[med-svn] r7632 - trunk/packages/mira/trunk/debian

[Steffen Möller]

Author: moeller
Date: 2011-09-03 00:22:37 +0000 (Sat, 03 Sep 2011)
New Revision: 7632

Modified:
   trunk/packages/mira/trunk/debian/README.source
   trunk/packages/mira/trunk/debian/changelog
   trunk/packages/mira/trunk/debian/control
Log:
Got Tim's changes into Debian. Thanks!!


Modified: trunk/packages/mira/trunk/debian/README.source
===================================================================
--- trunk/packages/mira/trunk/debian/README.source	2011-09-02 16:38:55 UTC (rev 7631)
+++ trunk/packages/mira/trunk/debian/README.source	2011-09-03 00:22:37 UTC (rev 7632)
@@ -7,6 +7,9 @@
     read.C:45:28: error: uninitialized const ‘Read::REA_bposhashstat_default’ [-fpermissive]
     ../../src/mira/read.H:159:10: note: ‘const struct Read::bposhashstat_t’ has no user-provided default constructor
 
+mira-3.4.0/doc/3rdparty/scaffolding_MIRA_BAMBUS.pdf
+was removed by a request from upstream.
+
  -- Steffen Moeller <moeller at debian.org>  Tue, 23 Aug 2011 22:56:50 +0200
 
 Basic packaging seems fine. There are issues with the location of 
@@ -21,3 +24,4 @@
 so instead I've made it build against the runtime.
 
  -- Tim Booth <tbooth at ceh.ac.uk> Thu, 18 Aug 2011 11:34:11 +0100
+

Modified: trunk/packages/mira/trunk/debian/changelog
===================================================================
--- trunk/packages/mira/trunk/debian/changelog	2011-09-02 16:38:55 UTC (rev 7631)
+++ trunk/packages/mira/trunk/debian/changelog	2011-09-03 00:22:37 UTC (rev 7632)
@@ -1,3 +1,9 @@
+mira (3.4.0-3) unstable; urgency=low
+
+  * Rendering Tim's additions available for Debian
+
+ -- Steffen Moeller <moeller at debian.org>  Sat, 03 Sep 2011 01:02:10 +0200
+
 mira (3.4.0-2ubuntu5) lucid; urgency=low
 
   * Small fix to clean target and suppress warnings
@@ -8,8 +14,14 @@
 
  -- Tim Booth <tbooth at ceh.ac.uk>  Tue, 30 Aug 2011 17:17:11 +0100
 
-mira (3.4.0-1) unstable; urgency=low
+mira (3.4.0-2) unstable; urgency=low
 
+  * Fixing source tree (removed PDF with no source)
+
+ -- Steffen Moeller <moeller at debian.org>  Mon, 29 Aug 2011 22:54:53 +0200
+
+mira (3.4.0-1) UNRELEASED; urgency=low
+
   * New upstream version.
     - added default constructor to avoid FTBFS
   * Sposoring Tim's work for Debian

Modified: trunk/packages/mira/trunk/debian/control
===================================================================
--- trunk/packages/mira/trunk/debian/control	2011-09-02 16:38:55 UTC (rev 7631)
+++ trunk/packages/mira/trunk/debian/control	2011-09-03 00:22:37 UTC (rev 7632)
@@ -32,24 +32,24 @@
  .
  The package provides the following executables:
  Binaries provided: 
-  - mira: for assembly of genome sequences
-  - miramem: estimating memory needed to assemble projects. Realised through
+  * mira: for assembly of genome sequences
+  * miramem: estimating memory needed to assemble projects. Realised through
     link to mira.
-  - convert_project: for converting project file types into other types
-  - caf2fasta, caf2gbf, caf2text, caf2html, gbf2caf and gbf2fasta are some
+  * convert_project: for converting project file types into other types
+  * caf2fasta, caf2gbf, caf2text, caf2html, gbf2caf and gbf2fasta are some
     frequently used file converters (realised through links to convert_project)
-  - scftool: set of tools useful when working with SCF trace files
-  - fastatool: set of tools useful when working with FASTA trace files
+  * scftool: set of tools useful when working with SCF trace files
+  * fastatool: set of tools useful when working with FASTA trace files
  .
  Scripts provided:
-  - fasta2frag.tcl: fragmenting sequences into smaller, overlapping
+  * fasta2frag.tcl: fragmenting sequences into smaller, overlapping
     subsequences. Useful for simulating shotgun sequences. Can create
     subsequences in both directions (/default) and also paired-end sequences.
-  - fastaselect.tcl: given a FASTA file (and possibly a FASTA quality file) and
+  * fastaselect.tcl: given a FASTA file (and possibly a FASTA quality file) and
     a file with names of reads, select the sequences from the input FASTA (and
     quality file) and writes them to an output FASTA
-  - fastqselect.tcl: like fastaselect.tcl, only for FASTQ
-  - fixACE4consed.tcl: Consed has a bug which incapacitates it from reading
+  * fastqselect.tcl: like fastaselect.tcl, only for FASTQ
+  * fixACE4consed.tcl: Consed has a bug which incapacitates it from reading
     consensus tags in ACE files written by the MIRA assembler (and possibly
     other programs). This script massages an ACE file so that consed can read
     the consensus tags.