[med-svn] [snpomatic] 01/02: fix manpage building
Sascha Steinbiss
sascha at steinbiss.name
Thu Mar 10 07:30:58 UTC 2016
This is an automated email from the git hooks/post-receive script.
sascha-guest pushed a commit to branch master
in repository snpomatic.
commit 3f39243a65302e285169a12571d4b7fbf4142906
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date: Wed Mar 9 23:11:50 2016 +0000
fix manpage building
---
debian/changelog | 8 ++
debian/control | 2 +-
.../{findknownsnps.1.ronn => findknownsnps.1.adoc} | 115 +++++++++++----------
debian/rules | 5 +-
4 files changed, 72 insertions(+), 58 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index 7981db3..5a5bb1e 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,11 @@
+snpomatic (1.0-3) unstable; urgency=medium
+
+ * Fix locale in attempt to ensure reproducible manpages.
+ * Switch to asciidoctor instead of ronn, which is unsupported
+ upstream and fails on some archs.
+
+ -- Sascha Steinbiss <sascha at steinbiss.name> Wed, 09 Mar 2016 23:10:54 +0000
+
snpomatic (1.0-2) unstable; urgency=medium
* Make manpage generation reproducible.
diff --git a/debian/control b/debian/control
index 26671be..d941ede 100644
--- a/debian/control
+++ b/debian/control
@@ -4,7 +4,7 @@ Uploaders: Sascha Steinbiss <sascha at steinbiss.name>
Section: science
Priority: optional
Build-Depends: debhelper (>= 9),
- ruby-ronn,
+ asciidoctor,
antiword
Standards-Version: 3.9.7
Testsuite: autopkgtest
diff --git a/debian/findknownsnps.1.ronn b/debian/findknownsnps.1.adoc
similarity index 72%
rename from debian/findknownsnps.1.ronn
rename to debian/findknownsnps.1.adoc
index 43e6507..b108b0b 100644
--- a/debian/findknownsnps.1.ronn
+++ b/debian/findknownsnps.1.adoc
@@ -1,167 +1,174 @@
-findknownsnps(1) -- main executable for snpomatic
-=================================================
+= findknownsnps(1)
+:doctype: manpage
+:man manual: SNP-o-matic Manual
+:man source: SNP-o-matic 1.0
+:page-layout: base
-## SYNOPSIS
+== NAME
-`findknownsnps` <options>
+findknownsnps - main executable for snpomatic
-## DESCRIPTION
+== SYNOPSIS
+
+*findknownsnps* <options>
+
+== DESCRIPTION
findknownsnps is the main executable for the **snpomatic** software.
-## OPTIONS
+== OPTIONS
These options control whether output is written to file(s), standard output, or
directly to a man pager.
- * `--genome=GENOME_FILE`:
- FASTA file with chromosomes (mandatory)
+ *--genome=GENOME_FILE*::
+ FASTA file with chromosomes (mandatory)
- * `--fasta=FASTA_FILE`:
+ *--fasta=FASTA_FILE*::
FASTA file with Solexa reads (mandatory, except when --fastq or --index is
used)
- * `--fasta=FASTA_FILE`:
+ *--fasta=FASTA_FILE*::
FASTA file with Solexa reads (mandatory, except when --fastq or --index is
used)
- * `--fastq=FASTQ_FILE`:
+ *--fastq=FASTQ_FILE*::
FASTQ file with Solexa reads (mandatory, except when --fasta or --index is
used)
- * `--fastq2=FASTQ_FILE2`:
+ *--fastq2=FASTQ_FILE2*::
FASTQ file with Solexa reads (optional; read mate)
- * `--nono=FILENAME`:
+ *--nono=FILENAME*::
File with list of read names (!) to ignore (optional)
- * `--regions=REGION_FILE`:
+ *--regions=REGION_FILE*::
Region file for finding new SNPs (optional) [DEPRECATED]
- * `--snps=SNP_FILE`:
+ *--snps=SNP_FILE*::
Simple SNP file (optional)
- * `--gff=GFF_FILE`:
+ *--gff=GFF_FILE*::
GFF file with SNPs (optional)
- * `--uniqueness=FILE`:
+ *--uniqueness=FILE*::
Output a uniqueness data file for the reference; no Solexa reads needed;
- implies `--noshortcuts` (optional)
+ implies--noshortcuts` (optional)
- * `--pileup=FILE`:
+ *--pileup=FILE*::
Outputs complete pileup into that file (optional)
- * `--cigar=FILE`:
+ *--cigar=FILE*::
Outputs alignment in CIGAR format (optional)
- * `--gffout=FILE`:
+ *--gffout=FILE*::
Outputs reads in GFF format (optional)
- * `--coverage=FILENAME`:
+ *--coverage=FILENAME*::
Outputs (high depth) coverage data (optional)
- * `--wobble=FILENAME`:
+ *--wobble=FILENAME*::
Outputs a list of possible variations (optional; paired reads only)
[UNDER CONSTRUCTION]
- * `--fragmentplot=FILENAME`:
+ *--fragmentplot=FILENAME*::
Outputs a plot of fragment size distribution to a file (optional)
- * `--snpsinreads=FILENAME`:
+ *--snpsinreads=FILENAME*::
Outputs a list of reads containing known SNPs to a file (optional)
- * `--indelplot=FILENAME`:
+ *--indelplot=FILENAME*::
Outputs indel data to a file (optional)
- * `--inversions=FILENAME`:
+ *--inversions=FILENAME*::
For paired reads, writes read matches indicating inversions into a file (optional)
- * `--faceaway=FILENAME`:
+ *--faceaway=FILENAME*::
For paired reads, writes read matches that "face away" from each other into a file (optional)
- * `--sqlite=FILENAME`:
+ *--sqlite=FILENAME*::
Creates a sqlite text file with alignment data [EXPERIMENTAL] (optional)
- * `--sam=FILENAME`:
+ *--sam=FILENAME*::
Creates a SAM alignment file (optional)
- * `--spancontigs=FILENAME`:
+ *--spancontigs=FILENAME*::
Outputs read pairs where "half" reads map uniquely to different
contigs (optional)
- * `--bins=FILE_PREFIX`:
+ *--bins=FILE_PREFIX*::
Outputs no-match, single-match and multi-match Solexa reads into prefixed
files (optional)
- * `--binmask=MASK`:
+ *--binmask=MASK*::
Mask of 1s and 0s to turn off individual bins. Order: No match, single
match, multi-match, IUPAC. Example: 0100 creates only single-match bin.
(optional; default:1111)
- * `--pair=NUMBER`:
+ *--pair=NUMBER*::
For paired reads, the length of the first part of the read (mandatory for
paired reads)
- * `--fragment=NUMBER`:
+ *--fragment=NUMBER*::
For paired reads, the average fragment length (mandatory for paired reads)
- * `--variance=NUMBER`:
+ *--variance=NUMBER*::
For paired reads, the variance of the fragment length to either side (optional; default: 1/4 of fragment size)
- * `--wobblemax=NUMBER`:
+ *--wobblemax=NUMBER*::
Maximum number of mismatches for wobble (optional; default 2; see --wobble)
- * `--mspi=NUMBER`:
+ *--mspi=NUMBER*::
Maximum number of SNPs per chromosomal index (optional; default:8)
- * `--index=FILENAME`:
+ *--index=FILENAME*::
Index filename (index will be created if it does not exist; optional)
- * `--noshortcuts`:
+ *--noshortcuts*::
Will process all chrososomal regions, even those with lots'o'repeats (optional;
no value)
- * `--snpsonly`:
+ *--snpsonly*::
Only lists found SNPs in the pileup (optional; no value)
- * `--chromosome=NAME`:
+ *--chromosome=NAME*::
Discards all chromosomes but NAME prior to run (optional)
- * `--index_from=NUMBER`:
+ *--index_from=NUMBER*::
Starts indexing at this position on all chromosomes (optional)
- * `--index_to=NUMBER`:
+ *--index_to=NUMBER*::
Stops indexing at this position on all chromosomes (optional)
- * `--chop=NUMBER`:
+ *--chop=NUMBER*::
For paired reads, if one but not the other matches, shorten the other by
- `NUMBER` bases (optional)
+ NUMBER` bases (optional)
- * `--index1=NUMBER` :
+ *--index1=NUMBER`*::
Length of internal index 1 (optional; default:10)
- * `--index2=NUMBER`:
+ *--index2=NUMBER*::
Length of internal index 2 (optional; default:16)
- * `--memory_save=NUMBER`:
+ *--memory_save=NUMBER*::
Indexes the genome every NUMBER of positions; saves memory and runtime, but
can have strange side effects (optional)
- * `--multimatch`:
+ *--multimatch*::
Puts a multiple-matching read to a random position (optional) [currently
paired reads only]
- * `--singlematch`:
+ *--singlematch*::
Only performs additional output functions for single matches (optional)
[currently paired reads only]
- * `--foum`:
+ *--foum*::
For paired reads, at least one read has to match uniquely in the genome
(force one unique match) (optional)
- * `--mismatch`:
+ *--mismatch*::
The number of mismatches allowed outside the index (index1+index2)
(optional)
- * `--rpa=FILENAME`:
+ *--rpa=FILENAME*::
Writes all read pair alignments into a file (optional)
diff --git a/debian/rules b/debian/rules
index 5f97697..261bd6e 100755
--- a/debian/rules
+++ b/debian/rules
@@ -4,9 +4,8 @@ export DH_VERBOSE := 1
mandir := $(CURDIR)/debian/man
debfolder := $(CURDIR)/debian
-DATE := $(shell dpkg-parsechangelog -S Date)
-SHORTDATE := $(shell date -d '$(DATE)' +%Y-%m-%d)
export LC_ALL=C
+SHORTDATE := $(shell LC_ALL=C date -d "$$(dpkg-parsechangelog -SDate)" +%Y-%m-%d)
%:
dh $@
@@ -36,5 +35,5 @@ override_dh_auto_install:
#cp ungap $(debfolder)/snpomatic/usr/bin
override_dh_installman:
- ronn --date=$(SHORTDATE) debian/findknownsnps.1.ronn
+ asciidoctor -a docdate=$(SHORTDATE) -b manpage debian/findknownsnps.1.adoc
dh_installman --
--
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