[med-svn] r11490 - in trunk/packages/meme/trunk/debian: . meme_manpages patches
Thorsten Alteholz
alteholz at alioth.debian.org
Wed Jun 27 20:32:32 UTC 2012
Author: alteholz
Date: 2012-06-27 20:32:32 +0000 (Wed, 27 Jun 2012)
New Revision: 11490
Added:
trunk/packages/meme/trunk/debian/meme.doc-base
trunk/packages/meme/trunk/debian/meme_manpages/meme-chip.1
trunk/packages/meme/trunk/debian/meme_manpages/meme2meme.1
trunk/packages/meme/trunk/debian/meme_manpages/meme_p.1
trunk/packages/meme/trunk/debian/patches/perl-include.patch
Modified:
trunk/packages/meme/trunk/debian/meme.install
trunk/packages/meme/trunk/debian/meme.manpages
trunk/packages/meme/trunk/debian/patches/series
trunk/packages/meme/trunk/debian/rules
Log:
lots of small tools are hidden in the source tree
Added: trunk/packages/meme/trunk/debian/meme.doc-base
===================================================================
--- trunk/packages/meme/trunk/debian/meme.doc-base (rev 0)
+++ trunk/packages/meme/trunk/debian/meme.doc-base 2012-06-27 20:32:32 UTC (rev 11490)
@@ -0,0 +1,13 @@
+Document: meme
+Title: meme manual
+Author: Tim Bailey
+Abstract: This manual documents The MEME suite.
+ The MEME Suite allows the biologist to discover novel motifs in
+ collections of unaligned DNA or protein sequences and to search for
+ motif occurrences in sequence databases. The suite is comprised of a
+ collection of tools that work together.
+Section: Science/Biology
+
+Format: HTML
+Index: /usr/share/doc/meme/meme.html
+Files: /usr/share/doc/meme/*
Modified: trunk/packages/meme/trunk/debian/meme.install
===================================================================
--- trunk/packages/meme/trunk/debian/meme.install 2012-06-27 19:55:59 UTC (rev 11489)
+++ trunk/packages/meme/trunk/debian/meme.install 2012-06-27 20:32:32 UTC (rev 11490)
@@ -1,5 +1,103 @@
+#only usable with website: usr/bin/metameme
+#use all tools: usr/bin/meme*
etc/*
-var
-usr/bin/meme*
+usr/bin/alphtype
+usr/bin/ama
+usr/bin/ama-qvalues
+usr/bin/ame
+usr/bin/beadstring
+usr/bin/beeml2meme
+usr/bin/cat_max
+usr/bin/centrimo
+usr/bin/ceqlogo
+usr/bin/changetoweb
+usr/bin/chen2meme
+usr/bin/clustalw-io
+usr/bin/clustalw2fasta
+usr/bin/clustalw2phylip
+usr/bin/compare_dates
+usr/bin/compute-prior-dist
+usr/bin/compute-uniform-priors
+usr/bin/download
+usr/bin/draw-mhmm
+usr/bin/dreme
+usr/bin/dust
+usr/bin/fasta-center
+usr/bin/fasta-dinucleotide-shuffle
+usr/bin/fasta-dinucleotide-shuffle.py
+usr/bin/fasta-fetch
+usr/bin/fasta-get-markov
+usr/bin/fasta-hamming-enrich
+usr/bin/fasta-hamming-enrich.py
+usr/bin/fasta-io
+usr/bin/fasta-make-index
+usr/bin/fasta-shuffle-letters
+usr/bin/fasta-subsample
+usr/bin/fasta-unique-names
+usr/bin/fimo
+usr/bin/fitevd
+usr/bin/gendb
+usr/bin/get_db_csv
+usr/bin/getsize
+usr/bin/gomo
+usr/bin/gomo_highlight
+usr/bin/hart2meme-bkg
+usr/bin/hartemink2psp
+usr/bin/hypergeometric.py
+usr/bin/iupac2meme
+usr/bin/jaspar2meme
+usr/bin/llr
+usr/bin/log-hmm
+usr/bin/mast
+usr/bin/mast2txt
+usr/bin/mcast
+usr/bin/meme
+usr/bin/meme-chip
+usr/bin/meme-get-motif
+usr/bin/meme-xml-html
+usr/bin/meme.bin
+usr/bin/meme2images
+usr/bin/meme2meme
+usr/bin/meme_p
usr/bin/metameme
+usr/bin/mhmm
+usr/bin/mhmm-io
+usr/bin/mhmm2html
+usr/bin/mhmme
+usr/bin/mhmms
+usr/bin/mhmmscan
+usr/bin/motiph
+usr/bin/nmica2meme
+usr/bin/oldmeme2meme
+usr/bin/plotgen
+usr/bin/pmp_bf
+usr/bin/prior_utils.pl
+usr/bin/priority2meme
+usr/bin/psp-gen
+usr/bin/purge
+usr/bin/qvalue
+usr/bin/ramen
+usr/bin/ranksum_test
+usr/bin/read_fasta_file.pl
+usr/bin/readseq
+usr/bin/reconcile-tree-alignment
+usr/bin/reduce-alignment
+usr/bin/remove-alignment-gaps
+usr/bin/rna2meme
+usr/bin/scpd2meme
+usr/bin/sd
+usr/bin/sequence.py
+usr/bin/shadow
+usr/bin/spamo
+usr/bin/taipale2meme
+usr/bin/tamo2meme
+usr/bin/tomtom
+usr/bin/transfac2meme
+usr/bin/tree
+usr/bin/uniprobe2meme
+usr/bin/update_db
+usr/bin/update_meme_tests
+usr/bin/xsltproc_lite
usr/share/doc/meme
+usr/share/perl5/Meme
+var
Modified: trunk/packages/meme/trunk/debian/meme.manpages
===================================================================
--- trunk/packages/meme/trunk/debian/meme.manpages 2012-06-27 19:55:59 UTC (rev 11489)
+++ trunk/packages/meme/trunk/debian/meme.manpages 2012-06-27 20:32:32 UTC (rev 11490)
@@ -1 +1,2 @@
debian/meme_manpages/*
+debian/tmp-manpages/*
Added: trunk/packages/meme/trunk/debian/meme_manpages/meme-chip.1
===================================================================
--- trunk/packages/meme/trunk/debian/meme_manpages/meme-chip.1 (rev 0)
+++ trunk/packages/meme/trunk/debian/meme_manpages/meme-chip.1 2012-06-27 20:32:32 UTC (rev 11490)
@@ -0,0 +1,86 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.10.
+.TH MEME\-CHIP "1" "June 2012" "DNA sequence analyser" "User Commands"
+.SH NAME
+meme\-chip \- automated analysis of a ChIPseq DNA sequence dataset
+.SH DESCRIPTION
+.SS "Usage:"
+.IP
+meme\-chip [options] <sequences>
+.SS
+Options:
+.TP
+\fB\-o\fR
+<dir> : output to the specified directory, failing if the directory exists
+.TP
+\fB\-oc\fR
+<dir> : output to the specified directory, overwriting if the directory exists
+.TP
+\fB\-index\-name\fR
+<name> : name of html index file; default: index.html
+.TP
+\fB\-db\fR
+<path> : target database for use by TOMTOM and AME, if not present then TOMTOM and AME are not run
+.TP
+\fB\-bfile\fR
+<path> : background file
+.TP
+\fB\-nmeme\fR
+<num> : limit of sequences to pass to MEME
+.TP
+\fB\-ccut\fR
+<num> : maximum size of a sequence before it is cut down
+to a centered section; a value of 0 indicates the
+sequences should not be cut down; default: 100
+.TP
+\fB\-desc\fR
+<text> : description of the job
+.TP
+\fB\-fdesc\fR
+<file> : file containing plain text description of the job
+.TP
+\fB\-run\-mast\fR
+: run MAST \- motif alignment & search tool
+.TP
+\fB\-run\-ama\fR
+: run AMA \- Average motif affinity.
+.TP
+\fB\-noecho\fR
+: don't echo the commands run
+.TP
+\fB\-tar\fR
+: create a tar.gz file of the outputs
+.TP
+\fB\-help\fR
+: display this help message
+.SS
+MEME Specific Options:
+.HP
+\fB\-meme\-mod\fR [oops|zoops|anr]: sites used in a single sequence
+.TP
+\fB\-meme\-minw\fR
+<num> : minimum motif width
+.TP
+\fB\-meme\-maxw\fR
+<num> : maximum motif width
+.TP
+\fB\-meme\-nmotifs\fR
+<num> : maximum number of motifs to find
+.TP
+\fB\-meme\-minsites\fR
+<num> : minimum number of sites per motif
+.TP
+\fB\-meme\-maxsites\fR
+<num> : maximum number of sites per motif
+.TP
+\fB\-meme\-time\fR
+<secs> : maximum time to run MEME in seconds
+.TP
+\fB\-meme\-p\fR
+<np> : use parallel version with <np> processors
+.TP
+\fB\-meme\-norevcomp\fR
+: search given strand only
+.TP
+\fB\-meme\-pal\fR
+: look for palindromes only
+
Added: trunk/packages/meme/trunk/debian/meme_manpages/meme2meme.1
===================================================================
--- trunk/packages/meme/trunk/debian/meme_manpages/meme2meme.1 (rev 0)
+++ trunk/packages/meme/trunk/debian/meme_manpages/meme2meme.1 2012-06-27 20:32:32 UTC (rev 11490)
@@ -0,0 +1,41 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.10.
+.TH MEME2MEME "1" "June 2012" "Meme converter" "User Commands"
+.SH NAME
+meme2meme \- convert file in meme format to other meme format
+.SH DESCRIPTION
+Takes meme motifs in many forms and makes a single database in
+minimal meme format.
+Note that this doesn't accept the old meme html format
+(prior to version 4.3.2).
+Writes to standard output.
+.SH
+Usage:
+.IP
+meme2meme [options] <meme file>+
+.SH
+Options:
+.TP
+\fB\-consensus\fR
+numeric names are swapped for an IUPAC
+consensus; default: use existing names
+.TP
+\fB\-numbers\fR
+use numbers instead of strings for motif names;
+default: use existing ID
+.TP
+\fB\-bg\fR <background file>
+file with background frequencies of letters;
+default: use first file background
+.TP
+\fB\-logodds\fR
+print log\-odds matrix as well as frequency matrix;
+default: frequency matrix only
+.TP
+\fB\-url\fR <website>
+website for the motif if it doesn't have one
+already; The motif name is substituted for
+MOTIF_NAME; default: use existing url
+.TP
+\fB\-forceurl\fR
+Existing urls are ignored
+
Added: trunk/packages/meme/trunk/debian/meme_manpages/meme_p.1
===================================================================
--- trunk/packages/meme/trunk/debian/meme_manpages/meme_p.1 (rev 0)
+++ trunk/packages/meme/trunk/debian/meme_manpages/meme_p.1 2012-06-27 20:32:32 UTC (rev 11490)
@@ -0,0 +1,147 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.10.
+.TH MEME_P "1" "June 2012" "meme_p" "User Commands"
+.SH NAME
+meme_p \- modify sequences
+.SH DESCRIPTION
+.PP
+USAGE:
+.TP
+meme_p <dataset> [optional arguments]
+.TP
+<dataset>
+file containing sequences in FASTA format
+.TP
+[\-h]
+print this message
+.TP
+[\-o <output dir>]
+name of directory for output files
+will not replace existing directory
+.TP
+[\-oc <output dir>]
+name of directory for output files
+will replace existing directory
+.TP
+[\-text]
+output in text format (default is HTML)
+.TP
+[\-dna]
+sequences use DNA alphabet
+.TP
+[\-protein]
+sequences use protein alphabet
+.TP
+[\-mod oops|zoops|anr]
+distribution of motifs
+.TP
+[\-nmotifs <nmotifs>]
+maximum number of motifs to find
+.TP
+[\-evt <ev>]
+stop if motif E\-value greater than <evt>
+.TP
+[\-nsites <sites>]
+number of sites for each motif
+.TP
+[\-minsites <minsites>]
+minimum number of sites for each motif
+.TP
+[\-maxsites <maxsites>]
+maximum number of sites for each motif
+.TP
+[\-wnsites <wnsites>]
+weight on expected number of sites
+.TP
+[\-w <w>]
+motif width
+.TP
+[\-minw <minw>]
+minimum motif width
+.TP
+[\-maxw <maxw>]
+maximum motif width
+.TP
+[\-nomatrim]
+do not adjust motif width using multiple
+alignment
+.TP
+[\-wg <wg>]
+gap opening cost for multiple alignments
+.TP
+[\-ws <ws>]
+gap extension cost for multiple alignments
+.TP
+[\-noendgaps]
+do not count end gaps in multiple alignments
+.TP
+[\-bfile <bfile>]
+name of background Markov model file
+.TP
+[\-revcomp]
+allow sites on + or \- DNA strands
+.TP
+[\-pal]
+force palindromes (requires \fB\-dna\fR)
+.TP
+[\-maxiter <maxiter>]
+maximum EM iterations to run
+.TP
+[\-distance <distance>]
+EM convergence criterion
+.TP
+[\-psp <pspfile>]
+name of positional priors file
+.IP
+[\-prior dirichlet|dmix|mega|megap|addone]
+.IP
+type of prior to use
+.TP
+[\-b <b>]
+strength of the prior
+.TP
+[\-plib <plib>]
+name of Dirichlet prior file
+.TP
+[\-spfuzz <spfuzz>]
+fuzziness of sequence to theta mapping
+.TP
+[\-spmap uni|pam]
+starting point seq to theta mapping type
+.TP
+[\-cons <cons>]
+consensus sequence to start EM from
+.TP
+[\-heapsize <hs>]
+size of heaps for widths where substring
+search occurs
+.TP
+[\-x_branch]
+perform x\-branching
+.TP
+[\-w_branch]
+perform width branching
+.TP
+[\-allw]
+include all motif widths from min to max
+.TP
+[\-bfactor <bf>]
+branching factor for branching search
+.TP
+[\-maxsize <maxsize>]
+maximum dataset size in characters
+.TP
+[\-nostatus]
+do not print progress reports to terminal
+.TP
+[\-p <np>]
+use parallel version with <np> processors
+.TP
+[\-time <t>]
+quit before <t> CPU seconds consumed
+.TP
+[\-sf <sf>]
+print <sf> as name of sequence file
+.TP
+[\-V]
+verbose mode
+
Added: trunk/packages/meme/trunk/debian/patches/perl-include.patch
===================================================================
--- trunk/packages/meme/trunk/debian/patches/perl-include.patch (rev 0)
+++ trunk/packages/meme/trunk/debian/patches/perl-include.patch 2012-06-27 20:32:32 UTC (rev 11490)
@@ -0,0 +1,49 @@
+Description: add meme directory to search path
+Index: meme_4.8.1.patch/scripts/meme-chip.pl.in
+===================================================================
+--- meme_4.8.1.patch.orig/scripts/meme-chip.pl.in 2012-02-07 04:26:29.000000000 +0100
++++ meme_4.8.1.patch/scripts/meme-chip.pl.in 2012-06-22 12:40:26.000000000 +0200
+@@ -4,6 +4,7 @@
+ use warnings;
+
+ use lib qw(@PERLLIBDIR@);
++use lib qw(/usr/share/perl5/Meme);
+
+ use Cwd qw(abs_path);
+ use Fcntl qw(O_CREAT O_RDONLY O_WRONLY O_TRUNC SEEK_SET);
+Index: meme_4.8.1.patch/scripts/meme-chip_webservice.pl.in
+===================================================================
+--- meme_4.8.1.patch.orig/scripts/meme-chip_webservice.pl.in 2012-01-27 07:05:09.000000000 +0100
++++ meme_4.8.1.patch/scripts/meme-chip_webservice.pl.in 2012-06-22 12:40:46.000000000 +0200
+@@ -4,6 +4,7 @@
+ use warnings;
+
+ use lib qw(@PERLLIBDIR@);
++use lib qw(/usr/share/perl5/Meme);
+
+ use Cwd;
+ use File::Basename qw(fileparse);
+Index: meme_4.8.1.patch/scripts/meme2meme.pl.in
+===================================================================
+--- meme_4.8.1.patch.orig/scripts/meme2meme.pl.in 2012-01-27 07:05:09.000000000 +0100
++++ meme_4.8.1.patch/scripts/meme2meme.pl.in 2012-06-22 13:12:53.000000000 +0200
+@@ -10,6 +10,7 @@
+ use strict;
+
+ use lib qw(@PERLLIBDIR@);
++use lib qw(/usr/share/perl5/Meme);
+
+ use MotifUtils qw(intern_to_iupac intern_to_meme read_background_file parse_double round);
+
+Index: meme_4.8.1.patch/website/scripts/metameme.txt
+===================================================================
+--- meme_4.8.1.patch.orig/website/scripts/metameme.txt 2012-01-27 07:05:12.000000000 +0100
++++ meme_4.8.1.patch/website/scripts/metameme.txt 2012-06-22 13:13:53.000000000 +0200
+@@ -16,6 +16,7 @@
+ # sorted scores for training set
+ # sorted scores for test set
+ use lib qw(.);
++use lib qw(/usr/share/perl5/Meme);
+ use mhmm_globals;
+
+ #########################################################################
Modified: trunk/packages/meme/trunk/debian/patches/series
===================================================================
--- trunk/packages/meme/trunk/debian/patches/series 2012-06-27 19:55:59 UTC (rev 11489)
+++ trunk/packages/meme/trunk/debian/patches/series 2012-06-27 20:32:32 UTC (rev 11490)
@@ -2,3 +2,4 @@
no_libxml_configure
fix_installer_paths
fix_plib_path
+perl-include.patch
Modified: trunk/packages/meme/trunk/debian/rules
===================================================================
--- trunk/packages/meme/trunk/debian/rules 2012-06-27 19:55:59 UTC (rev 11489)
+++ trunk/packages/meme/trunk/debian/rules 2012-06-27 20:32:32 UTC (rev 11490)
@@ -6,6 +6,7 @@
DBPATH=/var/lib/meme
LOGPATH=/var/log/meme
+MODULES=alphtype ama ama-qvalues ame beadstring beeml2meme cat_max centrimo ceqlogo changetoweb chen2meme clustalw-io clustalw2fasta clustalw2phylip compare_dates compute-prior-dist compute-uniform-priors download draw-mhmm dreme dust fasta-center fasta-dinucleotide-shuffle fasta-dinucleotide-shuffle.py fasta-fetch fasta-get-markov fasta-hamming-enrich fasta-hamming-enrich.py fasta-io fasta-make-index fasta-shuffle-letters fasta-subsample fasta-unique-names fimo fitevd gendb get_db_csv getsize gomo gomo_highlight hart2meme-bkg hartemink2psp hypergeometric.py iupac2meme jaspar2meme llr log-hmm mast mast2txt mcast meme meme-chip meme-get-motif meme-xml-html meme.bin meme2images meme2meme meme_p metameme mhmm mhmm-io mhmm2html mhmme mhmms mhmmscan motiph nmica2meme oldmeme2meme plotgen pmp_bf prior_utils.pl priority2meme psp-gen purge qvalue ramen ranksum_test read_fasta_file.pl readseq reconcile-tree-alignment reduce-alignment remove-alignment-gaps rna2meme scpd2meme sd sequence.py shadow spamo taipale2meme tamo2meme tomtom transfac2meme tree uniprobe2meme update_db update_meme_tests xsltproc_lite
%:
dh $@ --with autoreconf,python2
@@ -24,7 +25,14 @@
mkdir -p debian/tmp/usr/share/doc/meme ; mv debian/tmp/usr/doc/* debian/tmp/usr/share/doc/meme
mv debian/tmp/etc/meme/meme.doc debian/tmp/usr/share/doc/meme
find ./* -print|grep STRGGTCAN.meme|xargs chmod 644
+ find ./* -print
+ mkdir -p debian/tmp/usr/share/perl5/Meme
+ cp website/scripts/*.pm debian/tmp/usr/share/perl5/Meme
+ cp scripts/*.pm debian/tmp/usr/share/perl5/Meme
+ mkdir -p debian/tmp-manpages
+ $(foreach var,$(MODULES), /usr/bin/pod2man debian/tmp/usr/bin/$(var) > debian/tmp-manpages/$(var).1;)
dh_install -v --sourcedir=debian/tmp
+ find ./* -print
override_dh_auto_clean:
dh_auto_clean
@@ -35,7 +43,7 @@
rm -f aclocal.m4
find -type f -name Makefile -exec rm '{}' ';'
-#Disable testing temporarily to save time
+#XXX Disable testing temporarily to save time
override_dh_auto_test:
true
@@ -46,3 +54,5 @@
mkdir -p ../tarballs
uscan --verbose --force-download --destdir=../tarballs
+
+
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