[med-svn] r22013 - in trunk/packages/phylophlan/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2016-05-24 13:28:23 +0000 (Tue, 24 May 2016)
New Revision: 22013

Added:
   trunk/packages/phylophlan/trunk/debian/README.test
Modified:
   trunk/packages/phylophlan/trunk/debian/changelog
   trunk/packages/phylophlan/trunk/debian/patches/debian_tools.patch
   trunk/packages/phylophlan/trunk/debian/patches/series
   trunk/packages/phylophlan/trunk/debian/patches/use_vsearch.patch
Log:
Update TODO


Added: trunk/packages/phylophlan/trunk/debian/README.test
===================================================================
--- trunk/packages/phylophlan/trunk/debian/README.test	                        (rev 0)
+++ trunk/packages/phylophlan/trunk/debian/README.test	2016-05-24 13:28:23 UTC (rev 22013)
@@ -0,0 +1,8 @@
+
+
+   phylophlan -u example_corynebacteria --nproc 4
+
+    --> Requires usearch!
+    --> We need to install examples from input/ dir into examples package
+        and let the code point to the location
+

Modified: trunk/packages/phylophlan/trunk/debian/changelog
===================================================================
--- trunk/packages/phylophlan/trunk/debian/changelog	2016-05-24 07:25:26 UTC (rev 22012)
+++ trunk/packages/phylophlan/trunk/debian/changelog	2016-05-24 13:28:23 UTC (rev 22013)
@@ -1,5 +1,9 @@
 phylophlan (1.1.0-1) UNRELEASED; urgency=medium
 
   * Initial release (Closes: #<bug>)
+  TODO: 
+     * Find a replacement for usearch that can deal with proteins as well
+     * install examples from input/ dir into examples package and let the
+       code point to the location (see debian/README.test how to test this)
 
  -- Andreas Tille <tille at debian.org>  Mon, 23 May 2016 16:09:13 +0200

Modified: trunk/packages/phylophlan/trunk/debian/patches/debian_tools.patch
===================================================================
--- trunk/packages/phylophlan/trunk/debian/patches/debian_tools.patch	2016-05-24 07:25:26 UTC (rev 22012)
+++ trunk/packages/phylophlan/trunk/debian/patches/debian_tools.patch	2016-05-24 13:28:23 UTC (rev 22013)
@@ -9,7 +9,7 @@
  
  def dep_checks():
 -    for prog in ["FastTree", "usearch", "muscle", "tblastn"]:
-+    for prog in ["fasttree", "vsearch", "muscle", "tblastn"]:
++    for prog in ["fasttree", "usearch", "muscle", "tblastn"]:
          try:
              with open(os.devnull, 'w') as devnull:
                  sb.call([prog], stdout=devnull, stderr=devnull)

Modified: trunk/packages/phylophlan/trunk/debian/patches/series
===================================================================
--- trunk/packages/phylophlan/trunk/debian/patches/series	2016-05-24 07:25:26 UTC (rev 22012)
+++ trunk/packages/phylophlan/trunk/debian/patches/series	2016-05-24 13:28:23 UTC (rev 22013)
@@ -1,4 +1,4 @@
 debian_tools.patch
 datadir.patch
-use_vsearch.patch
+# use_vsearch.patch   --> see https://lists.debian.org/debian-med/2016/05/msg00091.html
 fasttree_name.patch

Modified: trunk/packages/phylophlan/trunk/debian/patches/use_vsearch.patch
===================================================================
--- trunk/packages/phylophlan/trunk/debian/patches/use_vsearch.patch	2016-05-24 07:25:26 UTC (rev 22012)
+++ trunk/packages/phylophlan/trunk/debian/patches/use_vsearch.patch	2016-05-24 13:28:23 UTC (rev 22013)
@@ -3,6 +3,10 @@
 Description: Debian can not package usearch which is non-free but it has
  the free replacement vsearch which is currently under active development
  and performs better than usearch
+Remark: According to
+  https://lists.debian.org/debian-med/2016/05/msg00091.html
+ in this case vsearch doese not serve as a replacement for usearch.
+ Thus for the moment the patch needs to be deactivated
 
 --- a/phylophlan.py
 +++ b/phylophlan.py