[med-svn] r5856 - in trunk/packages/bowtie/trunk/debian: . patches
Andreas Tille
tille at alioth.debian.org
Wed Feb 2 13:02:07 UTC 2011
Author: tille
Date: 2011-02-02 13:02:04 +0000 (Wed, 02 Feb 2011)
New Revision: 5856
Added:
trunk/packages/bowtie/trunk/debian/bowtie.dirs
trunk/packages/bowtie/trunk/debian/patches/
trunk/packages/bowtie/trunk/debian/patches/use_debian_seqan.patch
Removed:
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/bowtie.manpages
Modified:
trunk/packages/bowtie/trunk/debian/changelog
trunk/packages/bowtie/trunk/debian/control
trunk/packages/bowtie/trunk/debian/rules
Log:
Final polishing of bowtie and upload to unstable
Deleted: trunk/packages/bowtie/trunk/debian/bowtie-build.1
===================================================================
--- trunk/packages/bowtie/trunk/debian/bowtie-build.1 2011-02-02 12:16:56 UTC (rev 5855)
+++ trunk/packages/bowtie/trunk/debian/bowtie-build.1 2011-02-02 13:02:04 UTC (rev 5856)
@@ -1,94 +0,0 @@
-.\" 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.
Deleted: trunk/packages/bowtie/trunk/debian/bowtie-inspect.1
===================================================================
--- trunk/packages/bowtie/trunk/debian/bowtie-inspect.1 2011-02-02 12:16:56 UTC (rev 5855)
+++ trunk/packages/bowtie/trunk/debian/bowtie-inspect.1 2011-02-02 13:02:04 UTC (rev 5856)
@@ -1,56 +0,0 @@
-.\" 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.
Deleted: trunk/packages/bowtie/trunk/debian/bowtie.1
===================================================================
--- trunk/packages/bowtie/trunk/debian/bowtie.1 2011-02-02 12:16:56 UTC (rev 5855)
+++ trunk/packages/bowtie/trunk/debian/bowtie.1 2011-02-02 13:02:04 UTC (rev 5856)
@@ -1,241 +0,0 @@
-.\" 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 \- ultrafast memory-efficient short read aligner
-.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.
Added: trunk/packages/bowtie/trunk/debian/bowtie.dirs
===================================================================
--- trunk/packages/bowtie/trunk/debian/bowtie.dirs (rev 0)
+++ trunk/packages/bowtie/trunk/debian/bowtie.dirs 2011-02-02 13:02:04 UTC (rev 5856)
@@ -0,0 +1 @@
+usr/share/man/man1
Deleted: trunk/packages/bowtie/trunk/debian/bowtie.manpages
===================================================================
--- trunk/packages/bowtie/trunk/debian/bowtie.manpages 2011-02-02 12:16:56 UTC (rev 5855)
+++ trunk/packages/bowtie/trunk/debian/bowtie.manpages 2011-02-02 13:02:04 UTC (rev 5856)
@@ -1,3 +0,0 @@
-debian/bowtie.1
-debian/bowtie-build.1
-debian/bowtie-inspect.1
Modified: trunk/packages/bowtie/trunk/debian/changelog
===================================================================
--- trunk/packages/bowtie/trunk/debian/changelog 2011-02-02 12:16:56 UTC (rev 5855)
+++ trunk/packages/bowtie/trunk/debian/changelog 2011-02-02 13:02:04 UTC (rev 5856)
@@ -2,4 +2,4 @@
* Initial release (Closes: #604940)
- -- Steffen Moeller <moeller at debian.org> Thu, 25 Nov 2010 17:04:39 +0100
+ -- Andreas Tille <tille at debian.org> Wed, 02 Feb 2011 13:47:12 +0100
Modified: trunk/packages/bowtie/trunk/debian/control
===================================================================
--- trunk/packages/bowtie/trunk/debian/control 2011-02-02 12:16:56 UTC (rev 5855)
+++ trunk/packages/bowtie/trunk/debian/control 2011-02-02 13:02:04 UTC (rev 5856)
@@ -6,7 +6,7 @@
Uploaders: Steffen Moeller <moeller at debian.org>,
Yask Gupta <yask.gupta87 at gmail.com>,
Andreas Tille <tille at debian.org>
-Build-Depends: debhelper (>= 7.1)
+Build-Depends: debhelper (>= 7.1), help2man
Standards-Version: 3.9.1
Homepage: http://bowtie-bio.sourceforge.net/
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/bowtie/trunk
Added: trunk/packages/bowtie/trunk/debian/patches/use_debian_seqan.patch
===================================================================
--- trunk/packages/bowtie/trunk/debian/patches/use_debian_seqan.patch (rev 0)
+++ trunk/packages/bowtie/trunk/debian/patches/use_debian_seqan.patch 2011-02-02 13:02:04 UTC (rev 5856)
@@ -0,0 +1,26 @@
+Note: This patch is deactivated because the Debian packaged version of SeqAn 1.2
+ is not compatible with the version included into this package
+
+Author: Andreas Tille <tilleqdebian.org>
+Date: 2011-01-30
+Description: Use Debian packages SeqAn Librariy instead of copy in upstream source
+--- bowtie-0.12.7.orig/Makefile
++++ bowtie-0.12.7/Makefile
+@@ -2,7 +2,7 @@
+ # Makefile for bowtie, bowtie-build, bowtie-inspect
+ #
+
+-SEQAN_DIR = SeqAn-1.1
++SEQAN_DIR = /usr/include/seqan
+ SEQAN_INC = -I $(SEQAN_DIR)
+ INC = $(SEQAN_INC)
+ GCC_PREFIX = $(shell dirname `which gcc`)
+@@ -149,8 +149,6 @@
+ $(wildcard *.hh) \
+ $(wildcard *.c) \
+ $(wildcard *.cpp) \
+- $(shell $(FIND) SeqAn-1.1 -name "*.h") \
+- $(shell $(FIND) SeqAn-1.1 -name "*.txt") \
+ doc/strip_markdown.pl \
+ Makefile \
+ $(GENERAL_LIST)
Modified: trunk/packages/bowtie/trunk/debian/rules
===================================================================
--- trunk/packages/bowtie/trunk/debian/rules 2011-02-02 12:16:56 UTC (rev 5855)
+++ trunk/packages/bowtie/trunk/debian/rules 2011-02-02 13:02:04 UTC (rev 5856)
@@ -6,13 +6,25 @@
# Uncomment this to turn on verbose mode.
#export DH_VERBOSE=1
+pkg=bowtie
+
%:
- dh $@
+ dh $@
override_dh_auto_build:
- # dh_auto_build
$(MAKE) allall
+override_dh_auto_install:
+# for bin in bowtie bowtie-build bowtie-inspect ; do \
+# help2man $(CURDIR)/$${bin} > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/$${bin}.1 ; \
+# done
+ help2man --name="ultrafast memory-efficient short read aligner" \
+ $(CURDIR)/bowtie > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/bowtie.1
+ help2man --name="building a colorspace index for bowtie" \
+ $(CURDIR)/bowtie-build > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/bowtie-build.1
+ help2man --name="extracts information from a bowtie index" \
+ $(CURDIR)/bowtie-inspect > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/bowtie-inspect.1
+
override_dh_auto_clean:
rm -f .bowtie*
dh_auto_clean
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