mmseqs2: fix licenses & pkg install process

BioArchLinux/mmseqs2/PKGBUILD

@@ -4,14 +4,27 @@ pkgname=('mmseqs2-sse4' 'mmseqs2-avx2')
 _pkgbase=${pkgbase//mm/MM}
 pkgver=16.747c6
 _pkgver=16-747c6
-pkgrel=3
+pkgrel=4
 pkgdesc="ultra fast and sensitive search and clustering suite. https://doi.org/10.1038/nbt.3988"
 arch=('x86_64')
 url="https://github.com/soedinglab/mmseqs2"
-license=('GPL3')
-makedepends=('cmake' 'zlib' 'openmp' 'vim')
-source=("$_pkgbase-$_pkgver.tar.gz::https://github.com/soedinglab/MMseqs2/archive/refs/tags/${_pkgver}.tar.gz")
-sha256sums=('faeb6841feb8e028651c2391de1346c55c2091a96520b625525d27b99d07ef1d')
+license=('MIT')
+makedepends=('cmake' 'zlib' 'openmp' 'vim' 'perl')
+source=("$_pkgbase-$_pkgver.tar.gz::https://github.com/soedinglab/MMseqs2/archive/refs/tags/${_pkgver}.tar.gz"
+        "bash-completion.patch"
+        "fix_util_installation.patch"
+        )
+install=bash-completion.install
+sha256sums=('faeb6841feb8e028651c2391de1346c55c2091a96520b625525d27b99d07ef1d'
+            '39432896625dca6240e7f4f6dffebd05f40a1d0de2c724d7123cb63e2464e791'
+            'ca25afde5447ec6b72e0a6ca9874eb6b5b93c2ec52ff3f10e4b3929d1aea1e71')
+prepare() {
+  cd $_pkgbase-$_pkgver
+  # add package specific information needed to enable bash autocompletion
+  patch -p1 < ${srcdir}/bash-completion.patch
+  # Prevent CMake from installing util/ contents to nonstandard /usr/util location.
+  patch -p1 < ${srcdir}/fix_util_installation.patch
+}
 
 build() {
   cd $_pkgbase-$_pkgver
@@ -50,28 +63,36 @@ build() {
 
 package_mmseqs2-sse4() {
   depends=('gcc-libs' 'glibc' 'zlib' 'zstd' 'openmp' 'bzip2' 'bash')
+  optdepends=('r: For running bundled rscript file')
   provides=('mmseqs2')
   conflicts=('mmseqs2-avx2')
   pkgdesc="ultra fast and sensitive search and clustering suite optimised for SSE4 instructions. https://doi.org/10.1038/nbt.3988"
 
   cd $_pkgbase-$_pkgver
   DESTDIR="$pkgdir" cmake --install build1
+  install -Dm644 LICENSE.md -t "$pkgdir/usr/share/licenses/${pkgname}"
+  #install -Dm644 "${srcdir}"/mmseqs2.sh "${pkgdir}"/etc/profile.d/mmseqs2.sh
   cd util
-  install -Dm644 bash-completion.sh "${pkgdir}"/etc/profile.d/mmseqs2-completion.sh
-  install -Dm644 format_substitution_matrix.R ${pkgdir}/usr/share/${pkgbase}/format_substitution_matrix.R
-  rm -rf "${pkgdir}"/usr/util
+  #install -Dm644 bash-completion.sh "${pkgdir}"/etc/profile.d/mmseqs2-completion.sh
+  install -Dm755 bash-completion.sh "${pkgdir}"/usr/share/${pkgbase}/bash-completion.sh
+  install -Dm644 format_substitution_matrix.R "${pkgdir}"/usr/share/${pkgbase}/format_substitution_matrix.R
+  #rm -rf "${pkgdir}"/usr/util
 }
 
 package_mmseqs2-avx2() {
   depends=('gcc-libs' 'glibc' 'zlib' 'zstd' 'openmp' 'bzip2' 'bash')
+  optdepends=('r: For running bundled rscript file')
   provides=('mmseqs2')
   conflicts=('mmseqs2-sse4')
   pkgdesc="ultra fast and sensitive search and clustering suite optimised for AVX2 instructions. https://doi.org/10.1038/nbt.3988"
 
   cd $_pkgbase-$_pkgver
   DESTDIR="$pkgdir" cmake --install build2
+  install -Dm644 LICENSE.md -t "$pkgdir/usr/share/licenses/${pkgname}"
+  #install -Dm644 "${srcdir}"/mmseqs2.sh "${pkgdir}"/etc/profile.d/mmseqs2.sh
   cd util
-  install -Dm644 bash-completion.sh "${pkgdir}"/etc/profile.d/mmseqs2-completion.sh
-  install -Dm644 format_substitution_matrix.R ${pkgdir}/usr/share/${pkgbase}/format_substitution_matrix.R
-  rm -rf "${pkgdir}"/usr/util
+  #install -Dm644 bash-completion.sh "${pkgdir}"/etc/profile.d/mmseqs2-completion.sh
+  install -Dm755 bash-completion.sh "${pkgdir}"/usr/share/${pkgbase}/bash-completion.sh
+  install -Dm644 format_substitution_matrix.R "${pkgdir}"/usr/share/${pkgbase}/format_substitution_matrix.R
+  #rm -rf "${pkgdir}"/usr/util
 }

BioArchLinux/mmseqs2/bash-completion.install

@@ -0,0 +1,7 @@
+post_install() {
+	echo "Enable bash autocompletion by running  [echo \"source /usr/share/mmseqs2/bash-completion.sh\" >> ~/.bashrc] in a terminal  and reopen the shell"
+}
+
+post_remove() {
+	echo "to prevent error messages during bash startup remove  \"source /usr/share/mmseqs2/bash-completion.sh\" line from ~/.bashrc"
+}

BioArchLinux/mmseqs2/bash-completion.patch

@@ -0,0 +1,13 @@
+diff --git a/src/commons/Application.cpp b/src/commons/Application.cpp
+index bfa921bf..22f34920 100644
+--- a/src/commons/Application.cpp
++++ b/src/commons/Application.cpp
+@@ -119,7 +119,7 @@ void printUsage(bool showExtended) {
+         }
+     }
+     if (show_bash_info != NULL) {
+-        usage  << "\nBash completion for modules and parameters can be installed by adding \"source MMSEQS_HOME/util/bash-completion.sh\" to your \"$HOME/.bash_profile\".\nInclude the location of the " << tool_name << " binary in your \"$PATH\" environment variable.";
++        usage  << "\nBash completion for modules and parameters can be installed by adding \"source /usr/share/mmseqs2/bash-completion.sh\" to \"$HOME/.bashrc\".\n";
+     }
+     Debug(Debug::INFO) << usage.str() << "\n";
+ }

BioArchLinux/mmseqs2/fix_util_installation.patch

@@ -0,0 +1,13 @@
+diff --git a/util/CMakeLists.txt b/util/CMakeLists.txt
+index b1bc6f14..5a0a52f4 100644
+--- a/util/CMakeLists.txt
++++ b/util/CMakeLists.txt
+@@ -1,4 +1,4 @@
+-install(PROGRAMS
+-        bash-completion.sh
+-        DESTINATION util
+-        )
++#install(PROGRAMS
++#        bash-completion.sh
++#        DESTINATION util
++#        )