[med-svn] [kmer-tools] 08/08: Make kmer and libkmer-dev into metapackages

Sun May 24 09:29:42 UTC 2015

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afif-guest pushed a commit to branch master
in repository kmer-tools.

commit b295e1d20c0759dd82d91876831b207405a8e131
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Sun May 24 02:19:18 2015 -0700

    Make kmer and libkmer-dev into metapackages
    
    The former contents of these two have now
    been moved into meryl and libmeryl-dev.
    Until I better understand the relationships
    between the components of the kmer suite,
    I think this is the best first step. If
    it becomes apparent to me later that
    the base components are independent of
    meryl, I will then make the kmer-common
    and libkmer-common packages.
---
 debian/control                | 29 +++++-------------------
 debian/kmer-tools-doc.docs    |  1 -
 debian/kmer-tools-doc.install |  1 -
 debian/kmer.install           |  6 -----
 debian/kmer.manpages          |  2 --
 debian/libkmer-dev.install    |  9 --------
 debian/libmeryl-dev.install   | 52 +++++++++++++++++++++++++++++++++++++++++++
 debian/meryl.install          | 10 +++++++++
 debian/meryl.manpages         |  2 ++
 9 files changed, 70 insertions(+), 42 deletions(-)

diff --git a/debian/control b/debian/control
index 97e68fe..e804cf7 100644
--- a/debian/control
+++ b/debian/control
@@ -13,46 +13,29 @@ Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/kmer-tools.git
 Package: kmer
 Architecture: any
 Depends: ${shlibs:Depends},
-	 ${misc:Depends}
+	 ${misc:Depends},
+	 meryl
 Description: suite of tools for DNA sequence analysis
  The kmer package is a suite of tools for DNA sequence analysis.
  It provides tools for searching (ESTs, mRNAs, sequencing reads);
  aligning (ESTs, mRNAs, whole genomes); and a variety of analyses
  based on kmers.
-
-Package: kmer-doc
-Architecture: all
-Description: documentation for kmer
- The kmer package is a suite of tools for DNA sequence analysis.
- It provides tools for searching (ESTs, mRNAs, sequencing reads);
- aligning (ESTs, mRNAs, whole genomes); and a variety of analyses
- based on kmers.
  .
- This package contains documentation for kmer.
-
-Package: libkmer
-Architecture: any
-Section: libs
-Depends: ${shlibs:Depends},
-	 ${misc:Depends}
-Description: suite of tools for DNA sequence analysis
- The kmer package is a suite of tools for DNA sequence analysis.
- It provides tools for searching (ESTs, mRNAs, sequencing reads);
- aligning (ESTs, mRNAs, whole genomes); and a variety of analyses
- based on kmers.
+ This is a metapackage depending on the executable components of the kmer suite.
 
 Package: libkmer-dev
 Architecture: any
 Section: libdevel
 Depends: ${shlibs:Depends},
-	 ${misc:Depends}
+	 ${misc:Depends},
+	 libmeryl-dev
 Description: suite of tools for DNA sequence analysis (development lib)
  The kmer package is a suite of tools for DNA sequence analysis.
  It provides tools for searching (ESTs, mRNAs, sequencing reads);
  aligning (ESTs, mRNAs, whole genomes); and a variety of analyses
  based on kmers.
  .
- This package contains the static libraries and header files.
+ This is a metapackage package depending on the development components of kmer.
 
 Package: meryl
 Architecture: any
diff --git a/debian/kmer-tools-doc.docs b/debian/kmer-tools-doc.docs
deleted file mode 100644
index d4f4542..0000000
--- a/debian/kmer-tools-doc.docs
+++ /dev/null
@@ -1 +0,0 @@
-#DOCS#
diff --git a/debian/kmer-tools-doc.install b/debian/kmer-tools-doc.install
deleted file mode 100644
index d4f4542..0000000
--- a/debian/kmer-tools-doc.install
+++ /dev/null
@@ -1 +0,0 @@
-#DOCS#
diff --git a/debian/kmer.install b/debian/kmer.install
deleted file mode 100644
index c274d11..0000000
--- a/debian/kmer.install
+++ /dev/null
@@ -1,6 +0,0 @@
-# libutil (kazlib and its rdepends are currently not built)
-installdir/bin/mt19937ar-test	usr/bin
-# libseq
-installdir/bin/{test-merStream,test-seqCache,test-seqStream}	usr/bin
-# libkmer
-installdir/bin/{existDB,positionDB}	usr/bin
diff --git a/debian/kmer.manpages b/debian/kmer.manpages
deleted file mode 100644
index 00980dc..0000000
--- a/debian/kmer.manpages
+++ /dev/null
@@ -1,2 +0,0 @@
-debian/existDB.1
-debian/positionDB.1
diff --git a/debian/libkmer-dev.install b/debian/libkmer-dev.install
deleted file mode 100644
index 3afe4e5..0000000
--- a/debian/libkmer-dev.install
+++ /dev/null
@@ -1,9 +0,0 @@
-libutil/*.{h,H}	usr/include/kmer
-libutil/libutil.a	usr/include/kmer
-libutil/mt19937ar/libmt19937ar.a usr/include/kmer
-libbio/*.{h,H}	 usr/include/kmer
-libbio/libbio.a	 usr/include/kmer
-libseq/*.{h,H}	 usr/include/kmer
-libseq/libseq.a	 usr/include/kmer
-libkmer/*.{h,H}	 usr/include/kmer
-libkmer/libkmer.a	usr/include/kmer
diff --git a/debian/libmeryl-dev.install b/debian/libmeryl-dev.install
index 68fc00d..26921cf 100644
--- a/debian/libmeryl-dev.install
+++ b/debian/libmeryl-dev.install
@@ -2,3 +2,55 @@ meryl/meryl.H	usr/include
 meryl/libmerylguts.a	usr/include
 libmeryl/libmeryl.H	usr/include
 libmeryl/libmeryl.a	usr/include
+libutil/bigQueue.H	usr/include/kmer
+libutil/bitOperations.h	usr/include/kmer
+libutil/bitPackedArray.H	usr/include/kmer
+libutil/bitPackedFile.H		usr/include/kmer
+libutil/bitPacking.h		usr/include/kmer
+libutil/bzipBuffer.H		usr/include/kmer
+libutil/eliasDeltaEncoding.h	usr/include/kmer
+libutil/eliasGammaEncoding.h	usr/include/kmer
+libutil/endianess.H		usr/include/kmer
+libutil/fibonacciEncoding.h	usr/include/kmer
+libutil/generalizedUnaryEncoding.h	usr/include/kmer
+libutil/intervalList.H			usr/include/kmer
+libutil/logMsg.H			usr/include/kmer
+libutil/readBuffer.H			usr/include/kmer
+libutil/recordFile.H			usr/include/kmer
+libutil/speedCounter.H			usr/include/kmer
+libutil/splitToWords.H			usr/include/kmer
+libutil/sweatShop.H			usr/include/kmer
+libutil/uint32List.H			usr/include/kmer
+libutil/unaryEncoding.h			usr/include/kmer
+libutil/util.h				usr/include/kmer
+libutil/util++.H			usr/include/kmer
+libutil/libutil.a	usr/include/kmer
+libutil/mt19937ar/libmt19937ar.a	usr/include/kmer
+libbio/alphabet.h usr/include/kmer
+libbio/bio.h usr/include/kmer
+libbio/bio++.H usr/include/kmer
+libbio/kmer.H usr/include/kmer
+libbio/kmerhuge.H usr/include/kmer
+libbio/kmeriface.H usr/include/kmer
+libbio/kmertiny.H usr/include/kmer
+libbio/merCovering.H usr/include/kmer
+libbio/merList.H usr/include/kmer
+libbio/mers.h usr/include/kmer
+libbio/libbio.a	 usr/include/kmer
+libseq/fastaFile.H usr/include/kmer
+libseq/fastaStdin.H usr/include/kmer
+libseq/fastqFile.H usr/include/kmer
+libseq/fastqStdin.H usr/include/kmer
+libseq/merStream.H usr/include/kmer
+libseq/seqCache.H usr/include/kmer
+libseq/seqFactory.H usr/include/kmer
+libseq/seqFile.H usr/include/kmer
+libseq/seqStore.H usr/include/kmer
+libseq/seqStream.H usr/include/kmer
+libseq/sffFile.H usr/include/kmer
+libseq/test-correctSequence.H usr/include/kmer
+libseq/libseq.a	 usr/include/kmer
+libkmer/existDB.H usr/include/kmer
+libkmer/merTable.H usr/include/kmer
+libkmer/positionDB.H usr/include/kmer
+libkmer/libkmer.a	usr/include/kmer
diff --git a/debian/meryl.install b/debian/meryl.install
index 3c4086e..6566af5 100644
--- a/debian/meryl.install
+++ b/debian/meryl.install
@@ -1,5 +1,15 @@
+# From the meryl directories
 installdir/bin/meryl	usr/bin
 installdir/bin/simple	usr/bin
 installdir/bin/mapMers	usr/bin
 installdir/bin/mapMers-depth	usr/bin
 installdir/bin/kmer-mask	usr/bin
+# libutil (kazlib and its rdepends are currently not built)
+installdir/bin/mt19937ar-test	usr/bin
+# libseq
+installdir/bin/test-merStream	usr/bin
+installdir/bin/test-seqCache	usr/bin
+installdir/bin/test-seqStream	usr/bin
+# libkmer
+installdir/bin/existDB	usr/bin
+installdir/bin/positionDB	usr/bin
diff --git a/debian/meryl.manpages b/debian/meryl.manpages
index 001890b..a2a9a7d 100644
--- a/debian/meryl.manpages
+++ b/debian/meryl.manpages
@@ -2,3 +2,5 @@ debian/kmer-mask.1
 debian/mapMers.1
 debian/mapMers-depth.1
 debian/meryl.1
+debian/existDB.1
+debian/positionDB.1

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/kmer-tools.git

