[med-svn] [phylophlan] 02/10: Update TODO

[Andreas Tille]

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tille pushed a commit to branch master
in repository phylophlan.

commit 8b64eec10a3bd1ff262a868cd499d8c54bbb943e
Author: Andreas Tille <tille at debian.org>
Date:   Tue May 24 13:28:23 2016 +0000

    Update TODO
---
 debian/README.test                | 8 ++++++++
 debian/changelog                  | 4 ++++
 debian/patches/debian_tools.patch | 2 +-
 debian/patches/series             | 2 +-
 debian/patches/use_vsearch.patch  | 4 ++++
 5 files changed, 18 insertions(+), 2 deletions(-)

diff --git a/debian/README.test b/debian/README.test
new file mode 100644
index 0000000..c8cef4e
--- /dev/null
+++ b/debian/README.test
@@ -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
+
diff --git a/debian/changelog b/debian/changelog
index 89c718a..cbd3f38 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -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
diff --git a/debian/patches/debian_tools.patch b/debian/patches/debian_tools.patch
index 1817a55..aa1afce 100644
--- a/debian/patches/debian_tools.patch
+++ b/debian/patches/debian_tools.patch
@@ -9,7 +9,7 @@ Description: Use Debian packaged tools with correct names
  
  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)
diff --git a/debian/patches/series b/debian/patches/series
index 12c55fa..0d35121 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -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
diff --git a/debian/patches/use_vsearch.patch b/debian/patches/use_vsearch.patch
index 447acd0..57a8740 100644
--- a/debian/patches/use_vsearch.patch
+++ b/debian/patches/use_vsearch.patch
@@ -3,6 +3,10 @@ Last-Update: Mon, 23 May 2016 16:09:13 +0200
 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

-- 
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