Update t-coffee version

recipes/t-coffee/build.sh

@@ -9,9 +9,11 @@
 #
 set -eux -o pipefail
 # silence some LANG perl warning messages:
-export LANG=C.UTF-8
+export LC_ALL="en_US.UTF-8"
+export CPPFLAGS="${CPPFLAGS} -I${PREFIX}/include"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
 
-SHARE_DIR="${PREFIX}/libexec/${PKG_NAME}-${PKG_VERSION}-${PKG_BUILDNUM}"
+SHARE_DIR="${PREFIX}/share/${PKG_NAME}-${PKG_VERSION}-${PKG_BUILDNUM}"
 OS=$(./install get_os)
 
 # -fsigned-char is needed for aarch64; register needs to be hidden for os-x's C++ compiler
@@ -20,30 +22,34 @@ CFLAGS="${CFLAGS} -fsigned-char -Wno-write-strings -Dregister='' -O0"
 rm -fv bin/${OS}/*			# remove the download binaries - we rebuild
 
 cd t_coffee_source
-make -j ${CPU_COUNT} CFLAGS="${CFLAGS} -fsigned-char -Wno-write-strings -Dregister='' -O0" CC="${CXX}" LDFLAGS="${LDFLAGS}" FCC="${FC}" FFLAGS="${FFLAGS}" all
-cp t_coffee TMalign ../bin/${OS}/ # overwrite the distributed x86 linux binary 
+make CFLAGS="${CFLAGS} -fsigned-char -Wno-write-strings -Wno-return-type -Dregister='' -O0" CC="${CXX}" LDFLAGS="${LDFLAGS}" FCC="${FC}" FFLAGS="${FFLAGS}" all -j"${CPU_COUNT}"
+cp -f t_coffee TMalign ../bin/${OS}/ # overwrite the distributed x86 linux binary 
 cd ..
 
 mkdir -p "${PREFIX}/bin"
 
-# the t-coffee home only has plugins with x86_64 support; let's not 
-# download them. Instead use only bioconda's own installs.
-# the t_coffee application is the only one from the set required by Bio::Tools::Run::Alignment::TCoffee
-./install t_coffee -tcdir="${SHARE_DIR}" CC="${CXX}" CFLAGS="${CFLAGS}"
-
-# # llvm-otool -l fails for these plugins on macosx
-# if [ "$OS" = macosx ]
-# then
-#     for bad_plug in probconsRNA prank
-#     do
-# 	rm -fv "${SHARE_DIR}/plugins/macosx/${bad_plug}"
-#     done
-# fi
+./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 [[ "${OS}" == "Darwin" ]]; then
+    for bad_plug in probconsRNA prank
+    do
+	rm -f "${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 ${PREFIX}/bin/*
-
-sed -e "s|CHANGEME|${SHARE_DIR}|" -e "s|__OS__|${OS}|" "$RECIPE_DIR/t_coffee.sh" > "${PREFIX}/bin/t_coffee"
+# 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

@@ -1,14 +1,14 @@
-{% set version = "13.46.1.b8b01e06" %}
 {% set name = "t-coffee" %}
+{% set version = "13.46.1.b8b01e06" %}
+
 package:
   name: {{ name }}
   version: {{ version }}
 
 build:
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage('t-coffee', max_pin="x") }}
-  skip: True    # [osx]
 
 source:
   # The latest stable release is at http://www.tcoffee.org/Packages/Stable/Latest/ ,
@@ -24,10 +24,10 @@ requirements:
     - {{ compiler('c') }}
     - {{ compiler('cxx') }}
     - {{ compiler('fortran') }}
+    - perl
     - perl-xml-simple
-    - perl            ==5.32.1
   run:
-    - perl            ==5.32.1
+    - perl
     - clustalo        ==1.2.4
     - clustalw        ==2.1
     - consan          ==1.2 # [not osx]
@@ -60,13 +60,18 @@ 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:
   additional-platforms:
     - linux-aarch64
   identifiers:
     - doi:10.1006/jmbi.2000.4042
+    - biotools:tcoffee
+    - usegalaxy-eu:t_coffee