[Blends-commit] [SCM] med branch, master, updated. fd336d0206758e6a39802c6d2cbc80db0f7a79f3

[Andreas Tille]

The following commit has been merged in the master branch:
commit fd336d0206758e6a39802c6d2cbc80db0f7a79f3
Author: Andreas Tille <tille at debian.org>
Date:   Fri Dec 1 16:26:58 2017 +0100

    Remove non-distributable cap3

diff --git a/tasks/bio b/tasks/bio
index a81e564..9917929 100644
--- a/tasks/bio
+++ b/tasks/bio
@@ -2007,36 +2007,6 @@ Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
 Recommends: blixem, dotter, belvu
 Comment: These packages are all from source package seqtools
 
-Recommends: cap3
-Homepage: http://genome.cs.mtu.edu/cap/cap3.html
-License: free for governmental agency or a non-profit educational institution
-Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
-X-Category: Sequence assembly
-X-Importance: not a lot of alternatives
-Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
-Pkg-Description: DNA Sequence Assembly Program
- CAP3 contains the following improvements to the CAP sequence assembly
- program.
-  1. Use of forward-reverse constraints to correct assembly errors and
-     link contigs.
-  2. Use of base quality values in alignment of sequence reads.
-  3. Automatic clipping of 5' and 3' poor regions of reads.
-  4. Generation of assembly results in ace file format for Consed.
-  5. CAP3 can be used in GAP4 of the Staden package.
- These improvements allow CAP3 to take longer sequences of higher
- errors and produce more accurate consensus sequences.
-Remark: Obtaining the source requires to fill in a registration form
- Official distribution in Debian is probably impossible.  The
- package included in the BioLinux distribution
- http://envgen.nox.ac.uk/biolinux.html containins only the binaries
- cap3 and formcon, dated Aug 29, 2002.  This package exists purely for
- convenience to Bio-Linux users so that the files are placed in
- locations consistent with the Bio-Linux setup.
-
-Comment: BioLinux contains a clcworkbench package which is available
- at http://www.clcbio.com/index.php?id=28 but this seems to be only
- "free as in beer" binary download - so this is not for us ...
-
 Recommends: coalesce
 Homepage: http://evolution.gs.washington.edu/lamarc/coalesce.html
 License: not specified

-- 
Debian Med metapackages