[med-svn] r16022 - in trunk/packages/spades/trunk/debian: . mans

Thu Feb 13 10:38:16 UTC 2014

Author: tille
Date: 2014-02-13 10:38:16 +0000 (Thu, 13 Feb 2014)
New Revision: 16022

Added:
   trunk/packages/spades/trunk/debian/createmanpages
   trunk/packages/spades/trunk/debian/manpages
   trunk/packages/spades/trunk/debian/mans/
   trunk/packages/spades/trunk/debian/mans/dipspades.1
   trunk/packages/spades/trunk/debian/mans/spades.1
Log:
Add help2man based manpages


Added: trunk/packages/spades/trunk/debian/createmanpages
===================================================================

--- trunk/packages/spades/trunk/debian/createmanpages	                        (rev 0)
+++ trunk/packages/spades/trunk/debian/createmanpages	2014-02-13 10:38:16 UTC (rev 16022)
@@ -0,0 +1,10 @@
+#!/bin/sh
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//'`
+MANDIR=debian/mans
+mkdir -p $MANDIR
+help2man --no-info --no-discard-stderr \
+         --name='SPAdes genome assembler' \
+            --version-string="$VERSION" spades > $MANDIR/spades.1
+help2man --no-info --no-discard-stderr \
+         --name='genome assembler designed for diploid genomes with high heterozygosity rate' \
+            --version-string="$VERSION" dipspades > $MANDIR/dipspades.1


Property changes on: trunk/packages/spades/trunk/debian/createmanpages
___________________________________________________________________
Added: svn:executable
   + *

Added: trunk/packages/spades/trunk/debian/manpages
===================================================================
--- trunk/packages/spades/trunk/debian/manpages	                        (rev 0)
+++ trunk/packages/spades/trunk/debian/manpages	2014-02-13 10:38:16 UTC (rev 16022)
@@ -0,0 +1 @@
+debian/mans/*

Added: trunk/packages/spades/trunk/debian/mans/dipspades.1
===================================================================
--- trunk/packages/spades/trunk/debian/mans/dipspades.1	                        (rev 0)
+++ trunk/packages/spades/trunk/debian/mans/dipspades.1	2014-02-13 10:38:16 UTC (rev 16022)
@@ -0,0 +1,130 @@
+.TH DIPSPADES "1" "February 2014" "dipspades 3.0.0" "User Commands"
+.SH NAME
+dipspades \- genome assembler designed for diploid genomes with high heterozygosity rate
+.SH SYNOPSIS
+.B dipspades.py
+[\fIoptions\fR] \fI-o <output_dir>\fR
+.SH DESCRIPTION
+.P
+dipSPAdes: genome assembler designed for diploid genomes with high heterozygosity rate
+.P
+The dipSPAdes program belongs to the St. Petersburg genome assembler is
+intended for both standard isolates and single-cell MDA bacteria
+assemblies.  It  works  with Illumina  or IonTorrent reads and is
+capable of providing hybrid assemblies using PacBio and Sanger reads.
+You can  also  provide  additional contigs that will be used as long
+reads.
+.SH OPTIONS
+Basic options:
+.TP
+\fB\-o\fR <output_dir>
+directory to store all the resulting files (required)
+.TP
+\fB\-\-iontorrent\fR
+this flag is required for IonTorrent data
+.TP
+\fB\-\-test\fR
+runs SPAdes on toy dataset
+.TP
+\fB\-h\fR/\-\-help
+prints this usage message
+.PP
+Input reads:
+.TP
+\fB\-\-12\fR <filename>
+file with interlaced forward and reverse paired\-end reads
+.TP
+\fB\-1\fR <filename>
+file with forward paired\-end reads
+.TP
+\fB\-2\fR <filename>
+file with reverse paired\-end reads
+.TP
+\fB\-s\fR <filename>
+file with unpaired reads
+.TP
+\fB\-\-pe\fR<#>\-12 <filename>
+file with interlaced reads for paired\-end library number <#> (<#> = 1,2,3,4,5)
+.TP
+\fB\-\-pe\fR<#>\-1 <filename>
+file with forward reads for paired\-end library number <#> (<#> = 1,2,3,4,5)
+.TP
+\fB\-\-pe\fR<#>\-2 <filename>
+file with reverse reads for paired\-end library number <#> (<#> = 1,2,3,4,5)
+.TP
+\fB\-\-pe\fR<#>\-s <filename>
+file with unpaired reads for paired\-end library number <#> (<#> = 1,2,3,4,5)
+.TP
+\fB\-\-pe\fR<#>\-<or>
+orientation of reads for paired\-end library number <#> (<#> = 1,2,3,4,5; <or> = fr, rf, ff)
+.TP
+\fB\-\-mp\fR<#>\-12 <filename>
+file with interlaced reads for mate\-pair library number <#> (<#> = 1,2,3,4,5)
+.TP
+\fB\-\-mp\fR<#>\-1 <filename>
+file with forward reads for mate\-pair library number <#> (<#> = 1,2,3,4,5)
+.TP
+\fB\-\-mp\fR<#>\-2 <filename>
+file with reverse reads for mate\-pair library number <#> (<#> = 1,2,3,4,5)
+.TP
+\fB\-\-mp\fR<#>\-s <filename>
+file with unpaired reads for mate\-pair library number <#> (<#> = 1,2,3,4,5)
+.TP
+\fB\-\-mp\fR<#>\-<or>
+orientation of reads for mate\-pair library number <#> (<#> = 1,2,3,4,5; <or> = fr, rf, ff)
+.TP
+\fB\-\-sanger\fR <filename>
+file with Sanger reads
+.TP
+\fB\-\-pacbio\fR <filename>
+file with PacBio reads
+.TP
+\fB\-\-trusted\-contigs\fR <filename>
+file with trusted contigs
+.TP
+\fB\-\-untrusted\-contigs\fR <filename>
+file with untrusted contigs
+.PP
+Input haplocontigs:
+.TP
+\fB\-\-hap\fR <filename>
+file with haplocontigs
+.PP
+Pipeline options:
+.TP
+\fB\-\-only\-assembler\fR
+runs only assembling (without read error correction)
+.TP
+\fB\-\-disable\-gzip\-output\fR
+forces error correction not to compress the corrected reads
+.TP
+\fB\-\-disable\-rr\fR
+disables repeat resolution stage of assembling
+.PP
+DipSPAdes options:
+.TP
+\fB\-\-expect\-gaps\fR
+indicate that significant number of gaps in coverage is expected
+.TP
+\fB\-\-expect\-rearrangements\fR
+indicate that significant number of rearrangngements between haplomes of diploid genome is expected
+.PP
+Advanced options:
+.TP
+\fB\-\-dataset\fR <filename>
+file with dataset description in YAML format
+.TP
+\fB\-t\fR/\-\-threads <int>
+number of threads [default: 16]
+.TP
+\fB\-m\fR/\-\-memory <int>
+RAM limit for SPAdes in Gb (terminates if exceeded) [default: 250]
+.TP
+\fB\-\-tmp\-dir\fR <dirname>
+directory for temporary files [default: <output_dir>/tmp]
+.TP
+\fB\-k\fR <int,int,...>
+comma\-separated list of k\-mer sizes (must be odd and less than 128) [default: 'auto']
+.TP
+\fB\-\-phred\-offset\fR <33 or 64>
+PHRED quality offset in the input reads (33 or 64) [default: auto\-detect]

Added: trunk/packages/spades/trunk/debian/mans/spades.1
===================================================================
--- trunk/packages/spades/trunk/debian/mans/spades.1	                        (rev 0)
+++ trunk/packages/spades/trunk/debian/mans/spades.1	2014-02-13 10:38:16 UTC (rev 16022)
@@ -0,0 +1,128 @@
+.TH SPADES "1" "February 2014" "spades 3.0.0" "User Commands"
+.SH NAME
+spades \- SPAdes genome assembler
+.SH SYNOPSIS
+.B spades.py
+[\fIoptions\fR] \fI-o <output_dir>\fR
+.SH DESCRIPTION
+The SPAdes - St. Petersburg genome assembler is intended for both
+standard isolates and single-cell MDA bacteria assemblies.  It works
+with Illumina or IonTorrent reads and is capable of providing hybrid
+assemblies using PacBio and Sanger reads. You can also provide
+additional contigs that will be used as long reads.
+.SH OPTIONS
+Basic options:
+.TP
+\fB\-o\fR <output_dir>
+directory to store all the resulting files (required)
+.TP
+\fB\-\-sc\fR
+this flag is required for MDA (single\-cell) data
+.TP
+\fB\-\-iontorrent\fR
+this flag is required for IonTorrent data
+.TP
+\fB\-\-test\fR
+runs SPAdes on toy dataset
+.TP
+\fB\-h\fR/\-\-help
+prints this usage message
+.PP
+Input data:
+.TP
+\fB\-\-12\fR <filename>
+file with interlaced forward and reverse paired\-end reads
+.TP
+\fB\-1\fR <filename>
+file with forward paired\-end reads
+.TP
+\fB\-2\fR <filename>
+file with reverse paired\-end reads
+.TP
+\fB\-s\fR <filename>
+file with unpaired reads
+.TP
+\fB\-\-pe\fR<#>\-12 <filename>
+file with interlaced reads for paired\-end library number <#> (<#> = 1,2,3,4,5)
+.TP
+\fB\-\-pe\fR<#>\-1 <filename>
+file with forward reads for paired\-end library number <#> (<#> = 1,2,3,4,5)
+.TP
+\fB\-\-pe\fR<#>\-2 <filename>
+file with reverse reads for paired\-end library number <#> (<#> = 1,2,3,4,5)
+.TP
+\fB\-\-pe\fR<#>\-s <filename>
+file with unpaired reads for paired\-end library number <#> (<#> = 1,2,3,4,5)
+.TP
+\fB\-\-pe\fR<#>\-<or>
+orientation of reads for paired\-end library number <#> (<#> = 1,2,3,4,5; <or> = fr, rf, ff)
+.TP
+\fB\-\-mp\fR<#>\-12 <filename>
+file with interlaced reads for mate\-pair library number <#> (<#> = 1,2,3,4,5)
+.TP
+\fB\-\-mp\fR<#>\-1 <filename>
+file with forward reads for mate\-pair library number <#> (<#> = 1,2,3,4,5)
+.TP
+\fB\-\-mp\fR<#>\-2 <filename>
+file with reverse reads for mate\-pair library number <#> (<#> = 1,2,3,4,5)
+.TP
+\fB\-\-mp\fR<#>\-s <filename>
+file with unpaired reads for mate\-pair library number <#> (<#> = 1,2,3,4,5)
+.TP
+\fB\-\-mp\fR<#>\-<or>
+orientation of reads for mate\-pair library number <#> (<#> = 1,2,3,4,5; <or> = fr, rf, ff)
+.TP
+\fB\-\-sanger\fR <filename>
+file with Sanger reads
+.TP
+\fB\-\-pacbio\fR <filename>
+file with PacBio reads
+.TP
+\fB\-\-trusted\-contigs\fR <filename>
+file with trusted contigs
+.TP
+\fB\-\-untrusted\-contigs\fR <filename>
+file with untrusted contigs
+.PP
+Pipeline options:
+.TP
+\fB\-\-only\-error\-correction\fR
+runs only read error correction (without assembling)
+.TP
+\fB\-\-only\-assembler\fR
+runs only assembling (without read error correction)
+.TP
+\fB\-\-careful\fR
+tries to reduce number of mismatches and short indels
+.TP
+\fB\-\-continue\fR
+continue run from the last available check\-point
+.TP
+\fB\-\-restart\-from\fR <cp>
+restart run with updated options and from the specified check\-point ('ec', 'as', 'k<int>', 'mc')
+.TP
+\fB\-\-disable\-gzip\-output\fR
+forces error correction not to compress the corrected reads
+.TP
+\fB\-\-disable\-rr\fR
+disables repeat resolution stage of assembling
+.PP
+Advanced options:
+.TP
+\fB\-\-dataset\fR <filename>
+file with dataset description in YAML format
+.TP
+\fB\-t\fR/\-\-threads <int>
+number of threads [default: 16]
+.TP
+\fB\-m\fR/\-\-memory <int>
+RAM limit for SPAdes in Gb (terminates if exceeded) [default: 250]
+.TP
+\fB\-\-tmp\-dir\fR <dirname>
+directory for temporary files [default: <output_dir>/tmp]
+.TP
+\fB\-k\fR <int,int,...>
+comma\-separated list of k\-mer sizes (must be odd and less than 128) [default: 'auto']
+.TP
+\fB\-\-phred\-offset\fR <33 or 64>
+PHRED quality offset in the input reads (33 or 64) [default: auto\-detect]


