[med-svn] [Git][med-team/chip-seq][master] 9 commits: Add missing Depends
Andreas Tille
gitlab at salsa.debian.org
Thu Mar 26 16:07:26 GMT 2020
Andreas Tille pushed to branch master at Debian Med / chip-seq
Commits:
04e596b8 by Andreas Tille at 2020-03-26T16:27:26+01:00
Add missing Depends
- - - - -
064880d3 by Andreas Tille at 2020-03-26T16:33:20+01:00
More manpages
- - - - -
a26569d2 by Andreas Tille at 2020-03-26T16:34:46+01:00
Create data package since the data are actually used.
- - - - -
b538d7a4 by Andreas Tille at 2020-03-26T16:44:50+01:00
Adapt database installation PATH to Debian location
- - - - -
923b8372 by Andreas Tille at 2020-03-26T16:53:55+01:00
Fix installation of usr/bin and some *.pl manpages
- - - - -
d69d1c53 by Andreas Tille at 2020-03-26T16:56:26+01:00
Enhance description
- - - - -
29c107c4 by Andreas Tille at 2020-03-26T16:57:57+01:00
Fix permissions
- - - - -
ee6a173f by Andreas Tille at 2020-03-26T17:01:39+01:00
Some more manpages
- - - - -
5c1c2196 by Andreas Tille at 2020-03-26T17:04:23+01:00
Fif dh_fixperms
- - - - -
24 changed files:
- + debian/chip-seq-data.install
- debian/examples → debian/chip-seq.examples
- + debian/chip-seq.install
- debian/lintian-overrides → debian/chip-seq.lintian-overrides
- + debian/chip-seq.manpages
- debian/control
- + debian/createmanpages
- − debian/manpages
- + debian/mans/bed2bed_display.1
- + debian/mans/bed2sga.1
- + debian/mans/compactsga.1
- + debian/mans/countsga.1
- + debian/mans/featreplace.1
- + debian/mans/filter_counts.1
- + debian/mans/fps2sga.pl.1
- + debian/mans/gff2sga.pl.1
- + debian/mans/partit2bed.pl.1
- + debian/mans/sga2bed.1
- + debian/mans/sga2fps.pl.1
- + debian/mans/sga2gff.pl.1
- + debian/mans/sga2wig.1
- + debian/patches/data_location.patch
- debian/patches/series
- debian/rules
Changes:
=====================================
debian/chip-seq-data.install
=====================================
@@ -0,0 +1 @@
+share/* usr/share/chip-seq
=====================================
debian/examples → debian/chip-seq.examples
=====================================
=====================================
debian/chip-seq.install
=====================================
@@ -0,0 +1 @@
+usr/bin
=====================================
debian/lintian-overrides → debian/chip-seq.lintian-overrides
=====================================
=====================================
debian/chip-seq.manpages
=====================================
@@ -0,0 +1,2 @@
+*1.gz
+debian/mans/*.1
=====================================
debian/control
=====================================
@@ -12,7 +12,9 @@ Homepage: https://ccg.epfl.ch//chipseq
Package: chip-seq
Architecture: any
Depends: ${shlibs:Depends},
- ${misc:Depends}
+ ${misc:Depends},
+ chip-seq-data,
+ libmath-round-perl
Description: tools performing common ChIP-Seq data analysis tasks
The ChIP-Seq software provides a set of tools performing common genome-
wide ChIP- seq analysis tasks, including positional correlation
@@ -33,3 +35,29 @@ Description: tools performing common ChIP-Seq data analysis tasks
their own compact format for ChIP-seq data representation called SGA
(Simplified Genome Annotation). SGA is a line-oriented, tab-delimited
plain text format.
+
+Package: chip-seq-data
+Architecture: all
+Depends: ${misc:Depends}
+Description: tools performing common ChIP-Seq data analysis tasks (data)
+ The ChIP-Seq software provides a set of tools performing common genome-
+ wide ChIP- seq analysis tasks, including positional correlation
+ analysis, peak detection, and genome partitioning into signal-rich and
+ signal-poor regions. These tools exist as stand-alone C programs and
+ perform the following tasks:
+ .
+ 1. Positional correlation analysis and generation of an aggregation
+ plot (AP) (chipcor),
+ 2. Extraction of specific genome annotation features around reference
+ anchor points (chipextract),
+ 3. Read centering or shifting (chipcenter),
+ 4. Narrow peak caller using a fixed width peak size (chippeak),
+ 5. Broad peak caller used for large regions of enrichment (chippart),
+ 6. Feature selection tool based on a read count threshold (chipscore).
+ .
+ Because the ChIP-Seq tools are primarily optimized for speed, they use
+ their own compact format for ChIP-seq data representation called SGA
+ (Simplified Genome Annotation). SGA is a line-oriented, tab-delimited
+ plain text format.
+ .
+ This package contains the database files shipped with chip-seq.
=====================================
debian/createmanpages
=====================================
@@ -0,0 +1,109 @@
+#!/bin/sh
+MANDIR=debian/mans
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+NAME=`grep "^Description:" debian/control | sed 's/^Description: *//' | head -n1`
+PROGNAME=`grep "^Package:" debian/control | sed 's/^Package: *//' | head -n1`
+
+AUTHOR=".SH AUTHOR\n \
+This manpage was written by $DEBFULLNAME for the Debian distribution and\n \
+can be used for any other usage of the program.\
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=bed2bed_display
+help2man --no-info --no-discard-stderr --help-option=" -h" \
+ --name="Convert BED file to BED format suitable for displaying ChIP-seq peaks." \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=bed2sga
+help2man --no-info --no-discard-stderr --help-option=" -h" \
+ --name="Convert BED format into SGA format." \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+# Provided upstream:
+# chipcenter
+# chipcor
+# chipextract
+# chippart
+# chippeak
+# chipscore
+
+progname=compactsga
+help2man --no-info --no-discard-stderr --help-option=" -h" \
+ --name="reads a ChIP-seq data file and merges equal tag positions into a single line" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=countsga
+help2man --no-info --no-discard-stderr --help-option=" -h" \
+ --name="read a ChIP-seq data file and computes the total number of tag counts" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=featreplace
+help2man --no-info --no-discard-stderr --help-option=" -h" \
+ --name="read a ChIP-seq data file and changes the name of the feature field" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=filter_counts
+help2man --no-info --no-discard-stderr --help-option=" -h" \
+ --name="read a ChIP-seq data file and filters out all read counts" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=fps2sga.pl
+help2man --no-info --no-discard-stderr --help-option=" -h" \
+ --name="convert fps to sga" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=gff2sga.pl
+help2man --no-info --no-discard-stderr --help-option=" -h" \
+ --name="convert gff to sga" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=partit2bed.pl
+help2man --no-info --no-discard-stderr --help-option=" -h" \
+ --name="converts the output of the ChIP-Seq partitioning program to BED format" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=sga2bed
+help2man --no-info --no-discard-stderr --help-option=" -h" \
+ --name="Convert SGA format into BED format" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=sga2fps.pl
+help2man --no-info --no-discard-stderr --help-option=" -h" \
+ --name="Convert SGA format into FPS format" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=sga2gff.pl
+help2man --no-info --no-discard-stderr --help-option=" -h" \
+ --name="Convert SGA format into GFF format" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=sga2wig
+help2man --no-info --no-discard-stderr --help-option=" -h" \
+ --name="Convert SGA format into Wiggle Track format" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "*1.gz" > debian/${PROGNAME}.manpages
+echo "$MANDIR/*.1" >> debian/${PROGNAME}.manpages
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+ http://liw.fi/manpages/
+EOT
=====================================
debian/manpages deleted
=====================================
@@ -1 +0,0 @@
-*1.gz
=====================================
debian/mans/bed2bed_display.1
=====================================
@@ -0,0 +1,54 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.13.
+.TH BED2BED_DISPLAY "1" "March 2020" "bed2bed_display 1.5.5" "User Commands"
+.SH NAME
+bed2bed_display \- Convert BED file to BED format suitable for displaying ChIP-seq peaks.
+.SH SYNOPSIS
+.B bed2bed_display
+[\fI\,options\/\fR] [\fI\,-a <min BED score>\/\fR] [\fI\,-b <max BED score>\/\fR] [\fI\,<\/\fR] \fI\,<BED file|stdin>\/\fR
+.SH DESCRIPTION
+.IP
+\- version 1.5.5
+where options are:
+.TP
+\fB\-d\fR|\-\-debug
+Produce Debug information
+.TP
+\fB\-h\fR|\-\-help
+Show this Help text
+.TP
+\fB\-f\fR|\-\-feature <ft>
+Set Feature name <ft>
+.TP
+\fB\-o\fR|\-\-oformat <1|2>
+Set output Format (1:BED[Def] 2:BedGraph)
+.TP
+\fB\-\-name\fR <name>
+Set name for track name field [def. name=SGA\-feature]
+.TP
+\fB\-\-desc\fR <desc>
+Set track description field [def. desc="ChIP\-Seq Custom data"]
+.TP
+\fB\-\-color\fR <col>
+Define the track color in comma\-separated RGB values [def. 100,100,100]
+.TP
+\fB\-\-autoscale\fR
+<on|off> Data viewing paramenter: set auto\-scale to UCSC data view [def=OFF]
+.TP
+\fB\-\-always0\fR
+<on|off> Data viewing paramenter: always include zero [def=OFF]
+.TP
+\fB\-\-wfunction\fR
+<func> Data viewing paramenter: windowing function [def=mean+whiskers|maximum|mean|minimum]
+.TP
+\fB\-\-smoothing\fR
+<grade> Data viewing paramenter: smoothing window [def=OFF[0], <grade>=0,2..16]
+.TP
+\fB\-\-visibility\fR <mode>
+Display mode: [def=dense|full|hide] or [def=1|2|3]
+.IP
+Convert BED file to BED format suitable for displaying ChIP\-seq peaks.
+Two formats are supported: 1) BED Track with Score field; 2) BedGraph.
+For BED track format, only the graphical parameter 'visibility' can be set.
+.SH AUTHOR
+ This manpage was written by Andreas Tille for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/mans/bed2sga.1
=====================================
@@ -0,0 +1,57 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.13.
+.TH BED2SGA "1" "March 2020" "bed2sga 1.5.5" "User Commands"
+.SH NAME
+bed2sga \- Convert BED format into SGA format.
+.SH SYNOPSIS
+.B bed2sga
+[\fI\,options\/\fR] [\fI\,-s <s_assembly (e.g. hg19)>\/\fR] [\fI\,<\/\fR] \fI\,<BED file|stdin>\/\fR
+.SH DESCRIPTION
+.IP
+\- version 1.5.5
+where options are:
+.TP
+\fB\-d\fR|\-\-debug
+Produce Debug information
+.TP
+\fB\-h\fR|\-\-help
+Show this Help text
+.TP
+\fB\-i\fR|\-\-db <path>
+Use <path> to locate the assembly\-specific chr_NC_gi file
+[default is: $HOME/db/genome]
+.TP
+\fB\-f\fR|\-\-feature <ft>
+Set Feature name <ft>
+.TP
+\fB\-s\fR|\-\-species <spec>
+Assembly <spec> (i.e hg19)
+.TP
+\fB\-c\fR|\-\-center
+Generate a Centered SGA file
+.TP
+\fB\-u\fR|\-\-unoriented
+Generate an unoriented SGA file
+.TP
+\fB\-r\fR|\-\-regional
+Generate a 2\-line[+/\-] SGA file representing BED regions
+(e.g. RepeatMasker regions)
+.TP
+\fB\-e\fR|\-\-extend <f1,f2,...>
+Produce an extended SGA file with additional fields specified
+by a comma\-separated list of BED column numbers (from 1 to n)
+.TP
+\fB\-\-useScore\fR
+Use the BED 'score' field (#5) to set the SGA 'count' field
+.TP
+\fB\-\-useSigVal\fR
+Use the BED 'Signal Value' field (#7) to set the SGA 'count' field
+[This option is only valid for ENCODE narrowPeak]
+.TP
+\fB\-\-narrowPeak\fR
+Use this option for ENCODE narrowPeak format
+[Options \fB\-\-useScore\fR, \fB\-c\fR, and \fB\-u\fR are ignored]
+.IP
+Convert BED format into SGA format.
+.SH AUTHOR
+ This manpage was written by Andreas Tille for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/mans/compactsga.1
=====================================
@@ -0,0 +1,24 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.13.
+.TH COMPACTSGA "1" "March 2020" "compactsga 1.5.5" "User Commands"
+.SH NAME
+compactsga \- reads a ChIP-seq data file and merges equal tag positions into a single line
+.SH SYNOPSIS
+.B compactsga
+[\fI\,options\/\fR] \fI\,< <SGA File>\/\fR
+.SH DESCRIPTION
+.IP
+\- version 1.5.5
+where options are:
+.TP
+\fB\-h\fR
+Show this help text
+.TP
+\fB\-d\fR
+Print debug information
+.IP
+The program reads a ChIP\-seq data file in SGA format (<SGA File>),
+and merges equal tag positions into a single line adjusting the count
+field accordingly
+.SH AUTHOR
+ This manpage was written by Andreas Tille for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/mans/countsga.1
=====================================
@@ -0,0 +1,32 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.13.
+.TH COUNTSGA "1" "March 2020" "countsga 1.5.5" "User Commands"
+.SH NAME
+countsga \- read a ChIP-seq data file and computes the total number of tag counts
+.SH SYNOPSIS
+.B countsga
+[\fI\,options\/\fR] [\fI\,<\/\fR] \fI\,<SGA File>\/\fR
+.SH DESCRIPTION
+.IP
+\- version 1.5.5
+where options are:
+.TP
+\fB\-h\fR
+Show this help text
+.TP
+\fB\-d\fR
+Print debug information
+.TP
+\fB\-f\fR
+Feature specifications [name [+|\-]]
+.TP
+\fB\-c\fR
+Count Cut\-off (default is 1)
+.IP
+The program reads a ChIP\-seq data file (or from stdin [<]) in SGA format (<SGA File>),
+and computes the total number of tag counts as well as the total sequence length.
+The <Feature> parameter is a name that corresponds to the second field of the SGA file.
+It might optionally include the strand specification (+|\-).
+If no feature is given then all input tags are processed.
+.SH AUTHOR
+ This manpage was written by Andreas Tille for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/mans/featreplace.1
=====================================
@@ -0,0 +1,24 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.13.
+.TH FEATREPLACE "1" "March 2020" "featreplace 1.5.5" "User Commands"
+.SH NAME
+featreplace \- read a ChIP-seq data file and changes the name of the feature field
+.SH SYNOPSIS
+.B featreplace
+[\fI\,options\/\fR] \fI\,-f <feature name> \/\fR[\fI\,<\/\fR] \fI\,<SGA File>\/\fR
+.SH DESCRIPTION
+.IP
+\- version 1.5.5
+where options are:
+.TP
+\fB\-h\fR
+Show this help text
+.TP
+\fB\-d\fR
+Print debug information
+.IP
+The program reads a ChIP\-seq data file (or from stdin [<]) in SGA format (<SGA File>),
+and changes the name of the feature field according to the specified parameter <feature name>
+(by default <feature name>='FT').
+.SH AUTHOR
+ This manpage was written by Andreas Tille for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/mans/filter_counts.1
=====================================
@@ -0,0 +1,32 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.13.
+.TH FILTER_COUNTS "1" "March 2020" "filter_counts 1.5.5" "User Commands"
+.SH NAME
+filter_counts \- read a ChIP-seq data file and filters out all read counts
+.SH SYNOPSIS
+.B filter_counts
+[\fI\,options\/\fR] [\fI\,<\/\fR] \fI\,<SGA File>\/\fR
+.SH DESCRIPTION
+.IP
+\- version 1.5.5
+where options are:
+.TP
+\fB\-h\fR
+Show this help text
+.TP
+\fB\-d\fR
+Print debug information
+.TP
+\fB\-f\fR
+Feature defining the user\-defined regions of interest (default=RMSK)
+.TP
+\fB\-r\fR
+Retain Mode on
+.IP
+The program reads a ChIP\-seq data file (or from stdin [<]) in SGA format (<SGA File>)
+and filters out all read counts that occur within user\-defined regions of interest, such
+as Repeat Mask regions (feature=RMSK).
+If 'Retain Mode' is on, it only retains those lines that are within the user\-defined regions,
+in which case the annotation of the user\-defined regions is added to the output SGA file.
+.SH AUTHOR
+ This manpage was written by Andreas Tille for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/mans/fps2sga.pl.1
=====================================
@@ -0,0 +1,31 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.13.
+.TH FPS2SGA.PL "1" "March 2020" "fps2sga.pl 1.5.5" "User Commands"
+.SH NAME
+fps2sga.pl \- convert fps to sga
+.SH DESCRIPTION
+.IP
+fps2sga.pl [options] <FPS file>
+.IP
+where options are:
+.TP
+\fB\-h\fR|\-\-help
+Show this stuff
+.TP
+\fB\-f\fR|\-\-feature <feature>
+Set Feature name <feature>
+.TP
+\fB\-s\fR|\-\-species <species>
+Assembly <species> (i.e hg18)
+.TP
+\fB\-x\fR
+Generate an extended SGA file with the
+6th field equal to the FPS 'description' field
+.TP
+\fB\-\-ignore0flag\fR
+Ignore 0 flag at position 29 of the FP line,
+so keep orientation the same as original
+.PP
+
+.SH AUTHOR
+ This manpage was written by Andreas Tille for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/mans/gff2sga.pl.1
=====================================
@@ -0,0 +1,35 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.13.
+.TH GFF2SGA.PL "1" "March 2020" "gff2sga.pl 1.5.5" "User Commands"
+.SH NAME
+gff2sga.pl \- convert gff to sga
+.SH DESCRIPTION
+.IP
+gff2sga.pl [options] <GFF file>
+.IP
+where options are:
+.TP
+\fB\-h\fR|\-\-help
+Show this stuff
+.TP
+\fB\-\-db\fR <path>
+Use <path> to locate Chrom Id Storable File 'chro_idx.nstorage'
+.TP
+\fB\-f\fR|\-\-feature <feature>
+Set Feature name <feature>
+.TP
+\fB\-s\fR|\-\-species <species>
+Assembly <species> (i.e hg18)
+.TP
+\fB\-c\fR
+Generate a Centered SGA file
+.TP
+\fB\-u\fR
+Generate an Unoriented SGA file
+.TP
+\fB\-x\fR
+Generate an extended SGA file with the
+6th field equal to the GFF 'feature' field,
+and the feature field equal to the GFF 'source'
+.SH AUTHOR
+ This manpage was written by Andreas Tille for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/mans/partit2bed.pl.1
=====================================
@@ -0,0 +1,35 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.13.
+.TH PARTIT2BED.PL "1" "March 2020" "partit2bed.pl 1.5.5" "User Commands"
+.SH NAME
+partit2bed.pl \- converts the output of the ChIP-Seq partitioning program to BED format
+.SH DESCRIPTION
+.IP
+partit2bed.pl [options] <ChIP\-Part out file>
+.IP
+where options are:
+.TP
+\fB\-h\fR|\-\-help
+Show this stuff
+.TP
+\fB\-\-db\fR <path>
+Use <path> to locate Chrom Id Storable File 'chro_idx.nstorage'
+.TP
+\fB\-t\fR|\-\-track <track>
+BED track name [def: Test\-BED]
+.TP
+\fB\-d\fR|\-\-desc <desc>
+Description field of the BED header line [def: ChIP\-Seq]
+.TP
+\fB\-n\fR <int>
+Chromosome number (BED declaration lines) [def: 0 \- all chromosomes]
+.TP
+\fB\-b\fR <int>
+Chromosome start [def: \fB\-1\fR \- entire chrom region]
+.TP
+\fB\-e\fR <int>
+Chromosome end [def: \fB\-1\fR \- entire chrom region]
+.IP
+The program converts the output of the ChIP\-Seq partitioning program to BED format.
+.SH AUTHOR
+ This manpage was written by Andreas Tille for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/mans/sga2bed.1
=====================================
@@ -0,0 +1,59 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.13.
+.TH SGA2BED "1" "March 2020" "sga2bed 1.5.5" "User Commands"
+.SH NAME
+sga2bed \- Convert SGA format into BED format
+.SH SYNOPSIS
+.B sga2bed
+[\fI\,options\/\fR] [\fI\,<\/\fR] \fI\,<SGA file|stdin>\/\fR
+.SH DESCRIPTION
+.IP
+\- version 1.5.5
+where options are:
+.TP
+\fB\-d\fR|\-\-debug
+Produce Debug information
+.TP
+\fB\-h\fR|\-\-help
+Show this Help text
+.TP
+\fB\-i\fR|\-\-db <path>
+Use <path> to locate the chr_NC_gi file
+[default is: $HOME/db/genome]
+.TP
+\fB\-l\fR|\-\-readlen <len>
+Set Read length <len>
+Unoriented SGA files are extended by +/\-<len>/2
+.TP
+\fB\-c\fR|\-\-score <score>
+Normalisation factor for BED score field (5th) [score=1]
+.TP
+\fB\-n\fR|\-\-norm
+<normf> Normalisation factor for BED score field (7th) [normf=1]
+.TP
+\fB\-e\fR|\-\-extend f1:F1[,f2:F2] Set SGA optional field(s) f1(,f2,...) to BED field(s) F1,(F2,..)
+Fields are specified by column numbers
+Accepted BED field values are 4, 5, and 7
+Except BED field 5 (score field), BED fields 4 and 7
+can be used to set multiple extension values from SGA
+Fields 5 and 7 convert into numerical values whereas
+BED field 4 takes character strings as they are
+.TP
+\fB\-r\fR|\-\-nohdr
+BED format without annotation track header lines
+.TP
+\fB\-x\fR|\-\-expand
+Expand SGA lines into multiple BED lines
+.TP
+\fB\-\-name\fR <name>
+Set name for track name field [def. name=SGA\-feature]
+.TP
+\fB\-\-desc\fR <desc>
+Set track description field [def. desc="ChIP\-Seq Custom data"]
+.TP
+\fB\-\-color\fR <col>
+Define the track color in comma\-separated RGB values [def. 100,100,100]
+.IP
+Convert SGA format into BED format.
+.SH AUTHOR
+ This manpage was written by Andreas Tille for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/mans/sga2fps.pl.1
=====================================
@@ -0,0 +1,28 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.13.
+.TH SGA2FPS.PL "1" "March 2020" "sga2fps.pl 1.5.5" "User Commands"
+.SH NAME
+sga2fps.pl \- Convert SGA format into FPS format
+.SH DESCRIPTION
+.IP
+sga2fps.pl [options] <SGA file|stdin>
+.IP
+where options are:
+.TP
+\fB\-h\fR|\-\-help
+Show this stuff
+.TP
+\fB\-\-db\fR <path>
+Use <path> to locate Chrom Id Storable File 'chro_idx.nstorage'
+.TP
+\fB\-f\fR <feature>
+Set <feature> field
+.TP
+\fB\-s\fR|\-\-species <species>
+Assembly <species> (i.e hg18)
+.TP
+\fB\-\-set0flag\fR
+Set 0 flag at postion 29 of the FP line, forcing unoriented output
+(default : blank)
+.SH AUTHOR
+ This manpage was written by Andreas Tille for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/mans/sga2gff.pl.1
=====================================
@@ -0,0 +1,28 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.13.
+.TH SGA2GFF.PL "1" "March 2020" "sga2gff.pl 1.5.5" "User Commands"
+.SH NAME
+sga2gff.pl \- Convert SGA format into GFF format
+.SH DESCRIPTION
+.IP
+sga2gff.pl [options] <SGA file>
+.IP
+where options are:
+.TP
+\fB\-h\fR|\-\-help
+Show this stuff
+.TP
+\fB\-\-db\fR <path>
+Use <path> to locate Chrom Id Storable File 'chro_idx.nstorage'
+.TP
+\fB\-l\fR|\-\-taglen <taglen>
+Set Read length <taglen>
+.TP
+\fB\-x\fR
+Expand SGA lines into multiple GFF lines
+.TP
+\fB\-e\fR|\-\-ext <ext_flag>
+Use SGA 6th field to set GFF feature field
+and store SGA feature into GFF source field
+.SH AUTHOR
+ This manpage was written by Andreas Tille for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/mans/sga2wig.1
=====================================
@@ -0,0 +1,109 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.13.
+.TH SGA2WIG "1" "March 2020" "sga2wig 1.5.5" "User Commands"
+.SH NAME
+sga2wig \- Convert SGA format into Wiggle Track format
+.SH SYNOPSIS
+.B sga2wig
+[\fI\,options\/\fR] [\fI\,<\/\fR] \fI\,<SGA file|stdin>\/\fR
+.SH DESCRIPTION
+.IP
+\- version 1.5.5
+where options are:
+.TP
+\fB\-d\fR|\-\-debug
+Produce Debug information
+.TP
+\fB\-h\fR|\-\-help
+Show this Help text
+.TP
+\fB\-i\fR|\-\-db <path>
+Use <path> to locate the chr_NC_gi and chr_size files
+[default is: $HOME/db/genome]
+.TP
+\fB\-o\fR|\-\-format <0|1>
+Set Wiggle Track data format: variableStep[def=0]/fixedStep[1]
+.TP
+\fB\-n\fR|\-\-chrnb
+<int> Chromosome number [def: 0 (all chromosomes)]
+.TP
+\fB\-b\fR|\-\-start
+<int> Chromosome start [def: \fB\-1\fR (entire chromosome)]
+.TP
+\fB\-e\fR|\-\-end
+<int> Chromosome end [def: \fB\-1\fR (entire chromosome)]
+.TP
+\fB\-c\fR|\-\-coff
+<int> Count cut\-off for the SGA input file [def=99999]
+.TP
+\fB\-s\fR|\-\-span
+<int> Wiggle Track Span(\fI\,/stepInterval\/\fP) parameter [def=150]
+.IP
+For fixedStep data format, it defines the step parameter
+.TP
+\fB\-f\fR|\-\-norm
+<int> Normalization factor for total tag counts within step intervals [def=0]
+.IP
+This option is only valid for fixedStep data format
+.TP
+\fB\-\-peakf\fR
+Indicate that the The SGA input file represents a peak file
+[i.e. coordinates are peak centers]
+In such case, the span range begins upstream of [span=]150 bp
+chromosome position specified, and ends [span=]150 bp downstream
+.TP
+\fB\-\-name\fR <name>
+Set name for track name field [def. name=SGA\-feature]
+.TP
+\fB\-\-desc\fR <desc>
+Set track description field [def. desc="ChIP\-Seq Custom data"]
+.TP
+\fB\-\-color\fR <col>
+Define the track color in comma\-separated RGB values [def. 100,100,100]
+.TP
+\fB\-\-autoscale\fR
+<on|off> Data viewing paramenter: set auto\-scale to UCSC data view [def=OFF]
+.TP
+\fB\-\-always0\fR
+<on|off> Data viewing paramenter: always include zero [def=OFF]
+.TP
+\fB\-\-wfunction\fR
+<func> Data viewing paramenter: windowing function [def=mean+whiskers|maximum|mean|minimum]
+.TP
+\fB\-\-smoothing\fR
+<grade> Data viewing paramenter: smoothing window [def=OFF[0], <grade>=0,2..16]
+.TP
+\fB\-\-visibility\fR <mode>
+Display mode: [def=full|dense|hide]
+.IP
+Convert SGA format into Wiggle Track format (WIG).
+WIG format is line\-oriented, and is composed of declaration lines and data lines.
+.IP
+\- variableStep is for data with irregular intervals between new data points.
+.IP
+It begins with a declaration line and is followed by two columns containing chromosome positions and data values:
+.TP
+variableStep
+chrom=chrN [span=windowSize]
+.TP
+chromStartA
+dataValueA
+.TP
+chromStartB
+dataValueB
+.TP
+\&... etc ...
+\&... etc ...
+.IP
+\- fixedStep is for data with regular intervals between new data values.
+.IP
+It begins with a declaration line and is followed by a single column of data values:
+.TP
+fixedStep
+chrom=chrN start=position step=stepInterval [span=windowSize = stepInterval]
+.IP
+dataValue1
+dataValue2
+\&... etc ...
+.SH AUTHOR
+ This manpage was written by Andreas Tille for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/patches/data_location.patch
=====================================
@@ -0,0 +1,103 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Mon, 23 Mar 2020 20:55:38 +0100
+Description: Adapt database installation PATH to Debian location
+
+--- a/tools/chr_replace_sga.pl
++++ b/tools/chr_replace_sga.pl
+@@ -9,7 +9,7 @@ use Storable qw (retrieve nstore);
+
+ my %opts;
+ getopt('sf:', \%opts); # -s, & -f take arg. Values in %opts, Hash keys will be the switch names
+-my $DB = "/db/genome/";
++my $DB = "/usr/share/chip-seq/";
+ #my $DB = "/home/local/db/genome/";
+ my $chr2SV = retrieve($DB."chro_idx.nstorage");
+
+--- a/tools/sga2fps.pl
++++ b/tools/sga2fps.pl
+@@ -19,7 +19,7 @@ my $feature = "";
+ my $ft_flag = 0;
+ my $set0flag = 0;
+ #my $DB = "/home/local/db/genome/";
+-my $DB = "/db/genome/";
++my $DB = "/usr/share/chip-seq/";
+
+ if( ! GetOptions( \%opt, @options ) ) { &Usage(); }
+
+--- a/tools/sga2gff.pl
++++ b/tools/sga2gff.pl
+@@ -17,7 +17,7 @@ my $taglen = 0;
+ my $expand = 0;
+ my $ext_flag = 0;
+ #my $DB = "/home/local/db/genome/";
+-my $DB = "/db/genome/";
++my $DB = "/usr/share/chip-seq/";
+
+
+ if( ! GetOptions( \%opt, @options ) ) { &Usage(); }
+--- a/tools/check_bed.pl
++++ b/tools/check_bed.pl
+@@ -9,7 +9,7 @@ use Storable qw (retrieve nstore);
+
+ my %opts;
+ getopt('sf:', \%opts); # -s, & -f take arg. Values in %opts, Hash keys will be the switch names
+-my $DB = "/db/genome/";
++my $DB = "/usr/share/chip-seq/";
+ #my $DB = "/home/local/db/genome/";
+ my $chr2SV = retrieve($DB."chro_idx.nstorage");
+
+--- a/tools/eland2sga.pl
++++ b/tools/eland2sga.pl
+@@ -13,7 +13,7 @@ getopt('asf:', \%opts); # -a, -s, & -f
+ die("\nusage: eland2sga.pl -a feature -s species -f eland_file\n\n") unless (($opts{'f'})&&($opts{'a'})&&($opts{'s'}));
+
+ # hash defining chromosome from SV of chromosomes in current genome assemblies
+-my $DB = "/db/genome/";
++my $DB = "/usr/share/chip-seq/";
+ #my $DB = "/home/local/db/genome/";
+ my $chr2AC = retrieve($DB."chro_idx.nstorage");
+ # eventually add older assemblies?
+--- a/tools/gff2sga.pl
++++ b/tools/gff2sga.pl
+@@ -25,7 +25,7 @@ my $ext_sc = 0;
+ my $score = 0;
+
+ #my $DB = "/home/local/db/genome/";
+-my $DB = "/db/genome/";
++my $DB = "/usr/share/chip-seq/";
+
+ if( ! GetOptions( \%opt, @options ) ) { &Usage(); }
+
+--- a/tools/partit2bed.pl
++++ b/tools/partit2bed.pl
+@@ -17,7 +17,7 @@ my $chr_nb = "chr0";
+ my $chr_start = -1;
+ my $chr_end = -1;
+ #my $DB = "/home/local/db/genome/";
+-my $DB = "/db/genome/";
++my $DB = "/usr/share/chip-seq/";
+
+ if( ! GetOptions( \%opt, @options ) ) { &Usage(); }
+ &Usage() if defined($opt{'help'}) || defined($opt{'h'});
+--- a/tools/partit2gff.pl
++++ b/tools/partit2gff.pl
+@@ -10,7 +10,7 @@ use strict;
+ use Storable qw (retrieve nstore); # package to store persistently variables in files [http://search.cpan.org/author/AMS/Storable-2.07/Storable.pm]
+
+ # hash defining chromosome from SV of chromosomes in current genome assemblies
+-my $chr2SV = retrieve("/db/genome/chro_idx.nstorage");
++my $chr2SV = retrieve("/usr/share/chip-seq/chro_idx.nstorage");
+
+ my @pos = ();
+ my $count = 0;
+--- a/tools/partit2sga.pl
++++ b/tools/partit2sga.pl
+@@ -10,7 +10,7 @@ use Storable qw (retrieve nstore);
+ my %opt;
+ my @options = ("help", "h", "db=s");
+
+-my $DB = "/home/local/db/genome/";
++my $DB = "/usr/share/chip-seq/";
+ #my $DB = "/db/genome/";
+
+ if( ! GetOptions( \%opt, @options ) ) { &Usage(); }
=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
fix_makefile.patch
# fix_install.patch
+data_location.patch
=====================================
debian/rules
=====================================
@@ -2,6 +2,8 @@
# DH_VERBOSE := 1
+include /usr/share/dpkg/default.mk
+
%:
dh $@
@@ -10,3 +12,10 @@ override_dh_install:
for perlscript in `grep -lR '#!/usr/local/bin/perl' debian/*/usr` ; do \
sed -i '1s+#!/usr/local/bin/perl+#!/usr/bin/perl+' $${perlscript} ; \
done
+
+override_dh_installman:
+ dh_installman --language=C
+
+override_dh_fixperms:
+ dh_fixperms
+ find debian/$(DEB_SOURCE)-data/usr/share/$(DEB_SOURCE)/ -type f -exec chmod -x \{\} \;
View it on GitLab: https://salsa.debian.org/med-team/chip-seq/-/compare/340f7777e3fe3f28dc5c46e996d0b6d63ccb2411...5c1c219674ea08aaf558f4c88a3a52e40719e5ce
--
View it on GitLab: https://salsa.debian.org/med-team/chip-seq/-/compare/340f7777e3fe3f28dc5c46e996d0b6d63ccb2411...5c1c219674ea08aaf558f4c88a3a52e40719e5ce
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20200326/46f505ea/attachment-0001.html>
More information about the debian-med-commit
mailing list