From 90fad72c3dbe47ff0a1284a659afaa3dd7573062 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Thu, 20 Dec 2018 12:32:49 +0100
Subject: [PATCH] t-coffee-12.00.7fb08c2 (build 1) (#12601)

* t-coffee-12.00.7fb08c2 (build 1)

This commit add more deps required by t-coffee.

* Fixed pre-link confirmation

* Changed pre-link to post-link

* Disable Consan on OSX

* Added TMalign as a external dep
---
 recipes/t-coffee/build.sh                       |  5 -----
 recipes/t-coffee/meta.yaml                      | 17 ++++++++++++-----
 .../{bin/.t-coffee-pre-link.sh => post-link.sh} |  3 ---
 3 files changed, 12 insertions(+), 13 deletions(-)
 rename recipes/t-coffee/{bin/.t-coffee-pre-link.sh => post-link.sh} (67%)

diff --git a/recipes/t-coffee/build.sh b/recipes/t-coffee/build.sh
index 8558cd9c7ca0b..0cfb9c3b1c4fd 100644
--- a/recipes/t-coffee/build.sh
+++ b/recipes/t-coffee/build.sh
@@ -15,8 +15,3 @@ make
 # install tcoffee in the target bin directory 
 mkdir -p $PREFIX/bin
 cp t_coffee $PREFIX/bin
-
-# to be moved in a separate recipe in the future
-gfortran TMalign.f -o TMalign
-cp TMalign $PREFIX/bin
-
diff --git a/recipes/t-coffee/meta.yaml b/recipes/t-coffee/meta.yaml
index 5f213cb8cc685..a27a03f172acb 100644
--- a/recipes/t-coffee/meta.yaml
+++ b/recipes/t-coffee/meta.yaml
@@ -5,7 +5,7 @@ package:
   version: {{ version }}
 
 build:
-  number: 0
+  number: 1
 
 source:
   url: http://tcoffee.org/Packages/Stable/Latest/T-COFFEE_distribution_Version_{{ version }}.tar.gz
@@ -15,15 +15,22 @@ requirements:
   build:
     - {{ compiler('c') }}
     - {{ compiler('cxx') }}
-    - {{ compiler('fortran') }}
   run:
     - blast
     - clustalo
     - clustalw
-    - mafft
+    - dca
+    - dialign-tx=1.0.2
+    - mafft=7.310
     - muscle
-    - poa # [not osx]
-    - viennarna
+    - mustang=3.2.3
+    - poa=2.0 # [not osx]
+    - prank
+    - phylip
+    - viennarna=2.1.9
+    - consan # [not osx]
+    - pasta
+    - tmalign
 
 test:
   commands:
diff --git a/recipes/t-coffee/bin/.t-coffee-pre-link.sh b/recipes/t-coffee/post-link.sh
similarity index 67%
rename from recipes/t-coffee/bin/.t-coffee-pre-link.sh
rename to recipes/t-coffee/post-link.sh
index 885b2ee6665c7..b3e9b2836b760 100644
--- a/recipes/t-coffee/bin/.t-coffee-pre-link.sh
+++ b/recipes/t-coffee/post-link.sh
@@ -4,6 +4,3 @@ echo "It does not contain all required packages to use all T-Coffee modes."
 echo "We suggest to use the Bioconda 't_coffee' recipe instead or download it"
 echo "from the web site http://www.tcoffee.org"
 echo ""
-read -u 1 -p "* Please confirm you want to continue with the installation [y/n] " -n 1 -r
-echo ""
-if [[ ! $REPLY =~ ^[Yy]$ ]]; then exit 1; fi
\ No newline at end of file