[med-svn] [spades] 01/02: Revert "switch manpage building to asciidoctor"
Afif Elghraoui
afif at moszumanska.debian.org
Thu Mar 31 08:58:09 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 99dfb97bdf0506157bdc2d1a2237376444c0084d
Author: Afif Elghraoui <afif at ghraoui.name>
Date: Thu Mar 31 00:25:05 2016 -0700
Revert "switch manpage building to asciidoctor"
This reverts commit 6d53a34c5fbb818defa6e4e088d6b0138998b3b1.
jessie does not have a recent enough version of asciidoctor to
be able to generate the manpages. Until it's built for backports,
we'll switch back to using ronn.
---
debian/control | 2 +-
.../man_src/{dipspades.1.adoc => dipspades.1.ronn} | 101 ++++++++++----------
debian/man_src/{spades.1.adoc => spades.1.ronn} | 103 ++++++++++-----------
.../man_src/{truspades.1.adoc => truspades.1.ronn} | 27 +++---
debian/rules | 2 +-
5 files changed, 113 insertions(+), 122 deletions(-)
diff --git a/debian/control b/debian/control
index b01ce55..463cc16 100644
--- a/debian/control
+++ b/debian/control
@@ -18,7 +18,7 @@ Build-Depends: debhelper (>= 9),
libhts-dev,
python-yaml,
python-joblib,
- asciidoctor,
+ ruby-ronn,
bwa,
lynx
Standards-Version: 3.9.7
diff --git a/debian/man_src/dipspades.1.adoc b/debian/man_src/dipspades.1.ronn
similarity index 71%
rename from debian/man_src/dipspades.1.adoc
rename to debian/man_src/dipspades.1.ronn
index a81aac3..c2fc846 100644
--- a/debian/man_src/dipspades.1.adoc
+++ b/debian/man_src/dipspades.1.ronn
@@ -1,16 +1,13 @@
-= dipspades(1)
-
-## NAME
-
-dipspades - diploid genome assembler
+dipspades(1) -- 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>.
@@ -19,116 +16,116 @@ 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.adoc b/debian/man_src/spades.1.ronn
similarity index 70%
rename from debian/man_src/spades.1.adoc
rename to debian/man_src/spades.1.ronn
index 315a8a6..71adcf9 100644
--- a/debian/man_src/spades.1.adoc
+++ b/debian/man_src/spades.1.ronn
@@ -1,16 +1,13 @@
-= spades(1)
-
-## NAME
-
-spades - SPAdes genome assembler
+spades(1) -- 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>.
@@ -18,114 +15,114 @@ 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
-*--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.adoc b/debian/man_src/truspades.1.ronn
similarity index 61%
rename from debian/man_src/truspades.1.adoc
rename to debian/man_src/truspades.1.ronn
index ebe8699..ac4b443 100644
--- a/debian/man_src/truspades.1.adoc
+++ b/debian/man_src/truspades.1.ronn
@@ -1,16 +1,13 @@
-= truspades(1)
-
-## NAME
-
-truspades - truSPAdes genome assembler
+truspades(1) -- 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>.
@@ -18,28 +15,28 @@ 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>:w:
+ * `--dataset` <file>:
file with dataset description
diff --git a/debian/rules b/debian/rules
index 3a6b0c7..5b6301e 100755
--- a/debian/rules
+++ b/debian/rules
@@ -46,7 +46,7 @@ override_dh_auto_build:
override_dh_installman:
mkdir -p $(mandir)
- asciidoctor -a docdate='' -b manpage $(debfolder)/man_src/*.adoc
+ ronn $(debfolder)/man_src/*.ronn
cp $(debfolder)/man_src/*.? $(mandir)
dh_installman --
--
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