Update tcofffee version

recipes/t-coffee/build.sh

@@ -9,25 +9,33 @@
 #
 set -eux -o pipefail
 
-SHARE_DIR="${PREFIX}/libexec/${PKG_NAME}-${PKG_VERSION}-${PKG_BUILDNUM}"
+SHARE_DIR="${PREFIX}/share/${PKG_NAME}-${PKG_VERSION}-${PKG_BUILDNUM}"
 OS=$(./install get_os)
 
 mkdir -p "${PREFIX}/bin"
 
-./install all -tcdir="${SHARE_DIR}" CC="$CXX" CFLAGS="$CFLAGS"
+./install t_coffee -tcdir="${SHARE_DIR}" CC="$CXX" CFLAGS="$CFLAGS -O3 -Wno-register -L${PREFIX}/lib"
+./install tcoffee -tcdir="${SHARE_DIR}" CC="$CXX" CFLAGS="$CFLAGS -O3 -Wno-register -L${PREFIX}/lib"
+./install rcoffee -tcdir="${SHARE_DIR}" CC="$CXX" CFLAGS="$CFLAGS -O3 -Wno-register -L${PREFIX}/lib"
+./install seq_reformat -tcdir="${SHARE_DIR}" CC="$CXX" CFLAGS="$CFLAGS -O3 -Wno-register -L${PREFIX}/lib"
+./install expresso -tcdir="${SHARE_DIR}" CC="$CXX" CFLAGS="$CFLAGS -O3 -Wno-register -L${PREFIX}/lib"
+./install psicoffee -tcdir="${SHARE_DIR}" CC="$CXX" CFLAGS="$CFLAGS -O3 -Wno-register -L${PREFIX}/lib"
+./install trmsd -tcdir="${SHARE_DIR}" CC="$CXX" CFLAGS="$CFLAGS -O3 -Wno-register -L${PREFIX}/lib"
+./install accurate -tcdir="${SHARE_DIR}" CC="$CXX" CFLAGS="$CFLAGS -O3 -Wno-register -L${PREFIX}/lib"
+./install 3dcoffee -tcdir="${SHARE_DIR}" CC="$CXX" CFLAGS="$CFLAGS -O3 -Wno-register -L${PREFIX}/lib"
+./install mcoffee -tcdir="${SHARE_DIR}" CC="$CXX" CFLAGS="$CFLAGS -O3 -Wno-register -L${PREFIX}/lib"
 
 # llvm-otool -l fails for these plugins on macosx
-if [ "$OS" = macosx ]
-then
+if [[ `uname` == "Darwin" ]]; then
     for bad_plug in probconsRNA prank
     do
-	rm -fv "${SHARE_DIR}/plugins/macosx/${bad_plug}"
+	rm -f "${SHARE_DIR}/plugins/macosx/${bad_plug}"
     done
 fi
 
 # The installer may try to update dependencies and install them to bin/,
 # which will cause conflicts with the dependencies as separately packaged.
 # t_coffee itself is not installed here
-rm -fv ${PREFIX}/bin/*
+# rm -fv ${PREFIX}/bin/*
 
 sed -e "s|CHANGEME|${SHARE_DIR}|" -e "s|__OS__|${OS}|" "$RECIPE_DIR/t_coffee.sh" > "${PREFIX}/bin/t_coffee"

recipes/t-coffee/meta.yaml

@@ -1,7 +1,8 @@
-{% set version = "13.46.0.919e8c6b" %}
+{% set name = "t-coffee" %}
+{% set version = "13.46.1.b8b01e06" %}
 
 package:
-  name: t-coffee
+  name: {{ name }}
   version: {{ version }}
 
 build:
@@ -13,7 +14,7 @@ source:
   # The latest stable release is at http://www.tcoffee.org/Packages/Stable/Latest/ ,
   # but is then archived at http://www.tcoffee.org/Packages/Archives/
   url: https://s3.eu-central-1.amazonaws.com/tcoffee-packages/Archives/T-COFFEE_distribution_Version_{{ version }}.tar.gz
-  sha256: 31fd0ca0734974c93cb68bef6e394f463a4589c3315fd28cf2bd41b8a167db22
+  sha256: 54d2b00956af79a884fe7174522522c77e65796d5aa08974dad86e061e6d12d1
   patches:
     - expose-os-detection.patch
 
@@ -22,22 +23,24 @@ requirements:
     - make
     - {{ compiler('c') }}
     - {{ compiler('cxx') }}
+  host:
     - perl-xml-simple
+    - perl
+    - sphinx
     - blast
     - clustalo
     - clustalw
-    - consan # [not osx]
+    - consan  # [not osx]
     - dca
-    - dialign-tx 1.0.2
+    - dialign-tx ==1.0.2
     - famsa
     - kalign2
-    - mafft 7.310
+    - mafft ==7.526
     - muscle
-    - mustang 3.2.3
+    - mustang ==3.2.4
     - pasta
-    - perl
     - phylip
-    - poa 2.0 # [not osx]
+    - poa ==2.0  # [not osx]
     - prank
     - probcons
     - probconsrna
@@ -49,18 +52,18 @@ requirements:
     - blast
     - clustalo
     - clustalw
-    - consan # [not osx]
+    - consan  # [not osx]
     - dca
-    - dialign-tx 1.0.2
+    - dialign-tx ==1.0.2
     - famsa
     - kalign2
-    - mafft 7.310
+    - mafft ==7.526
     - muscle
-    - mustang 3.2.3
+    - mustang ==3.2.4
     - pasta
     - perl
     - phylip
-    - poa 2.0 # [not osx]
+    - poa ==2.0  # [not osx]
     - prank
     - probcons
     - probconsrna
@@ -80,11 +83,16 @@ test:
     - HOME=/tmp t_coffee 2>&1 | grep "sap is  Installed"  # [not osx]
 
 about:
-  home: http://www.tcoffee.org/Projects/tcoffee/
+  home: "https://tcoffee.org/Projects/tcoffee/index.html"
   license: GPL-2.0-only
+  license_family: GPL
   license_file: license.txt
-  summary: "A collection of tools for Multiple Alignments of DNA, RNA, Protein Sequence"
+  summary: "A collection of tools for Multiple Alignments of DNA, RNA, Protein Sequence."
+  dev_url: "https://github.com/cbcrg/tcoffee"
+  doc_url: "https://tcoffee.org/Projects/tcoffee/documentation/index.html"
 
 extra:
   identifiers:
     - doi:10.1006/jmbi.2000.4042
+    - biotools:tcoffee
+    - usegalaxy-eu:t_coffee