[med-svn] samtools 01/02: Build libbam-dev (only) from version 0.1.19 in a “legacy” source package.

Tue Sep 16 11:17:35 UTC 2014

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 <plessy at debian.org>
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 <plessy at debian.org>  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 <plessy at debian.org>  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 <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Charles Plessy <plessy at debian.org>,
-           Dominique Belhachemi <domibel at debian.org>
+Uploaders: Charles Plessy <plessy at debian.org>
 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

