This is an automated email from the git hooks/post-receive script. sascha-guest pushed a commit to branch master in repository ariba.
commit 46d486eb9e1e12416911aaaa244cdf665acf02f4 Author: Sascha Steinbiss <[email protected]> Date: Sun May 29 12:01:16 2016 +0000 complete manpage building --- debian/ariba.1.adoc | 48 +++++++++++++++++++++++++++++++++++++++++++++++ debian/control | 10 ++++++---- debian/extra-man-info.txt | 7 +++++++ debian/rules | 13 ++++++------- 4 files changed, 67 insertions(+), 11 deletions(-) diff --git a/debian/ariba.1.adoc b/debian/ariba.1.adoc new file mode 100644 index 0000000..425220c --- /dev/null +++ b/debian/ariba.1.adoc @@ -0,0 +1,48 @@ += ariba(1) + +== NAME + +ariba - Antibiotic Resistance Identification By Assembly + +## SYNOPSIS + +*ariba* <task> [options] + +## DESCRIPTION + +*ariba* is the main executable for the **ARIBA** software. The actual +functionality is provided by the subtools: + +*getref*:: + download reference data + +*prepareref*:: + prepare reference data for running the pipeline + +*run*:: + run the ARIBA local assembly pipeline + +*reportfilter*:: + Filter report.tsv file + +*summary*:: + summarise multiple reports made by "run" + +*flag*:: + translate the meaning of a flag output by the pipeline + +*aln2meta*:: + make metadata input to preparef, using multialignment and SNPs + +*test*:: + run on small test dataset + +*version*:: + print version and exit + +## SEE ALSO + +All subtools of ARIBA have their own respective manpages: + +ariba-aln2meta(1), ariba-flag(1), ariba-getref(1), ariba-prepareref(1), +ariba-reportfilter(1), ariba-run(1), ariba-summary(1), ariba-test(1) diff --git a/debian/control b/debian/control index c474bf7..b5c597d 100644 --- a/debian/control +++ b/debian/control @@ -13,14 +13,16 @@ Build-Depends: debhelper (>= 9), python3-lxml, bowtie2 (>= 2.1.0), r-cran-ape, - cd-hit, - samtools (>= 1.2), + cd-hit, + samtools (>= 1.2), bcftools (>= 1.2), - mummer, + mummer, spades, fastaq (>= 3.10.0), - help2man + help2man, + asciidoctor Standards-Version: 3.9.8 +Testsuite: autopkgtest Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/ariba.git Vcs-Git: https://anonscm.debian.org/git/debian-med/ariba.git Homepage: https://github.com/sanger-pathogens/ariba diff --git a/debian/extra-man-info.txt b/debian/extra-man-info.txt index 16ac644..a28db51 100644 --- a/debian/extra-man-info.txt +++ b/debian/extra-man-info.txt @@ -9,3 +9,10 @@ https://github.com/sanger-pathogens/ariba/wiki This tool is developed and maintained by the Pathogen Informatics group at the Wellcome Trust Sanger Institute under the GNU General Public License, version 3. + +[SEE ALSO] + +All subtools of ARIBA have their own respective manpages: + +ariba-aln2meta(1), ariba-flag(1), ariba-getref(1), ariba-prepareref(1), +ariba-reportfilter(1), ariba-run(1), ariba-summary(1), ariba-test(1), ariba(1) diff --git a/debian/rules b/debian/rules index 7f2af08..a0961ce 100755 --- a/debian/rules +++ b/debian/rules @@ -4,19 +4,18 @@ export PYBUILD_NAME=ariba mandir := $(CURDIR)/debian/man debfolder := $(CURDIR)/debian -ARIBA_VERSION := $(shell grep -Po "(?<=version=')([0-9.]+)" setup.py) %: dh $@ --with python3 --buildsystem=pybuild +override_dh_auto_clean: + rm -rf $(mandir) + dh_auto_clean -- + override_dh_installman: mkdir -p $(mandir) - PYTHONPATH=. help2man -N -o debian/man/ariba.1 \ - -n 'Antibiotic Resistance Identification by Assembly' \ - --no-discard-stderr \ - --version-string="$(ARIBA_VERSION)" scripts/ariba - sed -i 's/.SH DESCRIPTION/.SH DESCRIPTION\\n/' $(mandir)/ariba.1 - scripts/ariba 2>&1 | tail -n +13 | head -n 12 | debian/make_man + asciidoctor -a docdate='' -b manpage -o $(mandir)/ariba.1 $(debfolder)/ariba.1.adoc + PYTHONPATH=. scripts/ariba 2>&1 | tail -n +13 | head -n 12 | $(debfolder)/make_man dh_installman -- override_dh_auto_test: -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/ariba.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
