[med-svn] r13469 - in trunk/packages/ncbi-blast+: . branches branches/2.2.28_ubuntu branches/2.2.28_ubuntu/debian branches/2.2.28_ubuntu/debian/patches

2013-05-02 Thread Timothy Booth 
Author: tbooth-guest
Date: 2013-05-02 17:09:17 + (Thu, 02 May 2013)
New Revision: 13469

Added:
   trunk/packages/ncbi-blast+/branches/
   trunk/packages/ncbi-blast+/branches/2.2.28_ubuntu/
   trunk/packages/ncbi-blast+/branches/2.2.28_ubuntu/debian/
   
trunk/packages/ncbi-blast+/branches/2.2.28_ubuntu/debian/patches/enable_clean_after_failed_compile
   
trunk/packages/ncbi-blast+/branches/2.2.28_ubuntu/debian/patches/skip_services_unit_test
Modified:
   trunk/packages/ncbi-blast+/branches/2.2.28_ubuntu/debian/changelog
   trunk/packages/ncbi-blast+/branches/2.2.28_ubuntu/debian/control
   trunk/packages/ncbi-blast+/branches/2.2.28_ubuntu/debian/patches/fix_lib_deps
   trunk/packages/ncbi-blast+/branches/2.2.28_ubuntu/debian/patches/hurd_fixes
   
trunk/packages/ncbi-blast+/branches/2.2.28_ubuntu/debian/patches/no_multiarch_rpath
   trunk/packages/ncbi-blast+/branches/2.2.28_ubuntu/debian/patches/series
   trunk/packages/ncbi-blast+/branches/2.2.28_ubuntu/debian/rules
Log:
I've put my updates for 2.2.28 into this new subversion branch
/packages/ncbi-blast+/branches/2.2.28_ubuntu/ because:

1) They have changed the build system and I'm not 100%
   confident that my fixes to the patches are all correct.
2) Because of an oddity with the Boost libs on Ubuntu, and because
   Ubuntu LTS is getting old, the build dependencies are not right
   for Debian Sid, so you can't use my build unmodified in any case.

The thing I think you will find most useful is my new override_dh_clean
logic in rules. It took me about 8 attempts to get the package to build
and clean fully and I don't want you to waste the time repeating my mistakes!


Modified: trunk/packages/ncbi-blast+/branches/2.2.28_ubuntu/debian/changelog
===
--- trunk/packages/ncbi-blast+/trunk/debian/changelog   2013-05-01 20:09:53 UTC 
(rev 13468)
+++ trunk/packages/ncbi-blast+/branches/2.2.28_ubuntu/debian/changelog  
2013-05-02 17:09:17 UTC (rev 13469)
@@ -1,3 +1,14 @@
+ncbi-blast+ (2.2.28-3ubuntu1) precise; urgency=low
+
+  * New upstream
+  * Rebuild for Ubuntu
+  * Patch to skip test that needs network connection
+  * Re-jiggle shared build patch
+  * Drop mips patch as it is now in upstream
+  * Use newer Boost 1.48
+
+ -- Tim Booth tbo...@ceh.ac.uk  Tue, 30 Apr 2013 12:49:09 +0100
+
 ncbi-blast+ (2.2.27-3) unstable; urgency=low
 
   * debian/series: active patch fix_arm_mips_build (Closes: #688661).

Modified: trunk/packages/ncbi-blast+/branches/2.2.28_ubuntu/debian/control
===
--- trunk/packages/ncbi-blast+/trunk/debian/control 2013-05-01 20:09:53 UTC 
(rev 13468)
+++ trunk/packages/ncbi-blast+/branches/2.2.28_ubuntu/debian/control
2013-05-02 17:09:17 UTC (rev 13469)
@@ -4,7 +4,7 @@
 Build-Depends: autotools-dev (= 20100122),
debhelper (= 7.0.50~),
   dpkg-dev (= 1.16.1),
-   libboost-test-dev,
+   libboost-test1.48-dev,
libbz2-dev,
libc0.3-dev (= 2.13-9~) [hurd-i386],
libpcre3-dev,

Added: 
trunk/packages/ncbi-blast+/branches/2.2.28_ubuntu/debian/patches/enable_clean_after_failed_compile
===
--- 
trunk/packages/ncbi-blast+/branches/2.2.28_ubuntu/debian/patches/enable_clean_after_failed_compile
  (rev 0)
+++ 
trunk/packages/ncbi-blast+/branches/2.2.28_ubuntu/debian/patches/enable_clean_after_failed_compile
  2013-05-02 17:09:17 UTC (rev 13469)
@@ -0,0 +1,11 @@
+--- a/c++/src/build-system/new_module.sh.in
 b/c++/src/build-system/new_module.sh.in
+@@ -178,7 +178,7 @@
+ if test -x $bindir/datatool; then
+ datatool=$bindir/datatool
+ COMMON_AddRunpath $libdir
+-else
++elif [ $1 != purge_sources ] ; then
+ echo Unable to find datatool. 2
+ exit 2
+ fi

Modified: 
trunk/packages/ncbi-blast+/branches/2.2.28_ubuntu/debian/patches/fix_lib_deps
===
--- trunk/packages/ncbi-blast+/trunk/debian/patches/fix_lib_deps
2013-05-01 20:09:53 UTC (rev 13468)
+++ 
trunk/packages/ncbi-blast+/branches/2.2.28_ubuntu/debian/patches/fix_lib_deps   
2013-05-02 17:09:17 UTC (rev 13469)
@@ -37,7 +37,7 @@
  
  CPPFLAGS = $(ORIG_CPPFLAGS)
  
--DLL_LIB = blastxml xhtml xcgi
+-DLL_LIB = align_format blastxml xhtml xcgi
 +DLL_LIB = xblast align_format xalnmgr xobjmgr xnetblast scoremat blastxml \
 +  seq general xser tables xncbi
  
@@ -79,7 +79,7 @@
 +DLL_LIB = xnetblast xser xconnect xutil xncbi
 --- a/c++/src/objtools/align_format/Makefile.align_format.lib
 +++ b/c++/src/objtools/align_format/Makefile.align_format.lib
-@@ -10,6 +10,10 @@
+@@ -13,6 +13,10 @@
  
  CPPFLAGS = $(ORIG_CPPFLAGS)
  
@@ -88,8 +88,8 @@
 +  xcgi xhtml tables xncbi
 +
  ###  EXAMPLES OF OTHER SETTINGS THAT MIGHT BE OF INTEREST
- # CPPFLAGS =

[med-svn] r13470 - in trunk/packages/proalign/trunk/debian: . scripts

2013-05-02 Thread Thorsten Alteholz 
Author: alteholz
Date: 2013-05-02 17:49:18 + (Thu, 02 May 2013)
New Revision: 13470

Added:
   trunk/packages/proalign/trunk/debian/proalign.1
   trunk/packages/proalign/trunk/debian/proalign.manpages
Modified:
   trunk/packages/proalign/trunk/debian/changelog
   trunk/packages/proalign/trunk/debian/control
   trunk/packages/proalign/trunk/debian/rules
   trunk/packages/proalign/trunk/debian/scripts/proalign
Log:
ready for upload

Modified: trunk/packages/proalign/trunk/debian/changelog
===
--- trunk/packages/proalign/trunk/debian/changelog  2013-05-02 17:09:17 UTC 
(rev 13469)
+++ trunk/packages/proalign/trunk/debian/changelog  2013-05-02 17:49:18 UTC 
(rev 13470)
@@ -1,4 +1,4 @@
-proalign (0.603-1) UNRELEASED; urgency=low
+proalign (0.603-1) unstable; urgency=low
 
   * Initial release (Closes: #378290)
 

Modified: trunk/packages/proalign/trunk/debian/control
===
--- trunk/packages/proalign/trunk/debian/control2013-05-02 17:09:17 UTC 
(rev 13469)
+++ trunk/packages/proalign/trunk/debian/control2013-05-02 17:49:18 UTC 
(rev 13470)
@@ -5,7 +5,8 @@
 DM-Upload-Allowed: yes
 Uploaders: Andreas Tille ti...@debian.org,
  Thorsten Alteholz deb...@alteholz.de
-Build-Depends: debhelper (= 9)
+Build-Depends: debhelper (= 9),
+ default-jdk
 Standards-Version: 3.9.4
 Homepage: http://ueg.ulb.ac.be/ProAlign/
 Vcs-Browser: 
http://svn.debian.org/wsvn/debian-med/trunk/packages/proalign/trunk/
@@ -13,7 +14,8 @@
 
 Package: proalign
 Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
+Depends: ${shlibs:Depends}, ${misc:Depends},
+ default-jre
 Description: Probabilistic multiple alignment program
  ProAlign performs probabilistic sequence alignments using hidden Markov
  models (HMM). It includes a graphical interface (GUI) allowing to (i)

Added: trunk/packages/proalign/trunk/debian/proalign.1
===
--- trunk/packages/proalign/trunk/debian/proalign.1 
(rev 0)
+++ trunk/packages/proalign/trunk/debian/proalign.1 2013-05-02 17:49:18 UTC 
(rev 13470)
@@ -0,0 +1,79 @@
+.TH PROALIGN 1 May 2013 ProAlign User Commands
+.SH NAME
+proalign \- a probabilistic multiple alignment program
+.SH SYNOPSIS
+.B proalign [OPTIONS]
+.SH DESCRIPTION
+Only limited usage of the program is possible from command line. 
+Better use version with GUI (start without OPTIONS).
+.SH OPTIONS
+.TP
+\fB\-nogui\fR 
+force command line
+.TP
+\fB-seqfile=sequence file\fR
+.TP
+\fB-treefile=tree file\fR
+.TP
+\fB-newtree \fR
+compute a new guide tree
+.TP
+\fB-sample \fR
+sample traceback path; if not given, Viterbi is chosen
+.TP
+\fB-delta=HMM delta or \-delta=estimate \fR
+if not given, default is used
+.TP
+\fB-epsilon=HMM epsilon or \-epsilon=estimate \fR
+if not given, default is used
+.TP
+\fB-gapfreq=gap frequency \fR
+if not given, default is used
+.TP
+\fB-gapprob=gap substitution probability \fR
+if not given, default is used
+.TP
+\fB-bwidth=search band width \fR
+if not given, default is used
+.TP
+\fB-distscale=distance scale factor \fR
+for branch lengths
+.TP
+\fB-nocorrection \fR
+no correction for pairwise distances on guide tree computation
+.TP
+\fB-notrailing \fR
+no trailing sequence corrcection
+.TP
+\fB-trailing=trailing sequence correction length \fR
+for missing ends
+.TP
+\fB-penalize=true, or =false \fR
+penalize end gaps on pairwise alignments for guide tree
+.TP
+\fB-writemean \fR
+write mean posterior probability of sites
+.TP
+\fB-writeall \fR
+write posterior probability of each node
+.TP
+\fB-writeroot \fR
+write root node character probabilities
+.TP
+\fB-wag \fR
+use WAG probability table
+.TP
+\fB-dayhoff \fR
+use Dayhoff probability table
+.TP
+\fB-jtt \fR
+use JTT probability table
+.TP
+\fB-outfile=alignment file\fR
+.TP
+\fB\-outformat=pir, \-outformat=msf, \-outformat=phylip, or \-outformat=nexus 
\fR
+output format
+.TP
+\fB-quiet \fR
+no log
+

Added: trunk/packages/proalign/trunk/debian/proalign.manpages
===
--- trunk/packages/proalign/trunk/debian/proalign.manpages  
(rev 0)
+++ trunk/packages/proalign/trunk/debian/proalign.manpages  2013-05-02 
17:49:18 UTC (rev 13470)
@@ -0,0 +1 @@
+debian/proalign.1

Modified: trunk/packages/proalign/trunk/debian/rules
===
--- trunk/packages/proalign/trunk/debian/rules  2013-05-02 17:09:17 UTC (rev 
13469)
+++ trunk/packages/proalign/trunk/debian/rules  2013-05-02 17:49:18 UTC (rev 
13470)
@@ -8,15 +8,9 @@
 override_dh_auto_build:
mkdir -p build
javac -d ./build *.java
-   find
(cd build; jar cmvf ../debian/manifest.txt ProAlign.jar *)
#(cd build; jar cmvf ../debian/manifest.txt ProAlign.jar 
proalign/ProAlign.class

[med-svn] r13471 - in trunk/packages/infernal/trunk/debian: . patches

2013-05-02 Thread Steffen Möller 
Author: moeller
Date: 2013-05-02 20:17:12 + (Thu, 02 May 2013)
New Revision: 13471

Modified:
   trunk/packages/infernal/trunk/debian/changelog
   trunk/packages/infernal/trunk/debian/control
   trunk/packages/infernal/trunk/debian/infernal.docs
   trunk/packages/infernal/trunk/debian/infernal.install
   trunk/packages/infernal/trunk/debian/infernal.manpages
   trunk/packages/infernal/trunk/debian/patches/series
   trunk/packages/infernal/trunk/debian/rules
   trunk/packages/infernal/trunk/debian/watch
Log:
New upstream version.


Modified: trunk/packages/infernal/trunk/debian/changelog
===
--- trunk/packages/infernal/trunk/debian/changelog  2013-05-02 17:49:18 UTC 
(rev 13470)
+++ trunk/packages/infernal/trunk/debian/changelog  2013-05-02 20:17:12 UTC 
(rev 13471)
@@ -1,3 +1,14 @@
+infernal (1.1~rc2-1) unstable; urgency=low
+
+  * New upstream version - aiming to support RNAWorld BOINC project,
+with many thanks and regards to Yoyo!
+- cmscore no longer available
+  * Bumped policy to 3.9.4 (no changes needed)
+- introduced hardening, with it build dep on
+  dpkg-dev (= 1.16.1~)
+
+ -- Steffen Moeller moel...@debian.org  Wed, 01 May 2013 20:24:17 +0200
+
 infernal (1.0.2-3) UNRELEASED; urgency=low
 
   [ Steffen Moeller ]

Modified: trunk/packages/infernal/trunk/debian/control
===
--- trunk/packages/infernal/trunk/debian/control2013-05-02 17:49:18 UTC 
(rev 13470)
+++ trunk/packages/infernal/trunk/debian/control2013-05-02 20:17:12 UTC 
(rev 13471)
@@ -6,8 +6,8 @@
 Uploaders: Steffen Moeller moel...@debian.org,
  Charles Plessy ple...@debian.org,
  Andreas Tille ti...@debian.org
-Build-Depends: debhelper (= 7.0.50~), autotools-dev, quilt
-Standards-Version: 3.9.3
+Build-Depends: dpkg-dev (= 1.16.1~), debhelper (= 7.0.50~), autotools-dev, 
quilt
+Standards-Version: 3.9.4
 Vcs-Browser: 
http://svn.debian.org/wsvn/debian-med/trunk/packages/infernal/trunk/
 Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/infernal/trunk/
 Homepage: http://infernal.janelia.org/
@@ -16,9 +16,9 @@
 Architecture: any
 Depends: ${shlibs:Depends}, ${misc:Depends}
 Description: inference of RNA secondary structural alignments
- Infernal (INFERence of RNA ALignment) is for searching DNA sequence
- databases for RNA structure and sequence similarities. It is an
- implementation of a special case of profile stochastic context-free
+ Infernal (INFERence of RNA ALignment) searches DNA sequence
+ databases for RNA structure and sequence similarities. It provides an
+ implementation of a special variant of profile stochastic context-free
  grammars called covariance models (CMs). A CM is like a sequence
  profile, but it scores a combination of sequence consensus and RNA
  secondary structure consensus, so in many cases, it is more capable of
@@ -32,8 +32,8 @@
 Section: doc
 Depends: ${shlibs:Depends}, ${misc:Depends}
 Description: inference of RNA secondary structural alignments – documentation
- Infernal (INFERence of RNA ALignment) is for searching DNA sequence
- databases for RNA structure and sequence similarities. It is an
+ Infernal (INFERence of RNA ALignment) searches DNA sequence
+ databases for RNA structure and sequence similarities. It provides an
  implementation of a special case of profile stochastic context-free
  grammars called covariance models (CMs). A CM is like a sequence
  profile, but it scores a combination of sequence consensus and RNA

Modified: trunk/packages/infernal/trunk/debian/infernal.docs
===
--- trunk/packages/infernal/trunk/debian/infernal.docs  2013-05-02 17:49:18 UTC 
(rev 13470)
+++ trunk/packages/infernal/trunk/debian/infernal.docs  2013-05-02 20:17:12 UTC 
(rev 13471)
@@ -1,3 +1,2 @@
-00README
-00README-MPI
-documentation/release-notes/RELEASE-1.0
+README
+RELEASE-NOTES

Modified: trunk/packages/infernal/trunk/debian/infernal.install
===
--- trunk/packages/infernal/trunk/debian/infernal.install   2013-05-02 
17:49:18 UTC (rev 13470)
+++ trunk/packages/infernal/trunk/debian/infernal.install   2013-05-02 
20:17:12 UTC (rev 13471)
@@ -1,9 +1 @@
-src/cmalign   usr/bin
-src/cmbuild   usr/bin
-src/cmcalibrate   usr/bin
-src/cmemitusr/bin
-src/cmscore   usr/bin
-src/cmsearch  usr/bin
-src/cmstatusr/bin
-src/trcyk usr/bin
-src/truncyk_check usr/bin
+bin/*   usr/bin

Modified: trunk/packages/infernal/trunk/debian/infernal.manpages
===
--- trunk/packages/infernal/trunk/debian/infernal.manpages  2013-05-02 
17:49:18 UTC (rev 13470)
+++ trunk/packages/infernal/trunk/debian/infernal.manpages  2013-05-02 
20:17:12 UTC (rev 13471)
@@ -1 +1,3 @@
-documentation/manpages/*