Andreas Tille pushed to branch master at Debian Med / pilon-non-free
Commits: 9f715bf8 by Andreas Tille at 2018-06-12T14:43:17+02:00 Typo - - - - - 52c96edc by Andreas Tille at 2018-07-16T16:26:40+02:00 Document bug that is responsible why we can not build pilon - - - - - 97d870df by Andreas Tille at 2018-07-16T16:46:15+02:00 Upload to new - - - - - 5 changed files: - debian/changelog - debian/control - debian/copyright - debian/createmanpages - debian/pilon.1 Changes: ===================================== debian/changelog ===================================== --- a/debian/changelog +++ b/debian/changelog @@ -1,5 +1,5 @@ -pilon-non-free (1.22-1) UNRELEASED; urgency=medium +pilon-non-free (1.22-1) unstable; urgency=medium - * Initial release (Closes: #<bug>) + * Initial release (Closes: #903911) - -- Andreas Tille <[email protected]> Thu, 23 Feb 2017 16:48:18 +0100 + -- Andreas Tille <[email protected]> Mon, 16 Jul 2018 16:46:04 +0200 ===================================== debian/control ===================================== --- a/debian/control +++ b/debian/control @@ -4,7 +4,7 @@ Uploaders: Andreas Tille <[email protected]> Section: science Priority: optional Build-Depends: debhelper (>= 11~), -Standards-Version: 4.1.4 +Standards-Version: 4.1.5 Vcs-Browser: https://salsa.debian.org/med-team/pilon-non-free Vcs-Git: https://salsa.debian.org/med-team/pilon-non-free.git Homepage: https://github.com/broadinstitute/pilon/wiki @@ -36,5 +36,5 @@ Description: automated genome assembly improvement and variant detection tool The code of pilon is actually free but currently there is no method to build the JAR from the scala source in Debian. This package is supposed to be replaced by a pilon package once it can be build from - source. + source (see bug #873341). ===================================== debian/copyright ===================================== --- a/debian/copyright +++ b/debian/copyright @@ -3,7 +3,7 @@ Upstream-Name: pilon Upstream-Contact: https://github.com/broadinstitute/pilon/issues Source: https://github.com/broadinstitute/pilon/releases Comment: The code is actually free but currently there is no method - to build + to build (see bug #873341) Files: * Copyright: Copyright 2012-2017 Broad Institute, Inc. ===================================== debian/createmanpages ===================================== --- a/debian/createmanpages +++ b/debian/createmanpages @@ -18,7 +18,10 @@ help2man --no-info --no-discard-stderr --help-option=" --help" \ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1 echo $AUTHOR >> $MANDIR/${progname}.1 -sed -i 's/specifed/specified/' $MANDIR/${progname}.1 +sed -i \ + -e 's/specifed/specified/' \ + -e 's/minumum/minimum/' \ + $MANDIR/${progname}.1 cat <<EOT Please enhance the help2man output. ===================================== debian/pilon.1 ===================================== --- a/debian/pilon.1 +++ b/debian/pilon.1 @@ -187,7 +187,7 @@ Kmer size used by internal assembler (default 47). Variants (snps and indels) will only be called if there is coverage of good pairs at this depth or more; if this value is >= 1, it is an absolute depth, if it is a fraction < 1, then minimum depth is computed by multiplying this value by the mean -coverage for the region, with a minumum value of 5 (default 0.1: min depth to call +coverage for the region, with a minimum value of 5 (default 0.1: min depth to call is 10% of mean coverage or 5, whichever is greater). .IP \fB\-\-mingap\fR View it on GitLab: https://salsa.debian.org/med-team/pilon-non-free/compare/664bae39d91bf2c6380218b899559c33ba743ac5...97d870df6484d8e2ad8755c720bcc6e852428de0 -- View it on GitLab: https://salsa.debian.org/med-team/pilon-non-free/compare/664bae39d91bf2c6380218b899559c33ba743ac5...97d870df6484d8e2ad8755c720bcc6e852428de0 You're receiving this email because of your account on salsa.debian.org.
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