[med-svn] [spades] 02/03: Switch manpage building back to asciidoctor
Afif Elghraoui
afif at moszumanska.debian.org
Mon Jul 18 06:19:27 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a commit to branch debian/jessie-backports
in repository spades.
commit 12aeff3000e72d4f79059506cb9fefdb6e3998fc
Author: Afif Elghraoui <afif at ghraoui.name>
Date: Sun Jul 17 20:38:34 2016 -0700
Switch manpage building back to asciidoctor
asciidoctor has been backported to Jessie, so
we can reduce the delta with the version of spades in Stretch.
---
debian/control | 2 +-
.../man_src/{dipspades.1.ronn => dipspades.1.adoc} | 101 ++++++++++----------
debian/man_src/{spades.1.ronn => spades.1.adoc} | 103 +++++++++++----------
.../man_src/{truspades.1.ronn => truspades.1.adoc} | 27 +++---
debian/rules | 2 +-
5 files changed, 122 insertions(+), 113 deletions(-)
diff --git a/debian/control b/debian/control
index f4763fb..e02d81e 100644
--- a/debian/control
+++ b/debian/control
@@ -21,7 +21,7 @@ Build-Depends: debhelper (>= 9),
libssw-dev,
python-yaml,
python-joblib,
- ruby-ronn,
+ asciidoctor (>= 1.5.3),
bwa,
lynx
Standards-Version: 3.9.8
diff --git a/debian/man_src/dipspades.1.ronn b/debian/man_src/dipspades.1.adoc
similarity index 71%
rename from debian/man_src/dipspades.1.ronn
rename to debian/man_src/dipspades.1.adoc
index c2fc846..a81aac3 100644
--- a/debian/man_src/dipspades.1.ronn
+++ b/debian/man_src/dipspades.1.adoc
@@ -1,13 +1,16 @@
-dipspades(1) -- diploid genome assembler
-========================================
+= dipspades(1)
+
+## NAME
+
+dipspades - diploid genome assembler
## SYNOPSIS
-`dipspades` [options] -o <output_dir>
+*dipspades* [options] -o <output_dir>
## DESCRIPTION
-`dipspades` is the main executable for the **dipSPAdes** software, a genome
+*dipspades* is the main executable for the **dipSPAdes** software, a genome
assembler designed for diploid genomes with a high heterozygosity rate. It
assembles genomic reads given to it and places the resulting assembly in
<output_dir>.
@@ -16,116 +19,116 @@ assembles genomic reads given to it and places the resulting assembly in
### Basic options
- * `-o` <output_dir>:
+*-o* <output_dir>::
directory to store all the resulting files (required)
- * `--iontorrent`:
+*--iontorrent*::
this flag is required for IonTorrent data
- * `--test`:
+*--test*::
runs dipSPAdes on toy dataset
- * `-h`/`--help`:
+*-h*/*--help*::
prints this usage message
### Input data
- * `--12` <filename>:
+*--12* <filename>::
file with interlaced forward and reverse paired-end reads
- * `-1` <filename>:
+*-1* <filename>::
file with forward paired-end reads
- * `-2` <filename>:
+*-2* <filename>::
file with reverse paired-end reads
- * `-s` <filename>:
+*-s* <filename>::
file with unpaired reads
- * `--pe<#>-12` <filename>:
+*--pe<#>-12* <filename>::
file with interlaced reads for paired-end library number <#> (<#> = 1,2,3,4,5)
- * `--pe<#>-1` <filename>:
+*--pe<#>-1* <filename>::
file with forward reads for paired-end library number <#> (<#> = 1,2,3,4,5)
- * `--pe<#>-2` <filename>:
+*--pe<#>-2* <filename>::
file with reverse reads for paired-end library number <#> (<#> = 1,2,3,4,5)
- * `--pe<#>-s` <filename>:
+*--pe<#>-s* <filename>::
file with unpaired reads for paired-end library number <#> (<#> = 1,2,3,4,5)
- * `--pe<#>-<or>`:
+*--pe<#>-<or>*::
orientation of reads for paired-end library number <#> (<#> = 1,2,3,4,5; <or> = fr, rf, ff)
- * `--s<#>` <filename>:
+*--s<#>* <filename>::
file with unpaired reads for single reads library number <#> (<#> = 1,2,3,4,5)
- * `--mp<#>-12` <filename>:
+*--mp<#>-12* <filename>::
file with interlaced reads for mate-pair library number <#> (<#> = 1,2,3,4,5)
- * `--mp<#>-1` <filename>:
+*--mp<#>-1* <filename>::
file with forward reads for mate-pair library number <#> (<#> = 1,2,3,4,5)
- * `--mp<#>-2` <filename>:
+*--mp<#>-2* <filename>::
file with reverse reads for mate-pair library number <#> (<#> = 1,2,3,4,5)
- * `--mp<#>-s` <filename>:
+*--mp<#>-s* <filename>::
file with unpaired reads for mate-pair library number <#> (<#> = 1,2,3,4,5)
- * `--mp<#>-<or>`:
+*--mp<#>-<or>*::
orientation of reads for mate-pair library number <#> (<#> = 1,2,3,4,5; <or> = fr, rf, ff)
- * `--hqmp<#>-12` <filename>:
+*--hqmp<#>-12* <filename>::
file with interlaced reads for high-quality mate-pair library number <#> (<#> = 1,2,3,4,5)
- * `--hqmp<#>-1` <filename>:
+*--hqmp<#>-1* <filename>::
file with forward reads for high-quality mate-pair library number <#> (<#> = 1,2,3,4,5)
- * `--hqmp<#>-2` <filename>:
+*--hqmp<#>-2* <filename>::
file with reverse reads for high-quality mate-pair library number <#> (<#> = 1,2,3,4,5)
- * `--hqmp<#>-s` <filename>:
+*--hqmp<#>-s* <filename>::
file with unpaired reads for high-quality mate-pair library number <#> (<#> = 1,2,3,4,5)
- * `--hqmp<#>-<or>`:
+*--hqmp<#>-<or>*::
orientation of reads for high-quality mate-pair library number <#> (<#> = 1,2,3,4,5; <or> = fr, rf, ff)
- * `--nxmate<#>-1` <filename>:
+*--nxmate<#>-1* <filename>::
file with forward reads for Lucigen NxMate library number <#> (<#> = 1,2,3,4,5)
- * `--nxmate<#>-2` <filename>:
+*--nxmate<#>-2* <filename>::
file with reverse reads for Lucigen NxMate library number <#> (<#> = 1,2,3,4,5)
- * `--sanger` <filename>:
+*--sanger* <filename>::
file with Sanger reads
- * `--pacbio` <filename>:
+*--pacbio* <filename>::
file with PacBio reads
- * `--nanopore` <filename>:
+*--nanopore* <filename>::
file with Nanopore reads
- * `--trusted-contigs` <filename>:
+*--trusted-contigs* <filename>::
file with trusted contigs
- * `--untrusted-contigs` <filename>:
+*--untrusted-contigs* <filename>::
file with untrusted contigs
### Input haplocontigs
- * `--hap` <filename>:
+*--hap* <filename>::
file with haplocontigs
### Pipeline options
- * `--only-assembler`:
+*--only-assembler*::
runs only assembling (without read error correction)
- * `--disable-gzip-output`:
+*--disable-gzip-output*::
forces error correction not to compress the corrected reads
- * `--disable-rr`:
+*--disable-rr*::
disables repeat resolution stage of assembling
### dipSPAdes options
- * `--expect-gaps`:
+*--expect-gaps*::
indicates that significant number of gaps in coverage is expected
- * `--expect-rearrangements`:
+*--expect-rearrangements*::
indicates that significant number of rearrangements between haplomes of diploid genome is expected
- * `--hap-assembly`:
+*--hap-assembly*::
enables haplotype assembly phase
### Advanced options
- * `--dataset` <filename>:
+*--dataset* <filename>::
file with dataset description in YAML format
- * `-t`/`--threads` <int>:
+*-t*/*--threads* <int>::
number of threads [default: 16]
- * `-m`/`--memory` <int>:
+*-m*/*--memory* <int>::
RAM limit for SPAdes in Gb (terminates if exceeded) [default: 250]
- * `--tmp-dir` <dirname>:
+*--tmp-dir* <dirname>::
directory for temporary files [default: <output_dir>/tmp]
- * `-k` <int,int,...>:
+*-k* <int,int,...>::
comma-separated list of k-mer sizes (must be odd and less than 128) [default: 'auto']
- * `--cov-cutoff` <float>:
+*--cov-cutoff* <float>::
coverage cutoff value (a positive float number, or 'auto', or 'off') [default: 'off']
- * `--phred-offset` <33 or 64>:
+*--phred-offset* <33 or 64>::
PHRED quality offset in the input reads (33 or 64) [default: auto-detect]
diff --git a/debian/man_src/spades.1.ronn b/debian/man_src/spades.1.adoc
similarity index 71%
rename from debian/man_src/spades.1.ronn
rename to debian/man_src/spades.1.adoc
index adacdce..111dc93 100644
--- a/debian/man_src/spades.1.ronn
+++ b/debian/man_src/spades.1.adoc
@@ -1,13 +1,16 @@
-spades(1) -- SPAdes genome assembler
-====================================
+= spades(1)
+
+## NAME
+
+spades - SPAdes genome assembler
## SYNOPSIS
-`spades` [options] -o <output_dir>
+*spades* [options] -o <output_dir>
## DESCRIPTION
-`spades` is the main executable for the **SPAdes** software. It
+*spades* is the main executable for the **SPAdes** software. It
assembles genomic reads given to it and places the resulting assembly in
<output_dir>.
@@ -15,10 +18,10 @@ assembles genomic reads given to it and places the resulting assembly in
### Basic options
- * `-o` <output_dir>:
+*-o* <output_dir>::
directory to store all the resulting files (required)
- * `--sc`:
+*--sc*::
this flag is required for MDA (single-cell) data
* `--meta`:
@@ -27,108 +30,108 @@ assembles genomic reads given to it and places the resulting assembly in
* `--plasmid`:
Runs plasmidSPAdes pipeline for plasmid detection
- * `--iontorrent`:
+*--iontorrent*::
this flag is required for IonTorrent data
- * `--test`:
+*--test*::
runs SPAdes on toy dataset
- * `-h`/`--help`:
+*-h*/*--help*::
prints this usage message
### Input data
- * `--12` <filename>:
+*--12* <filename>::
file with interlaced forward and reverse paired-end reads
- * `-1` <filename>:
+*-1* <filename>::
file with forward paired-end reads
- * `-2` <filename>:
+*-2* <filename>::
file with reverse paired-end reads
- * `-s` <filename>:
+*-s* <filename>::
file with unpaired reads
- * `--pe<#>-12` <filename>:
+*--pe<#>-12* <filename>::
file with interlaced reads for paired-end library number <#> (<#> = 1,2,3,4,5)
- * `--pe<#>-1` <filename>:
+*--pe<#>-1* <filename>::
file with forward reads for paired-end library number <#> (<#> = 1,2,3,4,5)
- * `--pe<#>-2` <filename>:
+*--pe<#>-2* <filename>::
file with reverse reads for paired-end library number <#> (<#> = 1,2,3,4,5)
- * `--pe<#>-s` <filename>:
+*--pe<#>-s* <filename>::
file with unpaired reads for paired-end library number <#> (<#> = 1,2,3,4,5)
- * `--pe<#>-<or>`:
+*--pe<#>-<or>*::
orientation of reads for paired-end library number <#> (<#> = 1,2,3,4,5; <or> = fr, rf, ff)
- * `--s<#>` <filename>:
+*--s<#>* <filename>::
file with unpaired reads for single reads library number <#> (<#> = 1,2,3,4,5)
- * `--mp<#>-12` <filename>:
+*--mp<#>-12* <filename>::
file with interlaced reads for mate-pair library number <#> (<#> = 1,2,3,4,5)
- * `--mp<#>-1` <filename>:
+*--mp<#>-1* <filename>::
file with forward reads for mate-pair library number <#> (<#> = 1,2,3,4,5)
- * `--mp<#>-2` <filename>:
+*--mp<#>-2* <filename>::
file with reverse reads for mate-pair library number <#> (<#> = 1,2,3,4,5)
- * `--mp<#>-s` <filename>:
+*--mp<#>-s* <filename>::
file with unpaired reads for mate-pair library number <#> (<#> = 1,2,3,4,5)
- * `--mp<#>-<or>`:
+*--mp<#>-<or>*::
orientation of reads for mate-pair library number <#> (<#> = 1,2,3,4,5; <or> = fr, rf, ff)
- * `--hqmp<#>-12` <filename>:
+*--hqmp<#>-12* <filename>::
file with interlaced reads for high-quality mate-pair library number <#> (<#> = 1,2,3,4,5)
- * `--hqmp<#>-1` <filename>:
+*--hqmp<#>-1* <filename>::
file with forward reads for high-quality mate-pair library number <#> (<#> = 1,2,3,4,5)
- * `--hqmp<#>-2` <filename>:
+*--hqmp<#>-2* <filename>::
file with reverse reads for high-quality mate-pair library number <#> (<#> = 1,2,3,4,5)
- * `--hqmp<#>-s` <filename>:
+*--hqmp<#>-s* <filename>::
file with unpaired reads for high-quality mate-pair library number <#> (<#> = 1,2,3,4,5)
- * `--hqmp<#>-<or>`:
+*--hqmp<#>-<or>*::
orientation of reads for high-quality mate-pair library number <#> (<#> = 1,2,3,4,5; <or> = fr, rf, ff)
- * `--nxmate<#>-1` <filename>:
+*--nxmate<#>-1* <filename>::
file with forward reads for Lucigen NxMate library number <#> (<#> = 1,2,3,4,5)
- * `--nxmate<#>-2` <filename>:
+*--nxmate<#>-2* <filename>::
file with reverse reads for Lucigen NxMate library number <#> (<#> = 1,2,3,4,5)
- * `--sanger` <filename>:
+*--sanger* <filename>::
file with Sanger reads
- * `--pacbio` <filename>:
+*--pacbio* <filename>::
file with PacBio reads
- * `--nanopore` <filename>:
+*--nanopore* <filename>::
file with Nanopore reads
- * `--trusted-contigs` <filename>:
+*--trusted-contigs* <filename>::
file with trusted contigs
- * `--untrusted-contigs` <filename>:
+*--untrusted-contigs* <filename>::
file with untrusted contigs
### Pipeline options
- * `--only-error-correction`:
+*--only-error-correction*::
runs only read error correction (without assembling)
- * `--only-assembler`:
+*--only-assembler*::
runs only assembling (without read error correction)
- * `--careful`:
+*--careful*::
tries to reduce number of mismatches and short indels
- * `--continue`:
+*--continue*::
continue run from the last available check-point
- * `--restart-from` <cp>:
+*--restart-from* <cp>::
restart run with updated options and from the specified check-point ('ec', 'as', 'k<int>', 'mc')
- * `--disable-gzip-output`:
+*--disable-gzip-output*::
forces error correction not to compress the corrected reads
- * `--disable-rr`:
+*--disable-rr*::
disables repeat resolution stage of assembling
### Advanced options
- * `--dataset` <filename>:
+*--dataset* <filename>::
file with dataset description in YAML format
- * `-t`/`--threads` <int>:
+*-t*/*--threads* <int>::
number of threads [default: 16]
- * `-m`/`--memory` <int>:
+*-m*/*--memory* <int>::
RAM limit for SPAdes in Gb (terminates if exceeded) [default: 250]
- * `--tmp-dir` <dirname>:
+*--tmp-dir* <dirname>::
directory for temporary files [default: <output_dir>/tmp]
- * `-k` <int,int,...>:
+*-k* <int,int,...>::
comma-separated list of k-mer sizes (must be odd and less than 128) [default: 'auto']
- * `--cov-cutoff` <float>:
+*--cov-cutoff* <float>::
coverage cutoff value (a positive float number, or 'auto', or 'off') [default: 'off']
- * `--phred-offset` <33 or 64>:
+*--phred-offset* <33 or 64>::
PHRED quality offset in the input reads (33 or 64) [default: auto-detect]
diff --git a/debian/man_src/truspades.1.ronn b/debian/man_src/truspades.1.adoc
similarity index 61%
rename from debian/man_src/truspades.1.ronn
rename to debian/man_src/truspades.1.adoc
index ac4b443..ebe8699 100644
--- a/debian/man_src/truspades.1.ronn
+++ b/debian/man_src/truspades.1.adoc
@@ -1,13 +1,16 @@
-truspades(1) -- truSPAdes genome assembler
-==========================================
+= truspades(1)
+
+## NAME
+
+truspades - truSPAdes genome assembler
## SYNOPSIS
-`truspades` [options] -o <output_dir>
+*truspades* [options] -o <output_dir>
## DESCRIPTION
-`truspades` is the main executable for the **truSPAdes** software. It
+*truspades* is the main executable for the **truSPAdes** software. It
assembles genomic reads given to it and places the resulting assembly in
<output_dir>.
@@ -15,28 +18,28 @@ assembles genomic reads given to it and places the resulting assembly in
### Basic options
- * `-o` <output_dir>:
+*-o* <output_dir>::
directory to store all the resulting files (required)
- * `--test`:
+*--test*::
runs truSPAdes on toy dataset
- * `-h`/`--help`:
+*-h*/*--help*::
prints this usage message
- * `-t`/`--threads` <int>:
+*-t*/*--threads* <int>::
number of threads
- * `--continue`:
+*--continue*::
continue interrupted launch
- * `--construct-dataset`:
+*--construct-dataset*::
parse dataset from input folder
### Input options
- * `--input-dir` <directory>:
+*--input-dir* <directory>::
directory with input data. Note that the directory should contain only files with reads. This option can be used several times to provide several input directories.
- * `--dataset` <file>:
+*--dataset* <file>:w:
file with dataset description
diff --git a/debian/rules b/debian/rules
index ab730c2..756b4b7 100755
--- a/debian/rules
+++ b/debian/rules
@@ -47,7 +47,7 @@ override_dh_auto_build:
override_dh_installman:
mkdir -p $(mandir)
- ronn $(debfolder)/man_src/*.ronn
+ asciidoctor -a docdate='' -b manpage $(debfolder)/man_src/*.adoc
cp $(debfolder)/man_src/*.? $(mandir)
dh_installman --
--
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