[med-svn] r17389 - in trunk/packages/velvet/trunk/debian: . manpages
Andreas Tille
tille at moszumanska.debian.org
Tue Jul 1 14:38:05 UTC 2014
Author: tille
Date: 2014-07-01 14:38:05 +0000 (Tue, 01 Jul 2014)
New Revision: 17389
Added:
trunk/packages/velvet/trunk/debian/createmanpages
trunk/packages/velvet/trunk/debian/manpages/
trunk/packages/velvet/trunk/debian/manpages/velvetg.1
trunk/packages/velvet/trunk/debian/manpages/velvetg_63.1
trunk/packages/velvet/trunk/debian/manpages/velvetg_63_long.1
trunk/packages/velvet/trunk/debian/manpages/velvetg_de.1
trunk/packages/velvet/trunk/debian/manpages/velvetg_long.1
trunk/packages/velvet/trunk/debian/manpages/velveth.1
trunk/packages/velvet/trunk/debian/manpages/velveth_63.1
trunk/packages/velvet/trunk/debian/manpages/velveth_63_long.1
trunk/packages/velvet/trunk/debian/manpages/velveth_de.1
trunk/packages/velvet/trunk/debian/manpages/velveth_long.1
trunk/packages/velvet/trunk/debian/velvet-long.manpages
trunk/packages/velvet/trunk/debian/velvet.manpages
Modified:
trunk/packages/velvet/trunk/debian/changelog
trunk/packages/velvet/trunk/debian/control
trunk/packages/velvet/trunk/debian/rules
Log:
After realising that the manpages created at package build time have duplicated content I switched the manpage generation to a script which should be run before the final install. Manpages are created that way for all binaries.
Modified: trunk/packages/velvet/trunk/debian/changelog
===================================================================
--- trunk/packages/velvet/trunk/debian/changelog 2014-07-01 13:31:54 UTC (rev 17388)
+++ trunk/packages/velvet/trunk/debian/changelog 2014-07-01 14:38:05 UTC (rev 17389)
@@ -1,9 +1,11 @@
-velvet (1.2.10+dfsg1-1) UNRELEASED; urgency=medium
+velvet (1.2.10+dfsg1-1) unstable; urgency=medium
* Drop more stuff from upstream source via Files-Excluded
* cme fix dpkg-control
* Do not pack example data into another archive
* add autopkgtest (using new binary package velvet-tests)
+ * do not create manpages at package build time (which is error prone anyway
+ but rather prepare them before using debian/createmanpages script
-- Andreas Tille <tille at debian.org> Mon, 30 Jun 2014 13:56:46 +0200
Modified: trunk/packages/velvet/trunk/debian/control
===================================================================
--- trunk/packages/velvet/trunk/debian/control 2014-07-01 13:31:54 UTC (rev 17388)
+++ trunk/packages/velvet/trunk/debian/control 2014-07-01 14:38:05 UTC (rev 17389)
@@ -7,7 +7,6 @@
Testsuite: autopkgtest
Build-Depends: debhelper (>= 9),
zlib1g-dev,
- help2man,
texlive-latex-base,
texlive-latex-recommended
Standards-Version: 3.9.5
Added: trunk/packages/velvet/trunk/debian/createmanpages
===================================================================
--- trunk/packages/velvet/trunk/debian/createmanpages (rev 0)
+++ trunk/packages/velvet/trunk/debian/createmanpages 2014-07-01 14:38:05 UTC (rev 17389)
@@ -0,0 +1,35 @@
+#!/bin/sh
+MANDIR=debian/manpages
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+
+help2man --no-info --version-string="$VERSION" \
+ --name="simple hashing program" velveth > ${MANDIR}/velveth.1
+help2man --no-info --version-string="$VERSION" \
+ --name="simple hashing program (colorspace version)" velveth_de > ${MANDIR}/velveth_de.1
+help2man --no-info --version-option=" " --version-string="$VERSION" \
+ --name="de Bruijn graph construction, error removal and repeat resolution" velvetg > ${MANDIR}/velvetg.1
+help2man --no-info --version-option=" " --version-string="$VERSION" \
+ --name="de Bruijn graph construction, error removal and repeat resolution (colorspace version)" velvetg_de > ${MANDIR}/velvetg_de.1
+
+# for velvet-long
+help2man --no-info --version-option=" " --version-string="$VERSION" \
+ --name="de Bruijn graph construction, error removal and repeat resolution (MAXKMERLENGTH = 63)" velvetg_63 > ${MANDIR}/velvetg_63.1
+help2man --no-info --version-option=" " --version-string="$VERSION" \
+ --name="de Bruijn graph construction, error removal and repeat resolution (MAXKMERLENGTH = 63, LONGSEQUENCES)" velvetg_63_long > ${MANDIR}/velvetg_63_long.1
+help2man --no-info --version-option=" " --version-string="$VERSION" \
+ --name="de Bruijn graph construction, error removal and repeat resolution (LONGSEQUENCES)" velvetg_long > ${MANDIR}/velvetg_long.1
+help2man --no-info --version-string="$VERSION" \
+ --name="simple hashing program (MAXKMERLENGTH = 63)" velveth_63 > ${MANDIR}/velveth_63.1
+help2man --no-info --version-string="$VERSION" \
+ --name="simple hashing program (MAXKMERLENGTH = 63, LONGSEQUENCES)" velveth_63_long > ${MANDIR}/velveth_63_long.1
+help2man --no-info --version-string="$VERSION" \
+ --name="simple hashing program (LONGSEQUENCES)" velveth_long > ${MANDIR}/velveth_long.1
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+ http://liw.fi/manpages/
+EOT
+
Property changes on: trunk/packages/velvet/trunk/debian/createmanpages
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/velvet/trunk/debian/manpages/velvetg.1
===================================================================
--- trunk/packages/velvet/trunk/debian/manpages/velvetg.1 (rev 0)
+++ trunk/packages/velvet/trunk/debian/manpages/velvetg.1 2014-07-01 14:38:05 UTC (rev 17389)
@@ -0,0 +1,109 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.45.1.
+.TH VELVETG "1" "July 2014" "velvetg 1.2.10+dfsg1" "User Commands"
+.SH NAME
+velvetg \- de Bruijn graph construction, error removal and repeat resolution
+.SH DESCRIPTION
+Usage:
+\&./velvetg directory [options]
+.TP
+directory
+: working directory name
+.SS "Standard options:"
+.TP
+\fB\-cov_cutoff\fR <floating\-point|auto>
+: removal of low coverage nodes AFTER tour bus or allow the system to infer it
+.IP
+(default: no removal)
+.TP
+\fB\-ins_length\fR <integer>
+: expected distance between two paired end reads (default: no read pairing)
+.TP
+\fB\-read_trkg\fR <yes|no>
+: tracking of short read positions in assembly (default: no tracking)
+.TP
+\fB\-min_contig_lgth\fR <integer>
+: minimum contig length exported to contigs.fa file (default: hash length * 2)
+.TP
+\fB\-amos_file\fR <yes|no>
+: export assembly to AMOS file (default: no export)
+.TP
+\fB\-exp_cov\fR <floating point|auto>
+: expected coverage of unique regions or allow the system to infer it
+.IP
+(default: no long or paired\-end read resolution)
+.HP
+\fB\-long_cov_cutoff\fR <floating\-point>: removal of nodes with low long\-read coverage AFTER tour bus
+.IP
+(default: no removal)
+.SS "Advanced options:"
+.TP
+\fB\-ins_length\fR* <integer>
+: expected distance between two paired\-end reads in the respective short\-read dataset (default: no read pairing)
+.TP
+\fB\-ins_length_long\fR <integer>
+: expected distance between two long paired\-end reads (default: no read pairing)
+.TP
+\fB\-ins_length\fR*_sd <integer>
+: est. standard deviation of respective dataset (default: 10% of corresponding length)
+.IP
+[replace '*' by nothing, '2' or '_long' as necessary]
+.TP
+\fB\-scaffolding\fR <yes|no>
+: scaffolding of contigs used paired end information (default: on)
+.TP
+\fB\-max_branch_length\fR <integer>
+: maximum length in base pair of bubble (default: 100)
+.HP
+\fB\-max_divergence\fR <floating\-point>: maximum divergence rate between two branches in a bubble (default: 0.2)
+.TP
+\fB\-max_gap_count\fR <integer>
+: maximum number of gaps allowed in the alignment of the two branches of a bubble (default: 3)
+.TP
+\fB\-min_pair_count\fR <integer>
+: minimum number of paired end connections to justify the scaffolding of two long contigs (default: 5)
+.TP
+\fB\-max_coverage\fR <floating point>
+: removal of high coverage nodes AFTER tour bus (default: no removal)
+.TP
+\fB\-coverage_mask\fR <int>
+: minimum coverage required for confident regions of contigs (default: 1)
+.TP
+\fB\-long_mult_cutoff\fR <int>
+: minimum number of long reads required to merge contigs (default: 2)
+.TP
+\fB\-unused_reads\fR <yes|no>
+: export unused reads in UnusedReads.fa file (default: no)
+.TP
+\fB\-alignments\fR <yes|no>
+: export a summary of contig alignment to the reference sequences (default: no)
+.TP
+\fB\-exportFiltered\fR <yes|no>
+: export the long nodes which were eliminated by the coverage filters (default: no)
+.TP
+\fB\-clean\fR <yes|no>
+: remove all the intermediary files which are useless for recalculation (default : no)
+.TP
+\fB\-very_clean\fR <yes|no>
+: remove all the intermediary files (no recalculation possible) (default: no)
+.TP
+\fB\-paired_exp_fraction\fR <double>
+: remove all the paired end connections which less than the specified fraction of the expected count (default: 0.1)
+.TP
+\fB\-shortMatePaired\fR* <yes|no>
+: for mate\-pair libraries, indicate that the library might be contaminated with paired\-end reads (default no)
+.TP
+\fB\-conserveLong\fR <yes|no>
+: preserve sequences with long reads in them (default no)
+.SS "Output:"
+.TP
+directory/contigs.fa
+: fasta file of contigs longer than twice hash length
+.TP
+directory/stats.txt
+: stats file (tab\-spaced) useful for determining appropriate coverage cutoff
+.TP
+directory/LastGraph
+: special formatted file with all the information on the final graph
+.TP
+directory/velvet_asm.afg
+: (if requested) AMOS compatible assembly file
Added: trunk/packages/velvet/trunk/debian/manpages/velvetg_63.1
===================================================================
--- trunk/packages/velvet/trunk/debian/manpages/velvetg_63.1 (rev 0)
+++ trunk/packages/velvet/trunk/debian/manpages/velvetg_63.1 2014-07-01 14:38:05 UTC (rev 17389)
@@ -0,0 +1,109 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.45.1.
+.TH VELVETG_63 "1" "July 2014" "velvetg_63 1.2.10+dfsg1" "User Commands"
+.SH NAME
+velvetg_63 \- de Bruijn graph construction, error removal and repeat resolution (MAXKMERLENGTH = 63)
+.SH DESCRIPTION
+Usage:
+\&./velvetg directory [options]
+.TP
+directory
+: working directory name
+.SS "Standard options:"
+.TP
+\fB\-cov_cutoff\fR <floating\-point|auto>
+: removal of low coverage nodes AFTER tour bus or allow the system to infer it
+.IP
+(default: no removal)
+.TP
+\fB\-ins_length\fR <integer>
+: expected distance between two paired end reads (default: no read pairing)
+.TP
+\fB\-read_trkg\fR <yes|no>
+: tracking of short read positions in assembly (default: no tracking)
+.TP
+\fB\-min_contig_lgth\fR <integer>
+: minimum contig length exported to contigs.fa file (default: hash length * 2)
+.TP
+\fB\-amos_file\fR <yes|no>
+: export assembly to AMOS file (default: no export)
+.TP
+\fB\-exp_cov\fR <floating point|auto>
+: expected coverage of unique regions or allow the system to infer it
+.IP
+(default: no long or paired\-end read resolution)
+.HP
+\fB\-long_cov_cutoff\fR <floating\-point>: removal of nodes with low long\-read coverage AFTER tour bus
+.IP
+(default: no removal)
+.SS "Advanced options:"
+.TP
+\fB\-ins_length\fR* <integer>
+: expected distance between two paired\-end reads in the respective short\-read dataset (default: no read pairing)
+.TP
+\fB\-ins_length_long\fR <integer>
+: expected distance between two long paired\-end reads (default: no read pairing)
+.TP
+\fB\-ins_length\fR*_sd <integer>
+: est. standard deviation of respective dataset (default: 10% of corresponding length)
+.IP
+[replace '*' by nothing, '2' or '_long' as necessary]
+.TP
+\fB\-scaffolding\fR <yes|no>
+: scaffolding of contigs used paired end information (default: on)
+.TP
+\fB\-max_branch_length\fR <integer>
+: maximum length in base pair of bubble (default: 100)
+.HP
+\fB\-max_divergence\fR <floating\-point>: maximum divergence rate between two branches in a bubble (default: 0.2)
+.TP
+\fB\-max_gap_count\fR <integer>
+: maximum number of gaps allowed in the alignment of the two branches of a bubble (default: 3)
+.TP
+\fB\-min_pair_count\fR <integer>
+: minimum number of paired end connections to justify the scaffolding of two long contigs (default: 5)
+.TP
+\fB\-max_coverage\fR <floating point>
+: removal of high coverage nodes AFTER tour bus (default: no removal)
+.TP
+\fB\-coverage_mask\fR <int>
+: minimum coverage required for confident regions of contigs (default: 1)
+.TP
+\fB\-long_mult_cutoff\fR <int>
+: minimum number of long reads required to merge contigs (default: 2)
+.TP
+\fB\-unused_reads\fR <yes|no>
+: export unused reads in UnusedReads.fa file (default: no)
+.TP
+\fB\-alignments\fR <yes|no>
+: export a summary of contig alignment to the reference sequences (default: no)
+.TP
+\fB\-exportFiltered\fR <yes|no>
+: export the long nodes which were eliminated by the coverage filters (default: no)
+.TP
+\fB\-clean\fR <yes|no>
+: remove all the intermediary files which are useless for recalculation (default : no)
+.TP
+\fB\-very_clean\fR <yes|no>
+: remove all the intermediary files (no recalculation possible) (default: no)
+.TP
+\fB\-paired_exp_fraction\fR <double>
+: remove all the paired end connections which less than the specified fraction of the expected count (default: 0.1)
+.TP
+\fB\-shortMatePaired\fR* <yes|no>
+: for mate\-pair libraries, indicate that the library might be contaminated with paired\-end reads (default no)
+.TP
+\fB\-conserveLong\fR <yes|no>
+: preserve sequences with long reads in them (default no)
+.SS "Output:"
+.TP
+directory/contigs.fa
+: fasta file of contigs longer than twice hash length
+.TP
+directory/stats.txt
+: stats file (tab\-spaced) useful for determining appropriate coverage cutoff
+.TP
+directory/LastGraph
+: special formatted file with all the information on the final graph
+.TP
+directory/velvet_asm.afg
+: (if requested) AMOS compatible assembly file
Added: trunk/packages/velvet/trunk/debian/manpages/velvetg_63_long.1
===================================================================
--- trunk/packages/velvet/trunk/debian/manpages/velvetg_63_long.1 (rev 0)
+++ trunk/packages/velvet/trunk/debian/manpages/velvetg_63_long.1 2014-07-01 14:38:05 UTC (rev 17389)
@@ -0,0 +1,109 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.45.1.
+.TH VELVETG_63_LONG "1" "July 2014" "velvetg_63_long 1.2.10+dfsg1" "User Commands"
+.SH NAME
+velvetg_63_long \- de Bruijn graph construction, error removal and repeat resolution (MAXKMERLENGTH = 63, LONGSEQUENCES)
+.SH DESCRIPTION
+Usage:
+\&./velvetg directory [options]
+.TP
+directory
+: working directory name
+.SS "Standard options:"
+.TP
+\fB\-cov_cutoff\fR <floating\-point|auto>
+: removal of low coverage nodes AFTER tour bus or allow the system to infer it
+.IP
+(default: no removal)
+.TP
+\fB\-ins_length\fR <integer>
+: expected distance between two paired end reads (default: no read pairing)
+.TP
+\fB\-read_trkg\fR <yes|no>
+: tracking of short read positions in assembly (default: no tracking)
+.TP
+\fB\-min_contig_lgth\fR <integer>
+: minimum contig length exported to contigs.fa file (default: hash length * 2)
+.TP
+\fB\-amos_file\fR <yes|no>
+: export assembly to AMOS file (default: no export)
+.TP
+\fB\-exp_cov\fR <floating point|auto>
+: expected coverage of unique regions or allow the system to infer it
+.IP
+(default: no long or paired\-end read resolution)
+.HP
+\fB\-long_cov_cutoff\fR <floating\-point>: removal of nodes with low long\-read coverage AFTER tour bus
+.IP
+(default: no removal)
+.SS "Advanced options:"
+.TP
+\fB\-ins_length\fR* <integer>
+: expected distance between two paired\-end reads in the respective short\-read dataset (default: no read pairing)
+.TP
+\fB\-ins_length_long\fR <integer>
+: expected distance between two long paired\-end reads (default: no read pairing)
+.TP
+\fB\-ins_length\fR*_sd <integer>
+: est. standard deviation of respective dataset (default: 10% of corresponding length)
+.IP
+[replace '*' by nothing, '2' or '_long' as necessary]
+.TP
+\fB\-scaffolding\fR <yes|no>
+: scaffolding of contigs used paired end information (default: on)
+.TP
+\fB\-max_branch_length\fR <integer>
+: maximum length in base pair of bubble (default: 100)
+.HP
+\fB\-max_divergence\fR <floating\-point>: maximum divergence rate between two branches in a bubble (default: 0.2)
+.TP
+\fB\-max_gap_count\fR <integer>
+: maximum number of gaps allowed in the alignment of the two branches of a bubble (default: 3)
+.TP
+\fB\-min_pair_count\fR <integer>
+: minimum number of paired end connections to justify the scaffolding of two long contigs (default: 5)
+.TP
+\fB\-max_coverage\fR <floating point>
+: removal of high coverage nodes AFTER tour bus (default: no removal)
+.TP
+\fB\-coverage_mask\fR <int>
+: minimum coverage required for confident regions of contigs (default: 1)
+.TP
+\fB\-long_mult_cutoff\fR <int>
+: minimum number of long reads required to merge contigs (default: 2)
+.TP
+\fB\-unused_reads\fR <yes|no>
+: export unused reads in UnusedReads.fa file (default: no)
+.TP
+\fB\-alignments\fR <yes|no>
+: export a summary of contig alignment to the reference sequences (default: no)
+.TP
+\fB\-exportFiltered\fR <yes|no>
+: export the long nodes which were eliminated by the coverage filters (default: no)
+.TP
+\fB\-clean\fR <yes|no>
+: remove all the intermediary files which are useless for recalculation (default : no)
+.TP
+\fB\-very_clean\fR <yes|no>
+: remove all the intermediary files (no recalculation possible) (default: no)
+.TP
+\fB\-paired_exp_fraction\fR <double>
+: remove all the paired end connections which less than the specified fraction of the expected count (default: 0.1)
+.TP
+\fB\-shortMatePaired\fR* <yes|no>
+: for mate\-pair libraries, indicate that the library might be contaminated with paired\-end reads (default no)
+.TP
+\fB\-conserveLong\fR <yes|no>
+: preserve sequences with long reads in them (default no)
+.SS "Output:"
+.TP
+directory/contigs.fa
+: fasta file of contigs longer than twice hash length
+.TP
+directory/stats.txt
+: stats file (tab\-spaced) useful for determining appropriate coverage cutoff
+.TP
+directory/LastGraph
+: special formatted file with all the information on the final graph
+.TP
+directory/velvet_asm.afg
+: (if requested) AMOS compatible assembly file
Added: trunk/packages/velvet/trunk/debian/manpages/velvetg_de.1
===================================================================
--- trunk/packages/velvet/trunk/debian/manpages/velvetg_de.1 (rev 0)
+++ trunk/packages/velvet/trunk/debian/manpages/velvetg_de.1 2014-07-01 14:38:05 UTC (rev 17389)
@@ -0,0 +1,109 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.45.1.
+.TH VELVETG_DE "1" "July 2014" "velvetg_de 1.2.10+dfsg1" "User Commands"
+.SH NAME
+velvetg_de \- de Bruijn graph construction, error removal and repeat resolution (colorspace version)
+.SH DESCRIPTION
+Usage:
+\&./velvetg directory [options]
+.TP
+directory
+: working directory name
+.SS "Standard options:"
+.TP
+\fB\-cov_cutoff\fR <floating\-point|auto>
+: removal of low coverage nodes AFTER tour bus or allow the system to infer it
+.IP
+(default: no removal)
+.TP
+\fB\-ins_length\fR <integer>
+: expected distance between two paired end reads (default: no read pairing)
+.TP
+\fB\-read_trkg\fR <yes|no>
+: tracking of short read positions in assembly (default: no tracking)
+.TP
+\fB\-min_contig_lgth\fR <integer>
+: minimum contig length exported to contigs.fa file (default: hash length * 2)
+.TP
+\fB\-amos_file\fR <yes|no>
+: export assembly to AMOS file (default: no export)
+.TP
+\fB\-exp_cov\fR <floating point|auto>
+: expected coverage of unique regions or allow the system to infer it
+.IP
+(default: no long or paired\-end read resolution)
+.HP
+\fB\-long_cov_cutoff\fR <floating\-point>: removal of nodes with low long\-read coverage AFTER tour bus
+.IP
+(default: no removal)
+.SS "Advanced options:"
+.TP
+\fB\-ins_length\fR* <integer>
+: expected distance between two paired\-end reads in the respective short\-read dataset (default: no read pairing)
+.TP
+\fB\-ins_length_long\fR <integer>
+: expected distance between two long paired\-end reads (default: no read pairing)
+.TP
+\fB\-ins_length\fR*_sd <integer>
+: est. standard deviation of respective dataset (default: 10% of corresponding length)
+.IP
+[replace '*' by nothing, '2' or '_long' as necessary]
+.TP
+\fB\-scaffolding\fR <yes|no>
+: scaffolding of contigs used paired end information (default: on)
+.TP
+\fB\-max_branch_length\fR <integer>
+: maximum length in base pair of bubble (default: 100)
+.HP
+\fB\-max_divergence\fR <floating\-point>: maximum divergence rate between two branches in a bubble (default: 0.2)
+.TP
+\fB\-max_gap_count\fR <integer>
+: maximum number of gaps allowed in the alignment of the two branches of a bubble (default: 3)
+.TP
+\fB\-min_pair_count\fR <integer>
+: minimum number of paired end connections to justify the scaffolding of two long contigs (default: 5)
+.TP
+\fB\-max_coverage\fR <floating point>
+: removal of high coverage nodes AFTER tour bus (default: no removal)
+.TP
+\fB\-coverage_mask\fR <int>
+: minimum coverage required for confident regions of contigs (default: 1)
+.TP
+\fB\-long_mult_cutoff\fR <int>
+: minimum number of long reads required to merge contigs (default: 2)
+.TP
+\fB\-unused_reads\fR <yes|no>
+: export unused reads in UnusedReads.fa file (default: no)
+.TP
+\fB\-alignments\fR <yes|no>
+: export a summary of contig alignment to the reference sequences (default: no)
+.TP
+\fB\-exportFiltered\fR <yes|no>
+: export the long nodes which were eliminated by the coverage filters (default: no)
+.TP
+\fB\-clean\fR <yes|no>
+: remove all the intermediary files which are useless for recalculation (default : no)
+.TP
+\fB\-very_clean\fR <yes|no>
+: remove all the intermediary files (no recalculation possible) (default: no)
+.TP
+\fB\-paired_exp_fraction\fR <double>
+: remove all the paired end connections which less than the specified fraction of the expected count (default: 0.1)
+.TP
+\fB\-shortMatePaired\fR* <yes|no>
+: for mate\-pair libraries, indicate that the library might be contaminated with paired\-end reads (default no)
+.TP
+\fB\-conserveLong\fR <yes|no>
+: preserve sequences with long reads in them (default no)
+.SS "Output:"
+.TP
+directory/contigs.fa
+: fasta file of contigs longer than twice hash length
+.TP
+directory/stats.txt
+: stats file (tab\-spaced) useful for determining appropriate coverage cutoff
+.TP
+directory/LastGraph
+: special formatted file with all the information on the final graph
+.TP
+directory/velvet_asm.afg
+: (if requested) AMOS compatible assembly file
Added: trunk/packages/velvet/trunk/debian/manpages/velvetg_long.1
===================================================================
--- trunk/packages/velvet/trunk/debian/manpages/velvetg_long.1 (rev 0)
+++ trunk/packages/velvet/trunk/debian/manpages/velvetg_long.1 2014-07-01 14:38:05 UTC (rev 17389)
@@ -0,0 +1,109 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.45.1.
+.TH VELVETG_LONG "1" "July 2014" "velvetg_long 1.2.10+dfsg1" "User Commands"
+.SH NAME
+velvetg_long \- de Bruijn graph construction, error removal and repeat resolution (LONGSEQUENCES)
+.SH DESCRIPTION
+Usage:
+\&./velvetg directory [options]
+.TP
+directory
+: working directory name
+.SS "Standard options:"
+.TP
+\fB\-cov_cutoff\fR <floating\-point|auto>
+: removal of low coverage nodes AFTER tour bus or allow the system to infer it
+.IP
+(default: no removal)
+.TP
+\fB\-ins_length\fR <integer>
+: expected distance between two paired end reads (default: no read pairing)
+.TP
+\fB\-read_trkg\fR <yes|no>
+: tracking of short read positions in assembly (default: no tracking)
+.TP
+\fB\-min_contig_lgth\fR <integer>
+: minimum contig length exported to contigs.fa file (default: hash length * 2)
+.TP
+\fB\-amos_file\fR <yes|no>
+: export assembly to AMOS file (default: no export)
+.TP
+\fB\-exp_cov\fR <floating point|auto>
+: expected coverage of unique regions or allow the system to infer it
+.IP
+(default: no long or paired\-end read resolution)
+.HP
+\fB\-long_cov_cutoff\fR <floating\-point>: removal of nodes with low long\-read coverage AFTER tour bus
+.IP
+(default: no removal)
+.SS "Advanced options:"
+.TP
+\fB\-ins_length\fR* <integer>
+: expected distance between two paired\-end reads in the respective short\-read dataset (default: no read pairing)
+.TP
+\fB\-ins_length_long\fR <integer>
+: expected distance between two long paired\-end reads (default: no read pairing)
+.TP
+\fB\-ins_length\fR*_sd <integer>
+: est. standard deviation of respective dataset (default: 10% of corresponding length)
+.IP
+[replace '*' by nothing, '2' or '_long' as necessary]
+.TP
+\fB\-scaffolding\fR <yes|no>
+: scaffolding of contigs used paired end information (default: on)
+.TP
+\fB\-max_branch_length\fR <integer>
+: maximum length in base pair of bubble (default: 100)
+.HP
+\fB\-max_divergence\fR <floating\-point>: maximum divergence rate between two branches in a bubble (default: 0.2)
+.TP
+\fB\-max_gap_count\fR <integer>
+: maximum number of gaps allowed in the alignment of the two branches of a bubble (default: 3)
+.TP
+\fB\-min_pair_count\fR <integer>
+: minimum number of paired end connections to justify the scaffolding of two long contigs (default: 5)
+.TP
+\fB\-max_coverage\fR <floating point>
+: removal of high coverage nodes AFTER tour bus (default: no removal)
+.TP
+\fB\-coverage_mask\fR <int>
+: minimum coverage required for confident regions of contigs (default: 1)
+.TP
+\fB\-long_mult_cutoff\fR <int>
+: minimum number of long reads required to merge contigs (default: 2)
+.TP
+\fB\-unused_reads\fR <yes|no>
+: export unused reads in UnusedReads.fa file (default: no)
+.TP
+\fB\-alignments\fR <yes|no>
+: export a summary of contig alignment to the reference sequences (default: no)
+.TP
+\fB\-exportFiltered\fR <yes|no>
+: export the long nodes which were eliminated by the coverage filters (default: no)
+.TP
+\fB\-clean\fR <yes|no>
+: remove all the intermediary files which are useless for recalculation (default : no)
+.TP
+\fB\-very_clean\fR <yes|no>
+: remove all the intermediary files (no recalculation possible) (default: no)
+.TP
+\fB\-paired_exp_fraction\fR <double>
+: remove all the paired end connections which less than the specified fraction of the expected count (default: 0.1)
+.TP
+\fB\-shortMatePaired\fR* <yes|no>
+: for mate\-pair libraries, indicate that the library might be contaminated with paired\-end reads (default no)
+.TP
+\fB\-conserveLong\fR <yes|no>
+: preserve sequences with long reads in them (default no)
+.SS "Output:"
+.TP
+directory/contigs.fa
+: fasta file of contigs longer than twice hash length
+.TP
+directory/stats.txt
+: stats file (tab\-spaced) useful for determining appropriate coverage cutoff
+.TP
+directory/LastGraph
+: special formatted file with all the information on the final graph
+.TP
+directory/velvet_asm.afg
+: (if requested) AMOS compatible assembly file
Added: trunk/packages/velvet/trunk/debian/manpages/velveth.1
===================================================================
--- trunk/packages/velvet/trunk/debian/manpages/velveth.1 (rev 0)
+++ trunk/packages/velvet/trunk/debian/manpages/velveth.1 2014-07-01 14:38:05 UTC (rev 17389)
@@ -0,0 +1,92 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.45.1.
+.TH VELVETH "1" "July 2014" "velveth 1.2.10+dfsg1" "User Commands"
+.SH NAME
+velveth \- simple hashing program
+.SH DESCRIPTION
+velveth \- simple hashing program
+Version 1.2.09
+.SH OPTIONS
+.TP
+\fB\-strand_specific\fR
+: for strand specific transcriptome sequencing data (default: off)
+.TP
+\fB\-reuse_Sequences\fR
+: reuse Sequences file (or link) already in directory (no need to provide original filenames in this case (default: off)
+.TP
+\fB\-reuse_binary\fR
+: reuse binary sequences file (or link) already in directory (no need to provide original filenames in this case (default: off)
+.TP
+\fB\-noHash\fR
+: simply prepare Sequences file, do not hash reads or prepare Roadmaps file (default: off)
+.TP
+\fB\-create_binary\fR
+: create binary CnyUnifiedSeq file (default: off)
+.PP
+Synopsis:
+.SS "- Short single end reads:"
+.IP
+velveth Assem 29 \fB\-short\fR \fB\-fastq\fR s_1_sequence.txt
+.SS "- Paired-end short reads (remember to interleave paired reads):"
+.IP
+velveth Assem 31 \fB\-shortPaired\fR \fB\-fasta\fR interleaved.fna
+.PP
+\- Paired\-end short reads (using separate files for the paired reads)
+.IP
+velveth Assem 31 \fB\-shortPaired\fR \fB\-fasta\fR \fB\-separate\fR left.fa right.fa
+.SS "- Two channels and some long reads:"
+.IP
+velveth Assem 43 \fB\-short\fR \fB\-fastq\fR unmapped.fna \fB\-longPaired\fR \fB\-fasta\fR SangerReads.fasta
+.SS "- Three channels:"
+.IP
+velveth Assem 35 \fB\-shortPaired\fR \fB\-fasta\fR pe_lib1.fasta \fB\-shortPaired2\fR pe_lib2.fasta \fB\-short3\fR se_lib1.fa
+.SS "Output:"
+.IP
+directory/Roadmaps
+directory/Sequences
+.IP
+[Both files are picked up by graph, so please leave them there]
+.SH COPYRIGHT
+Copyright 2007, 2008 Daniel Zerbino (zerbino at ebi.ac.uk)
+.br
+This is free software; see the source for copying conditions. There is NO
+warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+.PP
+Compilation settings:
+CATEGORIES = 2
+MAXKMERLENGTH = 31
+.PP
+Usage:
+\&./velveth directory hash_length {[\-file_format][\-read_type][\-separate|\-interleaved] filename1 [filename2 ...]} {...} [options]
+.TP
+directory
+: directory name for output files
+.TP
+hash_length
+: EITHER an odd integer (if even, it will be decremented) <= 31 (if above, will be reduced)
+: OR: m,M,s where m and M are odd integers (if not, they will be decremented) with m < M <= 31 (if above, will be reduced)
+.IP
+and s is a step (even number). Velvet will then hash from k=m to k=M with a step of s
+.TP
+filename
+: path to sequence file or \- for standard input
+.SS "File format options:"
+.HP
+\fB\-fasta\fR \fB\-fastq\fR \fB\-raw\fR \fB\-fasta\fR.gz \fB\-fastq\fR.gz \fB\-raw\fR.gz \fB\-sam\fR \fB\-bam\fR \fB\-fmtAuto\fR
+.IP
+(Note: \fB\-fmtAuto\fR will detect fasta or fastq, and will try the following programs for decompression : gunzip, pbunzip2, bunzip2
+.SS "File layout options for paired reads (only for fasta and fastq formats):"
+.TP
+\fB\-interleaved\fR
+: File contains paired reads interleaved in the one file (default)
+.TP
+\fB\-separate\fR
+: Read 2 separate files for paired reads
+.SS "Read type options:"
+.HP
+\fB\-short\fR \fB\-shortPaired\fR
+.HP
+\fB\-short2\fR \fB\-shortPaired2\fR
+.HP
+\fB\-long\fR \fB\-longPaired\fR
+.HP
+\fB\-reference\fR
Added: trunk/packages/velvet/trunk/debian/manpages/velveth_63.1
===================================================================
--- trunk/packages/velvet/trunk/debian/manpages/velveth_63.1 (rev 0)
+++ trunk/packages/velvet/trunk/debian/manpages/velveth_63.1 2014-07-01 14:38:05 UTC (rev 17389)
@@ -0,0 +1,93 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.45.1.
+.TH VELVETH_63 "1" "July 2014" "velveth_63 1.2.10+dfsg1" "User Commands"
+.SH NAME
+velveth_63 \- simple hashing program (MAXKMERLENGTH = 63)
+.SH DESCRIPTION
+velveth \- simple hashing program
+Version 1.2.09
+.SH OPTIONS
+.TP
+\fB\-strand_specific\fR
+: for strand specific transcriptome sequencing data (default: off)
+.TP
+\fB\-reuse_Sequences\fR
+: reuse Sequences file (or link) already in directory (no need to provide original filenames in this case (default: off)
+.TP
+\fB\-reuse_binary\fR
+: reuse binary sequences file (or link) already in directory (no need to provide original filenames in this case (default: off)
+.TP
+\fB\-noHash\fR
+: simply prepare Sequences file, do not hash reads or prepare Roadmaps file (default: off)
+.TP
+\fB\-create_binary\fR
+: create binary CnyUnifiedSeq file (default: off)
+.PP
+Synopsis:
+.SS "- Short single end reads:"
+.IP
+velveth Assem 29 \fB\-short\fR \fB\-fastq\fR s_1_sequence.txt
+.SS "- Paired-end short reads (remember to interleave paired reads):"
+.IP
+velveth Assem 31 \fB\-shortPaired\fR \fB\-fasta\fR interleaved.fna
+.PP
+\- Paired\-end short reads (using separate files for the paired reads)
+.IP
+velveth Assem 31 \fB\-shortPaired\fR \fB\-fasta\fR \fB\-separate\fR left.fa right.fa
+.SS "- Two channels and some long reads:"
+.IP
+velveth Assem 43 \fB\-short\fR \fB\-fastq\fR unmapped.fna \fB\-longPaired\fR \fB\-fasta\fR SangerReads.fasta
+.SS "- Three channels:"
+.IP
+velveth Assem 35 \fB\-shortPaired\fR \fB\-fasta\fR pe_lib1.fasta \fB\-shortPaired2\fR pe_lib2.fasta \fB\-short3\fR se_lib1.fa
+.SS "Output:"
+.IP
+directory/Roadmaps
+directory/Sequences
+.IP
+[Both files are picked up by graph, so please leave them there]
+.SH COPYRIGHT
+Copyright 2007, 2008 Daniel Zerbino (zerbino at ebi.ac.uk)
+.br
+This is free software; see the source for copying conditions. There is NO
+warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+.PP
+Compilation settings:
+CATEGORIES = 2
+MAXKMERLENGTH = 63
+OPENMP
+.PP
+Usage:
+\&./velveth directory hash_length {[\-file_format][\-read_type][\-separate|\-interleaved] filename1 [filename2 ...]} {...} [options]
+.TP
+directory
+: directory name for output files
+.TP
+hash_length
+: EITHER an odd integer (if even, it will be decremented) <= 63 (if above, will be reduced)
+: OR: m,M,s where m and M are odd integers (if not, they will be decremented) with m < M <= 63 (if above, will be reduced)
+.IP
+and s is a step (even number). Velvet will then hash from k=m to k=M with a step of s
+.TP
+filename
+: path to sequence file or \- for standard input
+.SS "File format options:"
+.HP
+\fB\-fasta\fR \fB\-fastq\fR \fB\-raw\fR \fB\-fasta\fR.gz \fB\-fastq\fR.gz \fB\-raw\fR.gz \fB\-sam\fR \fB\-bam\fR \fB\-fmtAuto\fR
+.IP
+(Note: \fB\-fmtAuto\fR will detect fasta or fastq, and will try the following programs for decompression : gunzip, pbunzip2, bunzip2
+.SS "File layout options for paired reads (only for fasta and fastq formats):"
+.TP
+\fB\-interleaved\fR
+: File contains paired reads interleaved in the one file (default)
+.TP
+\fB\-separate\fR
+: Read 2 separate files for paired reads
+.SS "Read type options:"
+.HP
+\fB\-short\fR \fB\-shortPaired\fR
+.HP
+\fB\-short2\fR \fB\-shortPaired2\fR
+.HP
+\fB\-long\fR \fB\-longPaired\fR
+.HP
+\fB\-reference\fR
Added: trunk/packages/velvet/trunk/debian/manpages/velveth_63_long.1
===================================================================
--- trunk/packages/velvet/trunk/debian/manpages/velveth_63_long.1 (rev 0)
+++ trunk/packages/velvet/trunk/debian/manpages/velveth_63_long.1 2014-07-01 14:38:05 UTC (rev 17389)
@@ -0,0 +1,94 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.45.1.
+.TH VELVETH_63_LONG "1" "July 2014" "velveth_63_long 1.2.10+dfsg1" "User Commands"
+.SH NAME
+velveth_63_long \- simple hashing program (MAXKMERLENGTH = 63, LONGSEQUENCES)
+.SH DESCRIPTION
+velveth \- simple hashing program
+Version 1.2.09
+.SH OPTIONS
+.TP
+\fB\-strand_specific\fR
+: for strand specific transcriptome sequencing data (default: off)
+.TP
+\fB\-reuse_Sequences\fR
+: reuse Sequences file (or link) already in directory (no need to provide original filenames in this case (default: off)
+.TP
+\fB\-reuse_binary\fR
+: reuse binary sequences file (or link) already in directory (no need to provide original filenames in this case (default: off)
+.TP
+\fB\-noHash\fR
+: simply prepare Sequences file, do not hash reads or prepare Roadmaps file (default: off)
+.TP
+\fB\-create_binary\fR
+: create binary CnyUnifiedSeq file (default: off)
+.PP
+Synopsis:
+.SS "- Short single end reads:"
+.IP
+velveth Assem 29 \fB\-short\fR \fB\-fastq\fR s_1_sequence.txt
+.SS "- Paired-end short reads (remember to interleave paired reads):"
+.IP
+velveth Assem 31 \fB\-shortPaired\fR \fB\-fasta\fR interleaved.fna
+.PP
+\- Paired\-end short reads (using separate files for the paired reads)
+.IP
+velveth Assem 31 \fB\-shortPaired\fR \fB\-fasta\fR \fB\-separate\fR left.fa right.fa
+.SS "- Two channels and some long reads:"
+.IP
+velveth Assem 43 \fB\-short\fR \fB\-fastq\fR unmapped.fna \fB\-longPaired\fR \fB\-fasta\fR SangerReads.fasta
+.SS "- Three channels:"
+.IP
+velveth Assem 35 \fB\-shortPaired\fR \fB\-fasta\fR pe_lib1.fasta \fB\-shortPaired2\fR pe_lib2.fasta \fB\-short3\fR se_lib1.fa
+.SS "Output:"
+.IP
+directory/Roadmaps
+directory/Sequences
+.IP
+[Both files are picked up by graph, so please leave them there]
+.SH COPYRIGHT
+Copyright 2007, 2008 Daniel Zerbino (zerbino at ebi.ac.uk)
+.br
+This is free software; see the source for copying conditions. There is NO
+warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+.PP
+Compilation settings:
+CATEGORIES = 2
+MAXKMERLENGTH = 63
+OPENMP
+LONGSEQUENCES
+.PP
+Usage:
+\&./velveth directory hash_length {[\-file_format][\-read_type][\-separate|\-interleaved] filename1 [filename2 ...]} {...} [options]
+.TP
+directory
+: directory name for output files
+.TP
+hash_length
+: EITHER an odd integer (if even, it will be decremented) <= 63 (if above, will be reduced)
+: OR: m,M,s where m and M are odd integers (if not, they will be decremented) with m < M <= 63 (if above, will be reduced)
+.IP
+and s is a step (even number). Velvet will then hash from k=m to k=M with a step of s
+.TP
+filename
+: path to sequence file or \- for standard input
+.SS "File format options:"
+.HP
+\fB\-fasta\fR \fB\-fastq\fR \fB\-raw\fR \fB\-fasta\fR.gz \fB\-fastq\fR.gz \fB\-raw\fR.gz \fB\-sam\fR \fB\-bam\fR \fB\-fmtAuto\fR
+.IP
+(Note: \fB\-fmtAuto\fR will detect fasta or fastq, and will try the following programs for decompression : gunzip, pbunzip2, bunzip2
+.SS "File layout options for paired reads (only for fasta and fastq formats):"
+.TP
+\fB\-interleaved\fR
+: File contains paired reads interleaved in the one file (default)
+.TP
+\fB\-separate\fR
+: Read 2 separate files for paired reads
+.SS "Read type options:"
+.HP
+\fB\-short\fR \fB\-shortPaired\fR
+.HP
+\fB\-short2\fR \fB\-shortPaired2\fR
+.HP
+\fB\-long\fR \fB\-longPaired\fR
+.HP
+\fB\-reference\fR
Added: trunk/packages/velvet/trunk/debian/manpages/velveth_de.1
===================================================================
--- trunk/packages/velvet/trunk/debian/manpages/velveth_de.1 (rev 0)
+++ trunk/packages/velvet/trunk/debian/manpages/velveth_de.1 2014-07-01 14:38:05 UTC (rev 17389)
@@ -0,0 +1,94 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.45.1.
+.TH VELVETH_DE "1" "July 2014" "velveth_de 1.2.10+dfsg1" "User Commands"
+.SH NAME
+velveth_de \- simple hashing program (colorspace version)
+.SH DESCRIPTION
+velveth \- simple hashing program
+Version 1.2.09
+.SH OPTIONS
+.TP
+\fB\-strand_specific\fR
+: for strand specific transcriptome sequencing data (default: off)
+.TP
+\fB\-reuse_Sequences\fR
+: reuse Sequences file (or link) already in directory (no need to provide original filenames in this case (default: off)
+.TP
+\fB\-reuse_binary\fR
+: reuse binary sequences file (or link) already in directory (no need to provide original filenames in this case (default: off)
+.TP
+\fB\-noHash\fR
+: simply prepare Sequences file, do not hash reads or prepare Roadmaps file (default: off)
+.TP
+\fB\-create_binary\fR
+: create binary CnyUnifiedSeq file (default: off)
+.PP
+Synopsis:
+.SS "- Short single end reads:"
+.IP
+velveth Assem 29 \fB\-short\fR \fB\-fastq\fR s_1_sequence.txt
+.SS "- Paired-end short reads (remember to interleave paired reads):"
+.IP
+velveth Assem 31 \fB\-shortPaired\fR \fB\-fasta\fR interleaved.fna
+.PP
+\- Paired\-end short reads (using separate files for the paired reads)
+.IP
+velveth Assem 31 \fB\-shortPaired\fR \fB\-fasta\fR \fB\-separate\fR left.fa right.fa
+.SS "- Two channels and some long reads:"
+.IP
+velveth Assem 43 \fB\-short\fR \fB\-fastq\fR unmapped.fna \fB\-longPaired\fR \fB\-fasta\fR SangerReads.fasta
+.SS "- Three channels:"
+.IP
+velveth Assem 35 \fB\-shortPaired\fR \fB\-fasta\fR pe_lib1.fasta \fB\-shortPaired2\fR pe_lib2.fasta \fB\-short3\fR se_lib1.fa
+.SS "Output:"
+.IP
+directory/Roadmaps
+directory/Sequences
+.IP
+[Both files are picked up by graph, so please leave them there]
+.SH COPYRIGHT
+Copyright 2007, 2008 Daniel Zerbino (zerbino at ebi.ac.uk)
+.br
+This is free software; see the source for copying conditions. There is NO
+warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+.PP
+Compilation settings:
+CATEGORIES = 2
+MAXKMERLENGTH = 31
+OPENMP
+COLOR
+.PP
+Usage:
+\&./velveth directory hash_length {[\-file_format][\-read_type][\-separate|\-interleaved] filename1 [filename2 ...]} {...} [options]
+.TP
+directory
+: directory name for output files
+.TP
+hash_length
+: EITHER an odd integer (if even, it will be decremented) <= 31 (if above, will be reduced)
+: OR: m,M,s where m and M are odd integers (if not, they will be decremented) with m < M <= 31 (if above, will be reduced)
+.IP
+and s is a step (even number). Velvet will then hash from k=m to k=M with a step of s
+.TP
+filename
+: path to sequence file or \- for standard input
+.SS "File format options:"
+.HP
+\fB\-fasta\fR \fB\-fastq\fR \fB\-raw\fR \fB\-fasta\fR.gz \fB\-fastq\fR.gz \fB\-raw\fR.gz \fB\-sam\fR \fB\-bam\fR \fB\-fmtAuto\fR
+.IP
+(Note: \fB\-fmtAuto\fR will detect fasta or fastq, and will try the following programs for decompression : gunzip, pbunzip2, bunzip2
+.SS "File layout options for paired reads (only for fasta and fastq formats):"
+.TP
+\fB\-interleaved\fR
+: File contains paired reads interleaved in the one file (default)
+.TP
+\fB\-separate\fR
+: Read 2 separate files for paired reads
+.SS "Read type options:"
+.HP
+\fB\-short\fR \fB\-shortPaired\fR
+.HP
+\fB\-short2\fR \fB\-shortPaired2\fR
+.HP
+\fB\-long\fR \fB\-longPaired\fR
+.HP
+\fB\-reference\fR
Added: trunk/packages/velvet/trunk/debian/manpages/velveth_long.1
===================================================================
--- trunk/packages/velvet/trunk/debian/manpages/velveth_long.1 (rev 0)
+++ trunk/packages/velvet/trunk/debian/manpages/velveth_long.1 2014-07-01 14:38:05 UTC (rev 17389)
@@ -0,0 +1,94 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.45.1.
+.TH VELVETH_LONG "1" "July 2014" "velveth_long 1.2.10+dfsg1" "User Commands"
+.SH NAME
+velveth_long \- simple hashing program (LONGSEQUENCES)
+.SH DESCRIPTION
+velveth \- simple hashing program
+Version 1.2.09
+.SH OPTIONS
+.TP
+\fB\-strand_specific\fR
+: for strand specific transcriptome sequencing data (default: off)
+.TP
+\fB\-reuse_Sequences\fR
+: reuse Sequences file (or link) already in directory (no need to provide original filenames in this case (default: off)
+.TP
+\fB\-reuse_binary\fR
+: reuse binary sequences file (or link) already in directory (no need to provide original filenames in this case (default: off)
+.TP
+\fB\-noHash\fR
+: simply prepare Sequences file, do not hash reads or prepare Roadmaps file (default: off)
+.TP
+\fB\-create_binary\fR
+: create binary CnyUnifiedSeq file (default: off)
+.PP
+Synopsis:
+.SS "- Short single end reads:"
+.IP
+velveth Assem 29 \fB\-short\fR \fB\-fastq\fR s_1_sequence.txt
+.SS "- Paired-end short reads (remember to interleave paired reads):"
+.IP
+velveth Assem 31 \fB\-shortPaired\fR \fB\-fasta\fR interleaved.fna
+.PP
+\- Paired\-end short reads (using separate files for the paired reads)
+.IP
+velveth Assem 31 \fB\-shortPaired\fR \fB\-fasta\fR \fB\-separate\fR left.fa right.fa
+.SS "- Two channels and some long reads:"
+.IP
+velveth Assem 43 \fB\-short\fR \fB\-fastq\fR unmapped.fna \fB\-longPaired\fR \fB\-fasta\fR SangerReads.fasta
+.SS "- Three channels:"
+.IP
+velveth Assem 35 \fB\-shortPaired\fR \fB\-fasta\fR pe_lib1.fasta \fB\-shortPaired2\fR pe_lib2.fasta \fB\-short3\fR se_lib1.fa
+.SS "Output:"
+.IP
+directory/Roadmaps
+directory/Sequences
+.IP
+[Both files are picked up by graph, so please leave them there]
+.SH COPYRIGHT
+Copyright 2007, 2008 Daniel Zerbino (zerbino at ebi.ac.uk)
+.br
+This is free software; see the source for copying conditions. There is NO
+warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+.PP
+Compilation settings:
+CATEGORIES = 2
+MAXKMERLENGTH = 31
+OPENMP
+LONGSEQUENCES
+.PP
+Usage:
+\&./velveth directory hash_length {[\-file_format][\-read_type][\-separate|\-interleaved] filename1 [filename2 ...]} {...} [options]
+.TP
+directory
+: directory name for output files
+.TP
+hash_length
+: EITHER an odd integer (if even, it will be decremented) <= 31 (if above, will be reduced)
+: OR: m,M,s where m and M are odd integers (if not, they will be decremented) with m < M <= 31 (if above, will be reduced)
+.IP
+and s is a step (even number). Velvet will then hash from k=m to k=M with a step of s
+.TP
+filename
+: path to sequence file or \- for standard input
+.SS "File format options:"
+.HP
+\fB\-fasta\fR \fB\-fastq\fR \fB\-raw\fR \fB\-fasta\fR.gz \fB\-fastq\fR.gz \fB\-raw\fR.gz \fB\-sam\fR \fB\-bam\fR \fB\-fmtAuto\fR
+.IP
+(Note: \fB\-fmtAuto\fR will detect fasta or fastq, and will try the following programs for decompression : gunzip, pbunzip2, bunzip2
+.SS "File layout options for paired reads (only for fasta and fastq formats):"
+.TP
+\fB\-interleaved\fR
+: File contains paired reads interleaved in the one file (default)
+.TP
+\fB\-separate\fR
+: Read 2 separate files for paired reads
+.SS "Read type options:"
+.HP
+\fB\-short\fR \fB\-shortPaired\fR
+.HP
+\fB\-short2\fR \fB\-shortPaired2\fR
+.HP
+\fB\-long\fR \fB\-longPaired\fR
+.HP
+\fB\-reference\fR
Modified: trunk/packages/velvet/trunk/debian/rules
===================================================================
--- trunk/packages/velvet/trunk/debian/rules 2014-07-01 13:31:54 UTC (rev 17388)
+++ trunk/packages/velvet/trunk/debian/rules 2014-07-01 14:38:05 UTC (rev 17389)
@@ -37,17 +37,17 @@
dh_auto_build -- color OPENMP=1 CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)"
override_dh_install :
- mkdir -p debian/$(pkg)/usr/share/man/man1/
- help2man --no-info --name="simple hashing program" \
- ./velveth > debian/$(pkg)/usr/share/man/man1/velveth.1
- help2man --no-info --name="simple hashing program (colorspace version)" \
- ./velveth_de > debian/$(pkg)/usr/share/man/man1/velveth_de.1
- help2man --no-info --version-option=" " \
- --name="de Bruijn graph construction, error removal and repeat resolution" \
- ./velvetg > debian/$(pkg)/usr/share/man/man1/velvetg.1
- help2man --no-info --version-option=" " \
- --name="de Bruijn graph construction, error removal and repeat resolution (colorspace version)" \
- ./velvetg_de > debian/$(pkg)/usr/share/man/man1/velvetg_de.1
+# mkdir -p debian/$(pkg)/usr/share/man/man1/
+# help2man --no-info --name="simple hashing program" \
+# ./velveth > debian/$(pkg)/usr/share/man/man1/velveth.1
+# help2man --no-info --name="simple hashing program (colorspace version)" \
+# ./velveth_de > debian/$(pkg)/usr/share/man/man1/velveth_de.1
+# help2man --no-info --version-option=" " \
+# --name="de Bruijn graph construction, error removal and repeat resolution" \
+# ./velvetg > debian/$(pkg)/usr/share/man/man1/velvetg.1
+# help2man --no-info --version-option=" " \
+# --name="de Bruijn graph construction, error removal and repeat resolution (colorspace version)" \
+# ./velvetg_de > debian/$(pkg)/usr/share/man/man1/velvetg_de.1
dh_install
# remove extra copies of GPL
find $(CURDIR)/debian -type f -name 'LICENSE*' -delete
Added: trunk/packages/velvet/trunk/debian/velvet-long.manpages
===================================================================
--- trunk/packages/velvet/trunk/debian/velvet-long.manpages (rev 0)
+++ trunk/packages/velvet/trunk/debian/velvet-long.manpages 2014-07-01 14:38:05 UTC (rev 17389)
@@ -0,0 +1,2 @@
+debian/manpages/*63.1
+debian/manpages/*long.1
Added: trunk/packages/velvet/trunk/debian/velvet.manpages
===================================================================
--- trunk/packages/velvet/trunk/debian/velvet.manpages (rev 0)
+++ trunk/packages/velvet/trunk/debian/velvet.manpages 2014-07-01 14:38:05 UTC (rev 17389)
@@ -0,0 +1,2 @@
+debian/manpages/velvet[gh].1
+debian/manpages/velvet[gh]_de.1
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