.1 | 85 +++++++++++++
debian/mans/art_SOLiD.1 | 100 +++++++++++++++
debian/mans/art_illumina.1 | 183 +++++++++++++++++++++++++++
debian/mans/art_profiler_454.1 | 22 ++++
debian/mans/art_profiler_illumina.1 | 39 ++++++
debian/rules | 6 +
7 files changed, 436 insertions(+)
diff --git a/debian/art-nextgen-simulation-tools.manpages b/debian/art-nextgen-simulation-tools.manpages
new file mode 100644
index 0000000..63ab24a
--- /dev/null
+++ b/debian/art-nextgen-simulation-tools.manpages
@@ -0,0 +1 @@
+debian/mans/*
diff --git a/debian/mans/art_454.1 b/debian/mans/art_454.1
new file mode 100644
index 0000000..6b649aa
--- /dev/null
+++ b/debian/mans/art_454.1
@@ -0,0 +1,85 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.3.
+.TH ART_454 "1" "February 2016" "art_454 3.19.15" "User Commands"
+.SH NAME
+art_454 \- Simulation of 454 Pyrosequencing
+.SH DESCRIPTION
+ART is a set of simulation tools to generate synthetic next-generation
+sequencing reads. ART simulates sequencing reads by mimicking real
+sequencing process with empirical error models or quality profiles
+summarized from large recalibrated sequencing data.
+.P
+art_454 can be used for Simulation of 454 Pyrosequencing.
+.SH USAGE
+.SS SINGLE\-END SIMULATION
+.B art_454
+[\-s] [\-a ] [\-t] [\-r rand_seed] [ \fB\-p\fR read_profile ] [ \fB\-c\fR num_flow_cycles ] <INPUT_SEQ_FILE> <OUTPUT_FILE_PREFIX> <FOLD_COVERAGE>
+.SS PAIRED\-END SIMULATION
+.B art_454
+ [\-s] [\-a ] [\-t] [\-r rand_seed] [ \fB\-p\fR read_profile ] [ \fB\-c\fR num_flow_cycles ] <INPUT_SEQ_FILE> <OUTPUT_FILE_PREFIX> <FOLD_COVERAGE> <MEAN_FRAG_LEN> <STD_DEV>
+.SS AMPLICON SEQUENCING SIMULATION
+.B art_454
+[\-s] [\-a ] [\-t] [\-r rand_seed] [ \fB\-p\fR read_profile ] [ \fB\-c\fR num_flow_cycles ] <\-A|\-B> <INPUT_SEQ_FILE> <OUTPUT_FILE_PREFIX> <#_READS/#_READ_PAIRS_PER_AMPLICON>
+.SH OPTIONS
+.SS MANDATORY OPTIONS
+.TP
+INPUT_SEQ_FILE \- the filename of DNA/RNA reference sequences in FASTA format
+.TP
+OUTPUT_FILE_PREFIX \- the prefix or directory of output read data file (*.fq) and read alignment file (*.aln)
+.TP
+FOLD_COVERAGE \- the fold of read coverage over the reference sequences
+.TP
+MEAN_FRAG_LEN \- the average DNA fragment size for paired\-end read simulation
+.TP
+STD_DEV \- the standard deviation of the DNA fragment size for paired\-end read simulation
+.TP
+#READS_PER_AMPLICON \- number of reads per amplicon (for 5'end amplicon sequencing)
+.TP
+#READ_PAIRS_PER_AMPLICON \- number of read pairs per amplicon (for two\-end amplicon sequencing)
+.SS OPTIONAL PARAMETERS
+.TP
+\fB\-A\fR indicate to perform single\-end amplicon sequencing simulation
+.TP
+\fB\-B\fR indicate to perform paired\-end amplicon sequencing simulation
+.TP
+\fB\-M\fR indicate to use CIGAR 'M' instead of '=/X' for alignment match/mismatch
+.TP
+\fB\-a\fR indicate to output the ALN alignment file
+.TP
+\fB\-s\fR indicate to output the SAM alignment file
+.TP
+\fB\-d\fR print out warning messages for debugging
+.TP
+\fB\-t\fR indicate to simulate reads from the built\-in GS FLX Titanium profile [default: GS FLX profile]
+.TP
+\fB\-r\fR specify a fixed random seed for the simulation (to generate two identical datasets from two different runs)
+.TP
+\fB\-c\fR specify the number of flow cycles by the sequencer [ default: 100 for GS\-FLX, and 200 for GS\-FLX Titanium ]
+.TP
+\fB\-p\fR specify user's own read profile for simulation
+.P
+NOTE: the name of a read profile is the directory containing read profile data files.
+please read the REAME file about the format of 454 read profile data files and.
+and the default filenames of these data files.
+.SH EXAMPLES
+.TP
+1) singl\-end simulation with 20X coverage
+.IP
+art_454 \fB\-s\fR seq_reference.fa ./outdir/single_dat 20
+.TP
+2) paired\-end simulation with the mean fragment size 1500 and STD 20 using GS FLX Titanium platform
+.IP
+art_454 \fB\-s\fR \fB\-t\fR seq_reference.fa ./outdir/paired_dat 10 1500 20
+.TP
+3) paired\-end simulation with a fixed random seed
+.IP
+art_454 \fB\-s\fR \fB\-r\fR 777 seq_reference.fa ./outdir/paired_fxSeed 10 2500 50
+.TP
+4) single\-end amplicon sequencing with 10 reads per amplicon
+.IP
+art_454 \fB\-A\fR \fB\-s\fR amplicon_ref.fa ./outdir/amp_single 10
+.TP
+5) paired\-end amplicon sequencing with 10 read pairs per amplicon
+.IP
+art_454 \fB\-B\fR \fB\-s\fR amplicon_ref.fa ./outdir/amp_paired 10
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/art_SOLiD.1 b/debian/mans/art_SOLiD.1
new file mode 100644
index 0000000..522043d
--- /dev/null
+++ b/debian/mans/art_SOLiD.1
@@ -0,0 +1,100 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.3.
+.TH ART_SOLID "1" "February 2016" "art_SOLiD 3.19.15" "User Commands"
+.SH NAME
+art_SOLiD \- Simulation of Applied Biosystems SOLiD Sequencing
+.SH DESCRIPTION
+ART is a set of simulation tools to generate synthetic next-generation
+sequencing reads. ART simulates sequencing reads by mimicking real
+sequencing process with empirical error models or quality profiles
+summarized from large recalibrated sequencing data.
+.P
+art_SOLiD can be used for Simulation of Applied Biosystems SOLiD Sequencing.
+.SH USAGE
+.SS SINGLE\-END (F3 READ) SIMULATION
+.B art_SOLiD
+[ options ] <INPUT_SEQ_FILE> <OUTPUT_FILE_PREFIX> <LEN_READ> <FOLD_COVERAGE>
+.SS MATE\-PAIR READS (F3\-R3 PAIR) SIMULATION
+.B art_SOLiD
+[ options ] <INPUT_SEQ_FILE> <OUTPUT_FILE_PREFIX> <LEN_READ> <FOLD_COVERAGE> <MEAN_FRAG_LEN> <STD_DEV>
+.SS PAIRED\-END READS (F3\-F5 PAIR) SIMULATION
+.B art_SOLiD
+[ options ] <INPUT_SEQ_FILE> <OUTPUT_FILE_PREFIX> <LEN_READ_F3> <LEN_READ_F5> <FOLD_COVERAGE> <MEAN_FRAG_LEN> <STD_DEV>
+.SS AMPLICON SEQUENCING SIMULATION
+.B art_SOLiD
+[ options ] \fB\-A\fR s <INPUT_SEQ_FILE> <OUTPUT_FILE_PREFIX> <LEN_READ> <READS_PER_AMPLICON>
+.P
+.B art_SOLiD
+[ options ] \fB\-A\fR m <INPUT_SEQ_FILE> <OUTPUT_FILE_PREFIX> <LEN_READ> <READ_PAIRS_PER_AMPLICON>
+.P
+.B art_SOLiD
+[ options ] \fB\-A\fR p <INPUT_SEQ_FILE> <OUTPUT_FILE_PREFIX> <LEN_READ_F3> <LEN_READ_F5> <READ_PAIRS_PER_AMPLICON>
+.SH OPTIONS
+.SS MANDATORY OPTIONS
+.TP
+INPUT_SEQ_FILE \- filename of DNA/RNA reference sequences in FASTA format
+.TP
+OUTPUT_FILE_PREFIX \- prefix or directory for all output read data files
+.TP
+FOLD_COVERAGE \- fold of read coverage over the reference sequences
+.TP
+LEN_READ \- length of F3/R3 reads
+.TP
+LEN_READ_F3 \- length of F3 reads for paired\-end read simulation
+.TP
+LEN_READ_F5 \- length of F5 reads for paired\-end read simulation
+.TP
+READS_PER_AMPLICON \- number of reads per amplicon
+.TP
+READ_PAIRS_PER_AMPLICON \- number of read pairs per amplicon
+.TP
+MEAN_FRAG_LEN \- mean DNA/RNA fragment size for matepair/paired\-end read simulation
+.TP
+STD_DEV \- standard deviation of the DNA/RNA fragment sizes for matepair/paired\-end read simulation
+.SS OPTIONAL PARAMETERS
+.TP
+\fB\-A\fR specify the read type for amplicon sequencing simulation (s:single\-end, m: matepair, p: paired\-end)
+.TP
+\fB\-M\fR indicate to use CIGAR 'M' instead of '=/X' for alignment match/mismatch
+.TP
+\fB\-s\fR indicate to generate a SAM alignment file
+.TP
+\fB\-r\fR specify the random seed for the simulation
+.TP
+\fB\-f\fR specify the scale factor adjusting error rate (e.g., \fB\-f\fR 0 for zero\-error rate simulation)
+.TP
+\fB\-p\fR specify user's own read profile for simulation
+.SH EXAMPLES
+.TP
+1) singl\-end 25bp reads simulation at 10X coverage
+.IP
+art_SOLiD \fB\-s\fR seq_reference.fa ./outdir/single_dat 25 10
+.TP
+2) singl\-end 75bp reads simulation at 20X coverage with user's error profile
+.IP
+art_SOLiD \fB\-s\fR \fB\-p\fR ../SOLiD_profiles/profile_pseudo ./seq_reference.fa ./dat_userProfile 75 20
+.TP
+3) matepair 35bp (F3\-R3) reads simulation at 20X coverage with DNA/RNA MEAN fragment size 2000bp and STD 50
+.IP
+art_SOLiD \fB\-s\fR seq_reference.fa ./outdir/matepair_dat 35 20 2000 50
+.TP
+4) matepair reads simulation with a fixed random seed
+.IP
+art_SOLiD \fB\-r\fR 777 \fB\-s\fR seq_reference.fa ./outdir/matepair_fs 50 10 1500 50
+.TP
+5) paired\-end reads (75bp F3, 35bp F5) simulation with the MEAN fragment size 250 and STD 10 at 20X coverage
+.IP
+art_SOLiD \fB\-s\fR seq_reference.fa ./outdir/paired_dat 75 35 50 250 10
+.TP
+6) amplicon sequencing with 25bp single\-end reads at 100 reads per amplicon
+.IP
+art_SOLiD \fB\-A\fR s \fB\-s\fR amp_reference.fa ./outdir/amp_single 25 100
+.TP
+7) amplicon sequencing with 50bp matepair reads at 80 read pairs per amplicon
+.IP
+art_SOLiD \fB\-A\fR m \fB\-s\fR amp_reference.fa ./outdir/amp_matepair 50 80
+.TP
+8) amplicon sequencing with paired\-end reads (35bp F3, 25bp F5 reads) at 50 pairs per amplicon
+.IP
+art_SOLiD \fB\-A\fR p \fB\-s\fR amp_reference.fa ./outdir/amp_pair 35 25 50
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/art_illumina.1 b/debian/mans/art_illumina.1
new file mode 100644
index 0000000..83af2d3
--- /dev/null
+++ b/debian/mans/art_illumina.1
@@ -0,0 +1,183 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.3.
+.TH ART_ILLUMINA "1" "February 2016" "art_illumina 3.19.15" "User Commands"
+.SH NAME
+art_illumina \- Simulation of Illumina sequencers
+.SH DESCRIPTION
+ART is a set of simulation tools to generate synthetic next-generation
+sequencing reads. ART simulates sequencing reads by mimicking real
+sequencing process with empirical error models or quality profiles
+summarized from large recalibrated sequencing data.
+.P
+art_illumina can be used for Simulation of Illumina sequencers
+.SH USAGE
+.B art_illumina
+[options] \fB\-sam\fR \fB\-i\fR <seq_ref_file> \fB\-l\fR <read_length> \fB\-f\fR <fold_coverage> \fB\-ss\fR <sequencing_system> \fB\-o\fR <outfile_prefix>
+.P
+.B art_illumina
+[options] \fB\-sam\fR \fB\-i\fR <seq_ref_file> \fB\-l\fR <read_length> \fB\-f\fR <fold_coverage> \fB\-o\fR <outfile_prefix>
+.P
+.B art_illumina
+[options] \fB\-sam\fR \fB\-i\fR <seq_ref_file> \fB\-l\fR <read_length> \fB\-c\fR <total_num_reads> \fB\-o\fR <outfile_prefix>
+.P
+.B art_illumina
+[options] \fB\-sam\fR \fB\-i\fR <seq_ref_file> \fB\-l\fR <read_length> \fB\-f\fR <fold_coverage> \fB\-m\fR <mean_fragsize> \fB\-s\fR <std_fragsize> \fB\-o\fR <outfile_prefix>
+.P
+.B art_illumina
+[options] \fB\-sam\fR \fB\-i\fR <seq_ref_file> \fB\-l\fR <read_length> \fB\-c\fR <total_num_reads> \fB\-m\fR <mean_fragsize> \fB\-s\fR <std_fragsize> \fB\-o\fR <outfile_prefix>
+.SH OPTIONS
+.TP
+\fB\-1\fR \fB\-\-qprof1\fR
+the first\-read quality profile
+.TP
+\fB\-2\fR \fB\-\-qprof2\fR
+the second\-read quality profile
+.HP
+\fB\-amp\fR \fB\-\-amplicon\fR amplicon sequencing simulation
+.TP
+\fB\-c\fR \fB\-\-rcount\fR
+total number of reads/read pairs to be generated [per amplicon if for amplicon simulation](not be used together with \fB\-f\fR/\-\-fcov)
+.TP
+\fB\-d\fR \fB\-\-id\fR
+the prefix identification tag for read ID
+.TP
+\fB\-ef\fR \fB\-\-errfree\fR
+indicate to generate the zero sequencing errors SAM file as well the regular one
+.IP
+NOTE: the reads in the zero\-error SAM file have the same alignment positions
+as those in the regular SAM file, but have no sequencing errors
+.TP
+\fB\-f\fR \fB\-\-fcov\fR
+the fold of read coverage to be simulated or number of reads/read pairs generated for each amplicon
+.TP
+\fB\-h\fR \fB\-\-help\fR
+print out usage information
+.TP
+\fB\-i\fR \fB\-\-in\fR
+the filename of input DNA/RNA reference
+.TP
+\fB\-ir\fR \fB\-\-insRate\fR
+the first\-read insertion rate (default: 0.00009)
+.HP
+\fB\-ir2\fR \fB\-\-insRate2\fR the second\-read insertion rate (default: 0.00015)
+.TP
+\fB\-dr\fR \fB\-\-delRate\fR
+the first\-read deletion rate (default: 0.00011)
+.HP
+\fB\-dr2\fR \fB\-\-delRate2\fR the second\-read deletion rate (default: 0.00023)
+.TP
+\fB\-l\fR \fB\-\-len\fR
+the length of reads to be simulated
+.TP
+\fB\-m\fR \fB\-\-mflen\fR
+the mean size of DNA/RNA fragments for paired\-end simulations
+.HP
+\fB\-mp\fR \fB\-\-matepair\fR indicate a mate\-pair read simulation
+.TP
+\fB\-nf\fR \fB\-\-maskN\fR
+the cutoff frequency of 'N' in a window size of the read length for masking genomic regions
+.IP
+NOTE: default: '\-nf 1' to mask all regions with 'N'. Use '\-nf 0' to turn off masking
+.TP
+\fB\-na\fR \fB\-\-noALN\fR
+do not output ALN alignment file
+.TP
+\fB\-o\fR \fB\-\-out\fR
+the prefix of output filename
+.TP
+\fB\-p\fR \fB\-\-paired\fR
+indicate a paired\-end read simulation or to generate reads from both ends of amplicons
+.IP
+NOTE: art will automatically switch to a mate\-pair simulation if the given mean fragment size >= 2000
+.TP
+\fB\-q\fR \fB\-\-quiet\fR
+turn off end of run summary
+.TP
+\fB\-qs\fR \fB\-\-qShift\fR
+the amount to shift every first\-read quality score by
+.TP
+\fB\-qs2\fR \fB\-\-qShift2\fR
+the amount to shift every second\-read quality score by
+.IP
+NOTE: For \fB\-qs\fR/\-qs2 option, a positive number will shift up quality scores (the max is 93)
+that reduce substitution sequencing errors and a negative number will shift down
+quality scores that increase sequencing errors. If shifting scores by x, the error
+rate will be 1/(10^(x/10)) of the default profile.
+.TP
+\fB\-rs\fR \fB\-\-rndSeed\fR
+the seed for random number generator (default: system time in second)
+.IP
+NOTE: using a fixed seed to generate two identical datasets from different runs
+.TP
+\fB\-s\fR \fB\-\-sdev\fR
+the standard deviation of DNA/RNA fragment size for paired\-end simulations.
+.TP
+\fB\-sam\fR \fB\-\-samout\fR
+indicate to generate SAM alignment file
+.TP
+\fB\-sp\fR \fB\-\-sepProf\fR
+indicate to use separate quality profiles for different bases (ATGC)
+.TP
+\fB\-ss\fR \fB\-\-seqSys\fR
+The name of Illumina sequencing system of the built\-in profile used for simulation
+.IP
+NOTE: sequencing system id names are:
+.TP
+GA1 \- Genome Analyzer I, GA2 \- Genome Analyzer II
+.TP
+HS10 \- HiSeq 1000, HS20 \- HiSeq 2000, HS25 \- HiSeq 2500, MS \- MiSeq
+.TP
+\fB\-M\fR \fB\-\-cigarM\fR
+indicate to use CIGAR 'M' instead of '=/X' for alignment match/mismatch
+.SH NOTES
+.PP
+* ART by default selects a built\-in quality score profile according to the read length specified for the run.
+.PP
+* For single\-end simulation, ART requires input sequence file, outputfile prefix, read length, and read count/fold coverage.
+.PP
+* For paired\-end simulation (except for amplicon sequencing), ART also requires the parameter values of
+.IP
+the mean and standard deviation of DNA/RNA fragment lengths
+.PP
+.SH EXAMPLES
+.TP
+1) single\-end read simulation
+.IP
+art_illumina \fB\-sam\fR \fB\-i\fR reference.fa \fB\-l\fR 150 \fB\-ss\fR HS25 \fB\-f\fR 10 \fB\-o\fR single_dat
+.TP
+2) paired\-end read simulation
+.IP
+art_illumina \fB\-sam\fR \fB\-i\fR reference.fa \fB\-p\fR \fB\-l\fR 150 \fB\-ss\fR HS25 \fB\-f\fR 20 \fB\-m\fR 200 \fB\-s\fR 10 \fB\-o\fR paired_dat
+.TP
+3) mate\-pair read simulation
+.IP
+art_illumina \fB\-sam\fR \fB\-i\fR reference.fa \fB\-mp\fR \fB\-l\fR 50 \fB\-f\fR 20 \fB\-m\fR 2500 \fB\-s\fR 50 \fB\-o\fR matepair_dat
+.TP
+4) amplicon sequencing simulation with 5' end single\-end reads
+.IP
+art_illumina \fB\-amp\fR \fB\-sam\fR \fB\-na\fR \fB\-i\fR amp_reference.fa \fB\-l\fR 50 \fB\-f\fR 10 \fB\-o\fR amplicon_5end_dat
+.TP
+5) amplicon sequencing simulation with paired\-end reads
+.IP
+art_illumina \fB\-amp\fR \fB\-p\fR \fB\-sam\fR \fB\-na\fR \fB\-i\fR amp_reference.fa \fB\-l\fR 50 \fB\-f\fR 10 \fB\-o\fR amplicon_pair_dat
+.TP
+6) amplicon sequencing simulation with matepair reads
+.IP
+art_illumina \fB\-amp\fR \fB\-mp\fR \fB\-sam\fR \fB\-na\fR \fB\-i\fR amp_reference.fa \fB\-l\fR 50 \fB\-f\fR 10 \fB\-o\fR amplicon_mate_dat
+.TP
+7) generate an extra SAM file with zero\-sequencing errors for a paired\-end read simulation
+.IP
+art_illumina \fB\-ef\fR \fB\-i\fR reference.fa \fB\-p\fR \fB\-l\fR 50 \fB\-f\fR 20 \fB\-m\fR 200 \fB\-s\fR 10 \fB\-o\fR paired_twosam_dat
+.TP
+8) reduce the substitution error rate to one 10th of the default profile
+.IP
+art_illumina \fB\-i\fR reference.fa \fB\-qs\fR 10 \fB\-qs2\fR 10 \fB\-l\fR 50 \fB\-f\fR 10 \fB\-p\fR \fB\-m\fR 500 \fB\-s\fR 10 \fB\-sam\fR \fB\-o\fR reduce_error
+.TP
+9) turn off the masking of genomic regions with unknown nucleotides 'N'
+.IP
+art_illumina \fB\-nf\fR 0 \fB\-sam\fR \fB\-i\fR reference.fa \fB\-p\fR \fB\-l\fR 50 \fB\-f\fR 20 \fB\-m\fR 200 \fB\-s\fR 10 \fB\-o\fR paired_nomask
+.TP
+10) masking genomic regions with >=5 'N's within the read length 50
+.IP
+art_illumina \fB\-nf\fR 5 \fB\-sam\fR \fB\-i\fR reference.fa \fB\-p\fR \fB\-l\fR 50 \fB\-f\fR 20 \fB\-m\fR 200 \fB\-s\fR 10 \fB\-o\fR paired_maskN5
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/art_profiler_454.1 b/debian/mans/art_profiler_454.1
new file mode 100644
index 0000000..177a23e
--- /dev/null
+++ b/debian/mans/art_profiler_454.1
@@ -0,0 +1,22 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.3.
+.TH ART_PROFILER_454 "1" "February 2016" "art_profiler_454 3.19.15" "User Commands"
+.SH NAME
+art_profiler_454 \- create an illumina read quality profile from multiple fastq or gzipped fastq files
+.SH DESCRIPTION
+art_profiler_454 is a program for generating empirical 454 read profiles
+for ART 454 simulator from 454 read data files
+.SH USAGE
+.B art_profiler_454
+input_fastq_files_dir output_profile_dir [fastq_filename_extension]
+.SH EXAMPLES
+.IP
+/usr/bin/art_profiler_454 454_dat_dir 454_profile_dir
+.IP
+/usr/bin/art_profiler_454 454_dat_dir 454_profile_dir fastq
+.SH NOTES
+.TP
+1)the default filename extension for fastq files is fq
+.TP
+2)the program can read gzipped fastq data files with filename extension fq.gz
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/art_profiler_illumina.1 b/debian/mans/art_profiler_illumina.1
new file mode 100644
index 0000000..e58accb
--- /dev/null
+++ b/debian/mans/art_profiler_illumina.1
@@ -0,0 +1,39 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.3.
+.TH ART_PROFILER_ILLUMINA "1" "February 2016" "art_profiler_illumina 3.19.15" "User Commands"
+.SH NAME
+art_profiler_illumina \- program for generating empirical 454 read profiles
+.SH DESCRIPTION
+This tool is to create an illumina read quality profile from multiple fastq or gzipped fastq files
+.SH USAGE
+.B art_profiler_illumina
+out_profile_name input_fastq_dir [fastq_filename_extension (default: fq)]
+.SH OPTIONS
+.TP
+out_profile_name:
+the name of read quality profile
+.TP
+input_fastq_dir:
+the directory of input fastq or zipped fastq files
+.IP
+fastq_filename_extension: fastq or gzipped fastq filename extension (default: fq)
+.SH EXAMPLES
+.TP
+1) create hiseq2k profiles from all *.fq.gz in the directory fastq_dat_dir
+.IP
+art_profiler_illumina hiseq2k fastq_dat_dir fq.gz
+.TP
+2) create miseq2500 profiles from all *.fq in the directory fastq_dat_dir
+.IP
+art_profiler_illumina miseq250 fastq_dat_dir fq
+.TP
+3) create hiseq1k profiles from all *.fq in the directory fastq_dat_dir
+.IP
+art_profiler_illumina hiseq1k fastq_dat_dir
+.P
+NOTES: For paired\-end fastq files, e.g., *.fq or *.fq.gz,
+the filenames of the 1st reads must be *_1.fq/*_1.fq.gz, or *.1.fq/*.1.fq.gz
+and those of the 2nd reads must be *_2.fq./*_2.fq.gz, or *.2.fq or *.2.fq.gz
+.SH AUTHOR
+This program was written by Weichun Huang <whduke at gmail.com>
+.P
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/rules b/debian/rules
index 4622c8b..f90ddcd 100755
--- a/debian/rules
+++ b/debian/rules
@@ -18,6 +18,12 @@ else
rm -f *.aln *.fq *.bed *.map *.sam *.stat
endif
+override_dh_install-arch:
+ dh_install -a
+ for pl in debian/$(DEBPKGNAME)/usr/bin/*.pl ; do \
+ mv $${pl} debian/$(DEBPKGNAME)/usr/bin/`basename $${pl} .pl` ; \
+ done
+
override_dh_installexamples-arch:
dh_installexamples -a
mkdir -p debian/$(DATAPKG)/usr/share/doc/$(DEBPKGNAME)
--
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