Merge branch 'EESSI:2023.06-software.eessi.io' into siesta

Author: ocaisa

easystacks/software.eessi.io/2023.06/grace/eessi-2023.06-eb-4.9.4-2023a.yml

@@ -90,3 +90,13 @@ easyconfigs:
   - PostgreSQL-16.1-GCCcore-12.3.0.eb
   - ImageMagick-7.1.1-15-GCCcore-12.3.0.eb
   - GDAL-3.7.1-foss-2023a.eb
+  - ncdu-1.18-GCC-12.3.0.eb
+  - SAMtools-1.18-GCC-12.3.0.eb
+  - R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb
+  - ipympl-0.9.3-gfbf-2023a.eb
+  - ESPResSo-4.2.2-foss-2023a.eb
+  - GATK-4.5.0.0-GCCcore-12.3.0-Java-17.eb
+  - WhatsHap-2.2-foss-2023a.eb
+  - BLAST+-2.14.1-gompi-2023a.eb
+  - Valgrind-3.21.0-gompi-2023a.eb
+  - OrthoFinder-2.5.5-foss-2023a.eb

install_apptainer_ubuntu.sh

@@ -2,30 +2,13 @@
 
 set -e
 
-# see https://github.com/apptainer/singularity/issues/5390#issuecomment-899111181
-sudo apt-get install alien
-alien --version
-epel_subdir="pub/epel/8"
-apptainer_rpm=$(curl --silent -L https://dl.fedoraproject.org/${epel_subdir}/Everything/x86_64/Packages/a/ | grep 'apptainer-[0-9]' | sed 's/.*\(apptainer[0-9._a-z-]*.rpm\).*/\1/g')
-curl -OL https://dl.fedoraproject.org/${epel_subdir}/Everything/x86_64/Packages/a/${apptainer_rpm}
-sudo alien -d ${apptainer_rpm}
-sudo apt install ./apptainer*.deb
-# No unpriviledged user name spaces in Ubuntu 23.10+
-ubuntu_version=$(lsb_release -r | awk '{print $2}')
-if [[ $(echo -e "$ubuntu_version\n23.10" | sort -V | head -n 1) == "23.10" ]]; then
-    sudo tee /etc/apparmor.d/apptainer << 'EOF'
-# Permit unprivileged user namespace creation for apptainer starter
-abi <abi/4.0>,
-include <tunables/global>
-profile apptainer /usr/libexec/apptainer/bin/starter{,-suid}
-    flags=(unconfined) {
-  userns,
-  # Site-specific additions and overrides. See local/README for details.
-  include if exists <local/apptainer>
-}
-EOF
-    sudo systemctl reload apparmor
-fi
+sudo apt update
+sudo apt install -y software-properties-common
+
+sudo add-apt-repository -y ppa:apptainer/ppa
+sudo apt update
+sudo apt install -y apptainer-suid
+
 apptainer --version
 # also check whether 'singularity' command is still provided by Apptainer installation
 singularity --version