[med-svn] r5508 - trunk/packages/bowtie/trunk/debian
Steffen Möller
moeller at alioth.debian.org
Thu Nov 25 16:31:26 UTC 2010
Author: moeller
Date: 2010-11-25 16:31:22 +0000 (Thu, 25 Nov 2010)
New Revision: 5508
Added:
trunk/packages/bowtie/trunk/debian/bowtie-build.1
trunk/packages/bowtie/trunk/debian/bowtie-inspect.1
trunk/packages/bowtie/trunk/debian/bowtie.1
trunk/packages/bowtie/trunk/debian/manpages
Modified:
trunk/packages/bowtie/trunk/debian/copyright
Log:
Some improvements to packaging of bowtie ... yet untested.
Added: trunk/packages/bowtie/trunk/debian/bowtie-build.1
===================================================================
--- trunk/packages/bowtie/trunk/debian/bowtie-build.1 (rev 0)
+++ trunk/packages/bowtie/trunk/debian/bowtie-build.1 2010-11-25 16:31:22 UTC (rev 5508)
@@ -0,0 +1,94 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.38.2.
+.TH BOWTIE-BUILD "1" "November 2010" "bowtie-build version 0.12.7" "User Commands"
+.SH NAME
+bowtie-build \- manual page for bowtie-build version 0.12.7
+.SH SYNOPSIS
+.B bowtie-build
+[\fIoptions\fR]\fI* <reference_in> <ebwt_outfile_base>\fR
+.SH DESCRIPTION
+.TP
+reference_in
+comma\-separated list of files with ref sequences
+.TP
+ebwt_outfile_base
+write Ebwt data to files with this dir/basename
+.SH OPTIONS
+.TP
+\fB\-f\fR
+reference files are Fasta (default)
+.TP
+\fB\-c\fR
+reference sequences given on cmd line (as <seq_in>)
+.TP
+\fB\-C\fR/\-\-color
+build a colorspace index
+.TP
+\fB\-a\fR/\-\-noauto
+disable automatic \fB\-p\fR/\-\-bmax/\-\-dcv memory\-fitting
+.TP
+\fB\-p\fR/\-\-packed
+use packed strings internally; slower, uses less mem
+.TP
+\fB\-B\fR
+build both letter\- and colorspace indexes
+.TP
+\fB\-\-bmax\fR <int>
+max bucket sz for blockwise suffix\-array builder
+.TP
+\fB\-\-bmaxdivn\fR <int>
+max bucket sz as divisor of ref len (default: 4)
+.TP
+\fB\-\-dcv\fR <int>
+diff\-cover period for blockwise (default: 1024)
+.TP
+\fB\-\-nodc\fR
+disable diff\-cover (algorithm becomes quadratic)
+.TP
+\fB\-r\fR/\-\-noref
+don't build .3/.4.ebwt (packed reference) portion
+.TP
+\fB\-3\fR/\-\-justref
+just build .3/.4.ebwt (packed reference) portion
+.TP
+\fB\-o\fR/\-\-offrate <int>
+SA is sampled every 2^offRate BWT chars (default: 5)
+.TP
+\fB\-t\fR/\-\-ftabchars <int>
+# of chars consumed in initial lookup (default: 10)
+.TP
+\fB\-\-ntoa\fR
+convert Ns in reference to As
+.TP
+\fB\-\-seed\fR <int>
+seed for random number generator
+.TP
+\fB\-q\fR/\-\-quiet
+verbose output (for debugging)
+.TP
+\fB\-h\fR/\-\-help
+print detailed description of tool and its options
+.TP
+\fB\-\-usage\fR
+print this usage message
+.TP
+\fB\-\-version\fR
+print version information and quit
+.PP
+64\-bit
+Built on Toshiba
+Thu Nov 25 17:18:33 CET 2010
+Compiler: gcc version 4.4.5 (Debian 4.4.5\-8)
+Options: \fB\-O3\fR \fB\-Wl\fR,\-\-hash\-style=both
+Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}
+.SH "SEE ALSO"
+The full documentation for
+.B bowtie-build
+is maintained as a Texinfo manual. If the
+.B info
+and
+.B bowtie-build
+programs are properly installed at your site, the command
+.IP
+.B info bowtie-build
+.PP
+should give you access to the complete manual.
Added: trunk/packages/bowtie/trunk/debian/bowtie-inspect.1
===================================================================
--- trunk/packages/bowtie/trunk/debian/bowtie-inspect.1 (rev 0)
+++ trunk/packages/bowtie/trunk/debian/bowtie-inspect.1 2010-11-25 16:31:22 UTC (rev 5508)
@@ -0,0 +1,56 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.38.2.
+.TH BOWTIE-INSPECT "1" "November 2010" "bowtie-inspect version 0.12.7" "User Commands"
+.SH NAME
+bowtie-inspect \- manual page for bowtie-inspect version 0.12.7
+.SH SYNOPSIS
+.B bowtie-inspect
+[\fIoptions\fR]\fI* <ebwt_base>\fR
+.SH DESCRIPTION
+.TP
+<ebwt_base>
+ebwt filename minus trailing .1.ebwt/.2.ebwt
+.IP
+By default, prints FASTA records of the indexed nucleotide sequences to
+standard out. With \fB\-n\fR, just prints names. With \fB\-s\fR, just prints a summary of
+the index parameters and sequences. With \fB\-e\fR, preserves colors if applicable.
+.SH OPTIONS
+.TP
+\fB\-a\fR/\-\-across <int>
+Number of characters across in FASTA output (default: 60)
+.TP
+\fB\-n\fR/\-\-names
+Print reference sequence names only
+.TP
+\fB\-s\fR/\-\-summary
+Print summary incl. ref names, lengths, index properties
+.TP
+\fB\-e\fR/\-\-ebwt\-ref
+Reconstruct reference from ebwt (slow, preserves colors)
+.TP
+\fB\-v\fR/\-\-verbose
+Verbose output (for debugging)
+.TP
+\fB\-h\fR/\-\-help
+print detailed description of tool and its options
+.TP
+\fB\-\-help\fR
+print this usage message
+.PP
+64\-bit
+Built on Toshiba
+Thu Nov 25 17:21:19 CET 2010
+Compiler: gcc version 4.4.5 (Debian 4.4.5\-8)
+Options: \fB\-O3\fR \fB\-Wl\fR,\-\-hash\-style=both
+Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}
+.SH "SEE ALSO"
+The full documentation for
+.B bowtie-inspect
+is maintained as a Texinfo manual. If the
+.B info
+and
+.B bowtie-inspect
+programs are properly installed at your site, the command
+.IP
+.B info bowtie-inspect
+.PP
+should give you access to the complete manual.
Added: trunk/packages/bowtie/trunk/debian/bowtie.1
===================================================================
--- trunk/packages/bowtie/trunk/debian/bowtie.1 (rev 0)
+++ trunk/packages/bowtie/trunk/debian/bowtie.1 2010-11-25 16:31:22 UTC (rev 5508)
@@ -0,0 +1,241 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.38.2.
+.TH BOWTIE "1" "November 2010" "bowtie version 0.12.7" "User Commands"
+.SH NAME
+bowtie \- manual page for bowtie version 0.12.7
+.SH DESCRIPTION
+.SS "Usage:"
+.IP
+bowtie [options]* <ebwt> {\-1 <m1> \fB\-2\fR <m2> | \fB\-\-12\fR <r> | <s>} [<hit>]
+.TP
+<m1>
+Comma\-separated list of files containing upstream mates (or the
+sequences themselves, if \fB\-c\fR is set) paired with mates in <m2>
+.TP
+<m2>
+Comma\-separated list of files containing downstream mates (or the
+sequences themselves if \fB\-c\fR is set) paired with mates in <m1>
+.TP
+<r>
+Comma\-separated list of files containing Crossbow\-style reads. Can be
+a mixture of paired and unpaired. Specify "\-" for stdin.
+.TP
+<s>
+Comma\-separated list of files containing unpaired reads, or the
+sequences themselves, if \fB\-c\fR is set. Specify "\-" for stdin.
+.TP
+<hit>
+File to write hits to (default: stdout)
+.SS "Input:"
+.TP
+\fB\-q\fR
+query input files are FASTQ .fq/.fastq (default)
+.TP
+\fB\-f\fR
+query input files are (multi\-)FASTA .fa/.mfa
+.TP
+\fB\-r\fR
+query input files are raw one\-sequence\-per\-line
+.TP
+\fB\-c\fR
+query sequences given on cmd line (as <mates>, <singles>)
+.TP
+\fB\-C\fR
+reads and index are in colorspace
+.TP
+\fB\-Q\fR/\-\-quals <file>
+QV file(s) corresponding to CSFASTA inputs; use with \fB\-f\fR \fB\-C\fR
+.TP
+\fB\-\-Q1\fR/\-\-Q2 <file>
+same as \fB\-Q\fR, but for mate files 1 and 2 respectively
+.TP
+\fB\-s\fR/\-\-skip <int>
+skip the first <int> reads/pairs in the input
+.TP
+\fB\-u\fR/\-\-qupto <int>
+stop after first <int> reads/pairs (excl. skipped reads)
+.TP
+\fB\-5\fR/\-\-trim5 <int>
+trim <int> bases from 5' (left) end of reads
+.TP
+\fB\-3\fR/\-\-trim3 <int>
+trim <int> bases from 3' (right) end of reads
+.TP
+\fB\-\-phred33\-quals\fR
+input quals are Phred+33 (default)
+.TP
+\fB\-\-phred64\-quals\fR
+input quals are Phred+64 (same as \fB\-\-solexa1\fR.3\-quals)
+.TP
+\fB\-\-solexa\-quals\fR
+input quals are from GA Pipeline ver. < 1.3
+.TP
+\fB\-\-solexa1\fR.3\-quals
+input quals are from GA Pipeline ver. >= 1.3
+.TP
+\fB\-\-integer\-quals\fR
+qualities are given as space\-separated integers (not ASCII)
+.SS "Alignment:"
+.TP
+\fB\-v\fR <int>
+report end\-to\-end hits w/ <=v mismatches; ignore qualities
+.IP
+or
+.HP
+\fB\-n\fR/\-\-seedmms <int> max mismatches in seed (can be 0\-3, default: \fB\-n\fR 2)
+.TP
+\fB\-e\fR/\-\-maqerr <int>
+max sum of mismatch quals across alignment for \fB\-n\fR (def: 70)
+.HP
+\fB\-l\fR/\-\-seedlen <int> seed length for \fB\-n\fR (default: 28)
+.TP
+\fB\-\-nomaqround\fR
+disable Maq\-like quality rounding for \fB\-n\fR (nearest 10 <= 30)
+.TP
+\fB\-I\fR/\-\-minins <int>
+minimum insert size for paired\-end alignment (default: 0)
+.TP
+\fB\-X\fR/\-\-maxins <int>
+maximum insert size for paired\-end alignment (default: 250)
+.HP
+\fB\-\-fr\fR/\-\-rf/\-\-ff \fB\-1\fR, \fB\-2\fR mates align fw/rev, rev/fw, fw/fw (default: \fB\-\-fr\fR)
+.TP
+\fB\-\-nofw\fR/\-\-norc
+do not align to forward/reverse\-complement reference strand
+.TP
+\fB\-\-maxbts\fR <int>
+max # backtracks for \fB\-n\fR 2/3 (default: 125, 800 for \fB\-\-best\fR)
+.TP
+\fB\-\-pairtries\fR <int>
+max # attempts to find mate for anchor hit (default: 100)
+.TP
+\fB\-y\fR/\-\-tryhard
+try hard to find valid alignments, at the expense of speed
+.TP
+\fB\-\-chunkmbs\fR <int>
+max megabytes of RAM for best\-first search frames (def: 64)
+.SS "Reporting:"
+.TP
+\fB\-k\fR <int>
+report up to <int> good alignments per read (default: 1)
+.TP
+\fB\-a\fR/\-\-all
+report all alignments per read (much slower than low \fB\-k\fR)
+.TP
+\fB\-m\fR <int>
+suppress all alignments if > <int> exist (def: no limit)
+.TP
+\fB\-M\fR <int>
+like \fB\-m\fR, but reports 1 random hit (MAPQ=0); requires \fB\-\-best\fR
+.TP
+\fB\-\-best\fR
+hits guaranteed best stratum; ties broken by quality
+.TP
+\fB\-\-strata\fR
+hits in sub\-optimal strata aren't reported (requires \fB\-\-best\fR)
+.SS "Output:"
+.TP
+\fB\-t\fR/\-\-time
+print wall\-clock time taken by search phases
+.HP
+\fB\-B\fR/\-\-offbase <int> leftmost ref offset = <int> in bowtie output (default: 0)
+.TP
+\fB\-\-quiet\fR
+print nothing but the alignments
+.TP
+\fB\-\-refout\fR
+write alignments to files refXXXXX.map, 1 map per reference
+.TP
+\fB\-\-refidx\fR
+refer to ref. seqs by 0\-based index rather than name
+.TP
+\fB\-\-al\fR <fname>
+write aligned reads/pairs to file(s) <fname>
+.TP
+\fB\-\-un\fR <fname>
+write unaligned reads/pairs to file(s) <fname>
+.TP
+\fB\-\-max\fR <fname>
+write reads/pairs over \fB\-m\fR limit to file(s) <fname>
+.TP
+\fB\-\-suppress\fR <cols>
+suppresses given columns (comma\-delim'ed) in default output
+.TP
+\fB\-\-fullref\fR
+write entire ref name (default: only up to 1st space)
+.SS "Colorspace:"
+.TP
+\fB\-\-snpphred\fR <int>
+Phred penalty for SNP when decoding colorspace (def: 30)
+.IP
+or
+.TP
+\fB\-\-snpfrac\fR <dec>
+approx. fraction of SNP bases (e.g. 0.001); sets \fB\-\-snpphred\fR
+.TP
+\fB\-\-col\-cseq\fR
+print aligned colorspace seqs as colors, not decoded bases
+.TP
+\fB\-\-col\-cqual\fR
+print original colorspace quals, not decoded quals
+.TP
+\fB\-\-col\-keepends\fR
+keep nucleotides at extreme ends of decoded alignment
+.SS "SAM:"
+.TP
+\fB\-S\fR/\-\-sam
+write hits in SAM format
+.TP
+\fB\-\-mapq\fR <int>
+default mapping quality (MAPQ) to print for SAM alignments
+.TP
+\fB\-\-sam\-nohead\fR
+supppress header lines (starting with @) for SAM output
+.TP
+\fB\-\-sam\-nosq\fR
+supppress @SQ header lines for SAM output
+.TP
+\fB\-\-sam\-RG\fR <text>
+add <text> (usually "lab=value") to @RG line of SAM header
+.SS "Performance:"
+.HP
+\fB\-o\fR/\-\-offrate <int> override offrate of index; must be >= index's offrate
+.HP
+\fB\-p\fR/\-\-threads <int> number of alignment threads to launch (default: 1)
+.TP
+\fB\-\-mm\fR
+use memory\-mapped I/O for index; many 'bowtie's can share
+.TP
+\fB\-\-shmem\fR
+use shared mem for index; many 'bowtie's can share
+.SS "Other:"
+.TP
+\fB\-\-seed\fR <int>
+seed for random number generator
+.TP
+\fB\-\-verbose\fR
+verbose output (for debugging)
+.TP
+\fB\-\-version\fR
+print version information and quit
+.TP
+\fB\-h\fR/\-\-help
+print this usage message
+.PP
+64\-bit
+Built on Toshiba
+Thu Nov 25 17:19:21 CET 2010
+Compiler: gcc version 4.4.5 (Debian 4.4.5\-8)
+Options: \fB\-O3\fR \fB\-Wl\fR,\-\-hash\-style=both
+Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}
+.SH "SEE ALSO"
+The full documentation for
+.B bowtie
+is maintained as a Texinfo manual. If the
+.B info
+and
+.B bowtie
+programs are properly installed at your site, the command
+.IP
+.B info bowtie
+.PP
+should give you access to the complete manual.
Modified: trunk/packages/bowtie/trunk/debian/copyright
===================================================================
--- trunk/packages/bowtie/trunk/debian/copyright 2010-11-25 16:23:36 UTC (rev 5507)
+++ trunk/packages/bowtie/trunk/debian/copyright 2010-11-25 16:31:22 UTC (rev 5508)
@@ -6,15 +6,16 @@
<url://example.com>
-Upstream Author(s):
+Upstream Authors:
- <put author's name and email here>
- <likewise for another author>
+ Ben Langmead <email?>
Copyright:
- <Copyright (C) YYYY Firstname Lastname>
- <likewise for another author>
+ Copyright (C) 2009-2010 Ben Langmead
+ Copyright (C) 2009-2010 C. Trapnell
+ Copyright (C) 2009-2010 M. Pop
+ Copyright (C) 2009-2010 Steven L. Salzberg
License:
@@ -25,6 +26,15 @@
WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES
OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+Publication:
+
+ It is not a requirement of the license, but when you use this
+ package for your research, you should cite
+
+ Langmead B, Trapnell C, Pop M, Salzberg SL.
+ Ultrafast and memory-efficient alignment of short DNA
+ sequences to the human genome. Genome Biology 10:R25.
+
On Debian systems, the complete text of the Artistic License
can be found in "/usr/share/common-licenses/Artistic".
@@ -32,14 +42,5 @@
Copyright (C) 2010 Steffen Moeller <moeller at debian.org>
-# Please chose a license for your packaging work. If the program you package
-# uses a mainstream license, using the same license is the safest choice.
-# Please avoid to pick license terms that are more restrictive than the
-# packaged work, as it may make Debian's contributions unacceptable upstream.
-# If you just want it to be GPL version 3, leave the following lines in.
+and is licensed under the same license.
-and is licensed under the GPL version 3,
-see "/usr/share/common-licenses/GPL-3".
-
-# Please also look if there are files or directories which have a
-# different copyright/license attached and list them here.
Added: trunk/packages/bowtie/trunk/debian/manpages
===================================================================
--- trunk/packages/bowtie/trunk/debian/manpages (rev 0)
+++ trunk/packages/bowtie/trunk/debian/manpages 2010-11-25 16:31:22 UTC (rev 5508)
@@ -0,0 +1,3 @@
+debian/bowtie.1
+debian/bowtie-build.1
+debian/bowtie-inspect.1
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