[med-svn] r17932 - trunk/packages/bowtie/trunk/debian

[Andreas Tille]

Author: tille
Date: 2014-09-03 08:10:31 +0000 (Wed, 03 Sep 2014)
New Revision: 17932

Added:
   trunk/packages/bowtie/trunk/debian/README.Debian
Modified:
   trunk/packages/bowtie/trunk/debian/changelog
Log:
Add README.Debian informing users about the fact that we ignore copy of cpuid.h


Added: trunk/packages/bowtie/trunk/debian/README.Debian
===================================================================
--- trunk/packages/bowtie/trunk/debian/README.Debian	                        (rev 0)
+++ trunk/packages/bowtie/trunk/debian/README.Debian	2014-09-03 08:10:31 UTC (rev 17932)
@@ -0,0 +1,31 @@
+Bowtie for Debian
+=================
+
+Upstream has included an old copy of a gcc owned header file (cpuid.h).
+This should be generally considered a bad idea and it breaks compilation
+on other architectures than amd64 (most probably since a copy of the
+architecture specific header file was taken).  While we try to contact
+upstream about this the current package is using the original header
+file from gcc.  If you might observe any issues that might be caused
+by this change please report this using the command
+
+    reportbug bowtie
+
+
+Hint from manual:
+
+    If your computer has multiple processors/cores, use `-p`
+
+    The `-p` option causes Bowtie to launch a specified number of
+    parallel search threads.  Each thread runs on a different
+    processor/core and all threads find alignments in parallel,
+    increasing alignment throughput by approximately a multiple of the
+    number of threads (though in practice, speedup is somewhat worse
+    than linear).
+
+There might be a chance to write a shell wrapper detecting whether your
+computer has more processors and automatically inject the -p option in
+this case.  If you like this please file a bug report with severity
+wishlist to let us know.
+
+ -- Andreas Tille <tille at debian.org>  Wed, 03 Sep 2014 09:50:22 +0200

Modified: trunk/packages/bowtie/trunk/debian/changelog
===================================================================
--- trunk/packages/bowtie/trunk/debian/changelog	2014-09-03 07:53:19 UTC (rev 17931)
+++ trunk/packages/bowtie/trunk/debian/changelog	2014-09-03 08:10:31 UTC (rev 17932)
@@ -2,6 +2,8 @@
 
   * Do not use copy of outdated gcc header file which destroys portability
     to other architectures
+  * Add README.Debian informing users about the fact that we ignore copy
+    of cpuid.h
 
  -- Andreas Tille <tille at debian.org>  Wed, 03 Sep 2014 09:50:22 +0200