t-coffee 12.00.7fb08c2 (#12594)

* t-coffee 12.00.7fb08c2

* add viennarna to deps

Adding viennarna to runtime dependencies will include RNAplfold thus allowing -mode rcoffee to run.

* t-coffee 12.00.7fb08c2 (2)

This commit adds vienna packages
and remove TMalign copy command

* t-coffee 12.00.7fb08c2 (4)

Adding TMalign

recipes/t-coffee/bin/.t-coffee-pre-link.sh

@@ -0,0 +1,9 @@
+echo "** WARNING: This T-Coffee recipe is still under development **"
+echo ""
+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

recipes/t-coffee/build.sh

@@ -15,3 +15,8 @@ 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
+

recipes/t-coffee/meta.yaml

@@ -1,4 +1,4 @@
-{% set version = "11.00.8cbe486" %}
+{% set version = "12.00.7fb08c2" %}
 
 package:
   name: t-coffee
@@ -9,7 +9,7 @@ build:
 
 source:
   url: http://tcoffee.org/Packages/Stable/Latest/T-COFFEE_distribution_Version_{{ version }}.tar.gz
-  sha256: b8018433574ff7705c49cd974bebb06a48eb8bc5e38aaa9eb4f53f2e7778e72c
+  sha256: 6119514a0e36da4b4de88741b8c12f9c8ab653772b3952a011d4cb373beee44f
 
 requirements:
   build:
@@ -23,6 +23,7 @@ requirements:
     - mafft
     - muscle
     - poa # [not osx]
+    - viennarna
 
 test:
   commands: