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 <moel...@debian.org> Thu, 25 Nov 2010 17:04:39 +0100 + -- Andreas Tille <ti...@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 <moel...@debian.org>, Yask Gupta <yask.gupt...@gmail.com>, Andreas Tille <ti...@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 _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit