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commit 3f39243a65302e285169a12571d4b7fbf4142906 Author: Sascha Steinbiss <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 -- -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/snpomatic.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
