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 <[email protected]> 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 -- -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/spades.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
