This is an automated email from the git hooks/post-receive script. daube-guest pushed a commit to branch master in repository scythe.
commit a81c6001b5e8b551bdb928fc8b611b130bb01709 Author: Kevin Murray <[email protected]> Date: Mon May 11 17:19:32 2015 +1000 Remove RONN generation of scythe.1 manpage --- debian/control | 1 - debian/rules | 1 - debian/scythe.1.ronn | 39 --------------------------------------- 3 files changed, 41 deletions(-) diff --git a/debian/control b/debian/control index 1fbfe01..9b87b18 100644 --- a/debian/control +++ b/debian/control @@ -6,7 +6,6 @@ Priority: optional Build-Depends: debhelper (>= 9), zlib1g-dev, python-markdown, - ruby-ronn, check Standards-Version: 3.9.6 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/scythe.git diff --git a/debian/rules b/debian/rules index 65aa80d..579ce2b 100755 --- a/debian/rules +++ b/debian/rules @@ -7,7 +7,6 @@ include /usr/share/dpkg/buildflags.mk override_dh_auto_build: dh_auto_build - ronn -r --manual=scythe --organization='Vince Buffalo' debian/scythe.1.ronn markdown_py -f README.html README.md get-orig-source: diff --git a/debian/scythe.1.ronn b/debian/scythe.1.ronn deleted file mode 100644 index a0b03cc..0000000 --- a/debian/scythe.1.ronn +++ /dev/null @@ -1,39 +0,0 @@ -scythe(1) -- Bayesian adaptor trimmer -===================================== - - -## SYNOPSIS - - scythe -t sanger -a /path/to/adaptors.fasta [options] <sequences.fastq.gz> - - - Trim 3'-end adapter contaminants off sequence files. If no output file - is specified, scythe will use stdout. - -## USAGE - - -p, --prior prior (default: 0.300) - -q, --quality-type quality type, either illumina, solexa, or sanger (default: sanger) - -m, --matches-file matches file (default: no output) - -o, --output-file output trimmed sequences file (default: stdout) - -t, --tag add a tag to the header indicating Scythe cut a sequence (default: off) - -n, --min-match smallest contaminant to consider (default: 5) - -M, --min-keep filter sequnces less than or equal to this length (default: 35) - --quiet don't output statistics about trimming to stdout (default: off) - --help display this help and exit - --version output version information and exit - - Information on quality schemes: - phred PHRED quality scores (e.g. from Roche 454). ASCII with no offset, range: [4, 60]. - sanger Sanger are PHRED ASCII qualities with an offset of 33, range: [0, 93]. From - NCBI SRA, or Illumina pipeline 1.8+. - solexa Solexa (also very early Illumina - pipeline < 1.3). ASCII offset of - 64, range: [-5, 62]. Uses a different quality-to-probabilities conversion than other - schemes. - illumina Illumina output from pipeline versions between 1.3 and 1.7. ASCII offset of 64, - range: [0, 62] - -## AUTHOR - -Vince Bufflo wrote scythe itself, while Kevin Murray made this man page and the -Debian package -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/scythe.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
