This is an automated email from the git hooks/post-receive script. plessy pushed a commit to annotated tag debian/samtools-legacy/0.1.19-2 in repository samtools.
commit 1bb181e38b8408a69a80ab4668895535630a752f Author: Charles Plessy <[email protected]> Date: Tue Sep 16 20:02:18 2014 +0900 Build libbam-dev (only) from version 0.1.19 in a “legacy” source package. --- debian/README.Debian | 20 -------------------- debian/changelog | 6 ++++++ debian/control | 27 +++++++-------------------- debian/gbp.conf | 5 +++++ debian/{samtools.docs => libbam-dev.doc} | 0 debian/razip.1 | 28 ---------------------------- debian/rules | 11 ----------- debian/samtools.bash-completion | 21 --------------------- debian/samtools.examples | 6 ------ debian/samtools.install | 16 ---------------- debian/samtools.manpages | 2 -- debian/{upstream => upstream/metadata} | 0 debian/watch | 2 -- 13 files changed, 18 insertions(+), 126 deletions(-) diff --git a/debian/README.Debian b/debian/README.Debian index 6a6b574..7301fb3 100644 --- a/debian/README.Debian +++ b/debian/README.Debian @@ -1,15 +1,3 @@ -SAMtools for Debian. -━━━━━━━━━━━━━━━━━━━━ - - -Extra utilities. -──────────────── - -The extra utilities found in the ‘misc’ directory of the upstream archive are -placed in ‘/usr/share/samtools’ for the Perl and Python scripts, and -‘/usr/lib/samtools’ for the binary executables. - - The BAM library. ──────────────── @@ -18,12 +6,4 @@ whole package) is built with the -fPIC option, to allow the compilation of the Bio::SamTools Perl module on the amd64 platform (Debian package libbio-samtools-perl). - -Note about how this package is tested. -────────────────────────────────────── - -At build time, the regression tests of the package are ran. You can consult the -results on ‘http://buildd.debian.org/samtools’. - - -- Charles Plessy <[email protected]> Thu, 15 Jul 2010 08:37:41 +0900 diff --git a/debian/changelog b/debian/changelog index 59d4728..ce0735d 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,9 @@ +samtools-legacy (0.1.19-2) UNRELEASED; urgency=medium + + * + + -- Charles Plessy <[email protected]> Tue, 16 Sep 2014 19:45:49 +0900 + samtools (0.1.19-1) unstable; urgency=low cb9bd50 Imported https://github.com/samtools/samtools/archive/0.1.19.tar.gz diff --git a/debian/control b/debian/control index dc9dd76..de48a42 100644 --- a/debian/control +++ b/debian/control @@ -1,32 +1,18 @@ -Source: samtools +Source: samtools-legacy Maintainer: Debian Med Packaging Team <[email protected]> -Uploaders: Charles Plessy <[email protected]>, - Dominique Belhachemi <[email protected]> +Uploaders: Charles Plessy <[email protected]> Section: science Priority: optional Build-Depends: debhelper (>= 9), - bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev -Standards-Version: 3.9.4 +Standards-Version: 3.9.5 Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/samtools.git -Vcs-Git: git://anonscm.debian.org/debian-med/samtools.git +Vcs-Git: git://anonscm.debian.org/debian-med/samtools.git -b samtools-legacy Homepage: http://samtools.sourceforge.net -Package: samtools -Architecture: any -Depends: ${shlibs:Depends}, - ${misc:Depends} -Suggests: python -Description: processing sequence alignments in SAM and BAM formats - Samtools is a set of utilities that manipulate nucleotide sequence alignments - in the binary BAM format. It imports from and exports to the ascii SAM - (Sequence Alignment/Map) format, does sorting, merging and indexing, and allows - to retrieve reads in any regions swiftly. It is designed to work on a stream, - and is able to open a BAM (not SAM) file on a remote FTP or HTTP server. - Package: libbam-dev Architecture: any Section: libdevel @@ -39,5 +25,6 @@ Description: manipulates nucleotide sequence alignments in BAM or SAM format sorting, merging, generating pileup, and quickly retrieval of reads overlapped with a specified region. . - This library is part of SAMtools. - + This library is part of SAMtools version 0.1.19. It is obsolete and provided + only to build software that has not yet transitioned to the HTSlib, which + replaces this library. diff --git a/debian/gbp.conf b/debian/gbp.conf index f21acea..2ef5b53 100644 --- a/debian/gbp.conf +++ b/debian/gbp.conf @@ -1,6 +1,11 @@ # Configuration file for git-buildpackage and friends [DEFAULT] +upstream-branch = upstream +debian-branch = debian/samtools-legacy +upstream-tag = upstream/0.1.19 +pristine-tar = True + # use pristine-tar: pristine-tar = True diff --git a/debian/samtools.docs b/debian/libbam-dev.doc similarity index 100% rename from debian/samtools.docs rename to debian/libbam-dev.doc diff --git a/debian/razip.1 b/debian/razip.1 deleted file mode 100644 index aa06283..0000000 --- a/debian/razip.1 +++ /dev/null @@ -1,28 +0,0 @@ -.\" Generated by help2man 1.36 and edited later with vi. -.\" This manual page was forwarded upstream on November 17th, 2009. -.TH RAZIP "1" "November 2009" "razip " "Bioinformatics tools" -.SH NAME -razip \- Compress and decompress files in RAZip format -.SH SYNOPSIS -.B razip -[\fIoptions\fR] [\fIfile\fR] ... -.SH DESCRIPTION -razip is a program to compress and decopmress files in RAZip format. -The corresponding file suffix is `.rz'. -.SH OPTIONS -\fB\-c\fR write on standard output, keep original files unchanged -.TP -\fB\-d\fR -decompress -.TP -\fB\-l\fR -list compressed file contents -.TP -\fB\-b\fR INT -decompress at INT position in the uncompressed file -.TP -\fB\-s\fR INT -decompress INT bytes in the uncompressed file -.TP -\fB\-h\fR -give this help diff --git a/debian/rules b/debian/rules index f4dc09e..f3817ce 100755 --- a/debian/rules +++ b/debian/rules @@ -9,16 +9,5 @@ CFLAGS += -fPIC $(LDFLAGS) $(CPPFLAGS) DEB_MAKE_BUILD_TARGET = all all-recur razip lib DEB_MAKE_CHECK_TARGET = -C examples all -DEB_COMPRESS_EXCLUDE = .bam -DEB_DH_BUILDDEB_ARGS = -- -Z=xz -DEB_INSTALL_CHANGELOGS_ALL = NEWS clean:: $(RM) examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fai examples/ex1.glf examples/ex1.glfview.gz examples/ex1.pileup.gz examples/ex1a.bam examples/ex1b.bam examples/ex1f-rmduppe.bam examples/ex1f-rmdupse.bam examples/ex1f.bam examples/ex1f.rg examples/ex1.bcf - -binary-install/samtools:: - install -m 644 bcftools/README $(CURDIR)/debian/samtools/usr/share/doc/samtools/README.bcftools - ln -s samtools.1.gz $(CURDIR)/debian/samtools/usr/share/man/man1/bcftools.1.gz - dh_bash-completion - -binary-fixup/samtools:: - sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' $(CURDIR)/debian/samtools/usr/share/samtools/varfilter.py diff --git a/debian/samtools.bash-completion b/debian/samtools.bash-completion deleted file mode 100644 index cae64e6..0000000 --- a/debian/samtools.bash-completion +++ /dev/null @@ -1,21 +0,0 @@ -# From https://raw.github.com/arq5x/bash_completion/master/samtools revision e931a8b46d9582672cc506e45ad9b4f4d6fbd743 -_samtools() -{ - local cur prev opts - COMPREPLY=() - cur="${COMP_WORDS[COMP_CWORD]}" - prev="${COMP_WORDS[COMP_CWORD-1]}" - opts="view sort mpileup depth - faidx tview index idxstats - fixmate flagstat calmd merge - rmdup reheader cat targetcut - phase pad2unpad" - - case $prev in - samtools) - COMPREPLY=( $(compgen -W "${opts}" -- ${cur}) ) - ;; - esac - return 0 -} -complete -F _samtools -o default samtools diff --git a/debian/samtools.examples b/debian/samtools.examples deleted file mode 100644 index 5a25472..0000000 --- a/debian/samtools.examples +++ /dev/null @@ -1,6 +0,0 @@ -examples/ex1.bam -examples/ex1.fa -examples/ex1.sam.gz -examples/00README.txt -examples/toy.fa -examples/toy.sam diff --git a/debian/samtools.install b/debian/samtools.install deleted file mode 100644 index 7bd879b..0000000 --- a/debian/samtools.install +++ /dev/null @@ -1,16 +0,0 @@ -#bgzip usr/bin -bcftools/bcftools usr/bin -razip usr/bin -samtools usr/bin -bcftools/vcfutils.pl usr/share/samtools -misc/*.pl usr/share/samtools -misc/*.py usr/share/samtools -misc/*.lua usr/share/samtools -misc/plot-bamcheck usr/share/samtools -misc/wgsim usr/lib/samtools -misc/ace2sam usr/lib/samtools -misc/bamcheck usr/lib/samtools -misc/maq2sam-long usr/lib/samtools -misc/maq2sam-short usr/lib/samtools -misc/md5fa usr/lib/samtools -misc/md5sum-lite usr/lib/samtools diff --git a/debian/samtools.manpages b/debian/samtools.manpages deleted file mode 100644 index 18d2896..0000000 --- a/debian/samtools.manpages +++ /dev/null @@ -1,2 +0,0 @@ -samtools.1 -debian/razip.1 diff --git a/debian/upstream b/debian/upstream/metadata similarity index 100% rename from debian/upstream rename to debian/upstream/metadata diff --git a/debian/watch b/debian/watch deleted file mode 100644 index 3d2e134..0000000 --- a/debian/watch +++ /dev/null @@ -1,2 +0,0 @@ -version=3 -https://github.com/samtools/samtools/tags .*/v?(\d[\d\.]+)\.tar\.gz -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/samtools.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
