diff --git a/EM/PEET/README.md b/EM/PEET/README.md index 9828d75..fb5b585 100644 --- a/EM/PEET/README.md +++ b/EM/PEET/README.md @@ -6,9 +6,7 @@ PEET is shipped as a self-expanding installation script. Run `./build` to install. - -An experimental config.yaml files is included using Pmodules/1.1.10 syntax. -This should probably not be used until yaml support in modbuild stabilizes. +This module is usually used in combination with IMOD (etomo GUI). ## Testing @@ -16,12 +14,17 @@ This should probably not be used until yaml support in modbuild stabilizes. ## Build notes -Building was successful with Pmodules 1.1.8 but not 1.1.9 or 1.1.10. Linking the binary is a bit of a pain. It requires gcc to be loaded to provide relatively recent versions of libstdc++.so.6. I didn't fine what exact version Matlab MCR expects, but 9.5.0 seemed to work. MCR is linked dynamically at runtime through LD_LIBRARY_PATH. This is not set in the modulefile as expected, but rather in wrapper scripts which source particle.cfg. Sed commands in -pbuild::install update this file so that it reads the loaded modules correctly. +pbuild::install update this file so that it reads the loaded modules correctly. +(Remark Nov. 2024: still true for version 1.17.0) +## Versions + +According to the website (INSTALL.TXT) the following Matlab is needed : + +-1.17.0 : 2022b (Merlin7, automatically loads matlab) diff --git a/EM/PEET/build b/EM/PEET/build index 27d7f66..caceb01 100755 --- a/EM/PEET/build +++ b/EM/PEET/build @@ -1,6 +1,5 @@ #!/usr/bin/env modbuild -pbuild::add_to_group 'EM' pbuild::prep() { @@ -13,6 +12,7 @@ pbuild::prep() { --fail \ --output "$dst" \ "https://bio3d.colorado.edu/ftp/PEET/linux/Particle_${V_PKG}_linux.sh" + --no-check-certificate fi } diff --git a/EM/PEET/files/_config.yaml.disable b/EM/PEET/files/_config.yaml.disable deleted file mode 100644 index 64da532..0000000 --- a/EM/PEET/files/_config.yaml.disable +++ /dev/null @@ -1,8 +0,0 @@ -overlay: base -relstage: stable -group: EM -shasums: - PEET/1.15.1a: de4e9104f90b9379502a34b58be33eafd5514d554002a94efe2adba6f44785e6 - -PEET/1.15.1a: - - relstage: unstable diff --git a/EM/PEET/files/config.yaml b/EM/PEET/files/config.yaml new file mode 100644 index 0000000..5470687 --- /dev/null +++ b/EM/PEET/files/config.yaml @@ -0,0 +1,16 @@ +--- +format: 1 +PEET: + defaults: + group: EM + overlay: base + relstage: unstable + versions: + 1.17.0: + variants: + - overlay: Alps + systems: [.*.merlin7.psi.ch] + relstage: unstable + runtime_deps: + - gcc/12.3.0 + - matlab/2022b diff --git a/EM/PEET/files/variants b/EM/PEET/files/variants deleted file mode 100644 index 05b2b61..0000000 --- a/EM/PEET/files/variants +++ /dev/null @@ -1,2 +0,0 @@ -PEET/1.15.1a stable gcc/9.5.0 matlab/2020b -PEET/1.16.0 stable gcc/9.5.0 matlab/2021b diff --git a/EM/PEET/modulefile b/EM/PEET/modulefile index 7510133..f95a274 100644 --- a/EM/PEET/modulefile +++ b/EM/PEET/modulefile @@ -3,7 +3,7 @@ module-whatis "PEET (Particle Estimation for Electron Tomography) is an open-source package for aligning and averaging particles in 3-D subvolumes extracted from tomograms." module-url "https://bio3d.colorado.edu/PEET/" module-license "GPLv2 license" -module-maintainer "Spencer Bliven " +module-maintainer "Greta Assmann " module-help " PEET (Particle Estimation for Electron Tomography) is an open-source package