diff --git a/EM/crYOLO/README.md b/EM/crYOLO/README.md index 9845306..0af8110 100644 --- a/EM/crYOLO/README.md +++ b/EM/crYOLO/README.md @@ -1,14 +1,15 @@ # crYOLO crYOLO/1.2.3 was built as a miniconda independent environment. -Subsequent versions are deployed as central conda environments. -This significantly changed the build process. +Subsequent versions (up to 1.6.1) are deployed as central conda environments + +crYOLO/1.9.9 (Merlin7, oct 2024) is installed with an independent miniconda setup again. + +From crYOLO/1.9.9 crYOLO exists as two different conda envs, one crYOLO (code itself) env, one napari (visualization) env. +The installation notes recommend to link one into another, on Merlin7 simply two different modules and envs exist. +Users need to load one env in one terminal ( crYOLO itself) and another for visualization (napari). ## Adding New Versions -To add a new version, first create the conda environment, as described in -../../Programming/anaconda/2019.07/conda-env-defs/cryolo/. - -Next, update files/variants with the new version and run `./build ` to -install the modulefile +Adding new versions: change the environment file in the build folder accordingly (and the config.yaml file) and run the build script. diff --git a/EM/crYOLO/build b/EM/crYOLO/build index 6f1766a..789c7bd 100755 --- a/EM/crYOLO/build +++ b/EM/crYOLO/build @@ -1,20 +1,27 @@ #!/usr/bin/env modbuild -pbuild::add_to_group 'EM' -pbuild::prep() { - : -} - pbuild::configure() { + #MINICONDA INSTALL + mkdir -p "$PREFIX/miniconda" + wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O "$PREFIX/miniconda/miniconda.sh" + bash "$PREFIX/miniconda/miniconda.sh" -b -u -p "$PREFIX/miniconda/" + + + #CREATE ENV , make sure to source the "correct" conda.sh + "$PREFIX/miniconda/condabin/conda" env create --name "${P}_${V}" -f "$BUILDBLOCK_DIR/environment.yaml" + +} + +#DO NOTHING +pbuild::compile(){ : } -pbuild::compile() { +pbuild::install(){ : } -pbuild::install() { - : -} + + diff --git a/EM/crYOLO/files/config-1.2.3.sh b/EM/crYOLO/files/config-1.2.3.sh deleted file mode 100644 index 319d977..0000000 --- a/EM/crYOLO/files/config-1.2.3.sh +++ /dev/null @@ -1,10 +0,0 @@ -# crYOLO configuration variables - -# Miniconda installer filename. Defaults to 'latest' -MINICONDA_VERSION='Miniconda2-4.5.12-Linux-x86_64.sh' - -# cryoloBM download url -CRYOLOBM_URL='ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_BM_V1_1_1/cryoloBM-1.1.1.tar.gz' -# cryolo download url. Default: -#CRYOLO_URL='ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_V1_2_3/cryolo-1.2.3.tar.gz' - diff --git a/EM/crYOLO/files/config.yaml b/EM/crYOLO/files/config.yaml new file mode 100644 index 0000000..8b6b49a --- /dev/null +++ b/EM/crYOLO/files/config.yaml @@ -0,0 +1,13 @@ +--- +format: 1 +crYOLO: + defaults: + group: EM + overlay: base + relstage: unstable + versions: + 1.9.9: + variants: + - overlay: Alps + systems: [.*.merlin7.psi.ch] + relstage: unstable diff --git a/EM/crYOLO/files/variants b/EM/crYOLO/files/variants deleted file mode 100644 index 3248392..0000000 --- a/EM/crYOLO/files/variants +++ /dev/null @@ -1,5 +0,0 @@ -crYOLO/1.2.3 deprecated cuda/9.0.176 -crYOLO/1.5.6_gpu stable anaconda/2019.07 -crYOLO/1.6.1_gpu stable anaconda/2019.07 -crYOLO/1.6.1_cpu stable anaconda/2019.07 - diff --git a/EM/crYOLO/modulefile b/EM/crYOLO/modulefile index 41cf27a..4a9df37 100644 --- a/EM/crYOLO/modulefile +++ b/EM/crYOLO/modulefile @@ -3,7 +3,7 @@ module-whatis "crYOLO is a fast and accurate particle picking procedure for electron microscopy" module-url "http://sphire.mpg.de/wiki/doku.php?id=pipeline:window:cryolo" module-license "SPHIRE-crYOLO Complimentary Science Software License (http://sphire.mpg.de/wiki/doku.php?id=cryolo_license). Non-commercial academic and research purposes only" -module-maintainer "Spencer Bliven " +module-maintainer "Greta Assmann " module-help " CrYOLO is a fast and accurate particle picking procedure. It's based on @@ -26,28 +26,20 @@ convolutional neural networks and utilizes the popular You Only Look Once set shelltype [module-info shelltype] switch -- $shelltype { "sh" { - puts stdout "source \"\${ANACONDA_PREFIX}\"/admintools/conda_setup.sh;\n" + puts stdout "conda(){ :; };" + puts stdout "set +u" + puts stdout "source \"${PREFIX}\"/miniconda/etc/profile.d/conda.sh;\n" } default { puts stderr "Shells of type '$shelltype' are NOT supported!" } } -# Determine useflags and construct conda env name -set list [split $V "_"] -set version [lindex ${list} 0] -set useflags [lrange ${list} 1 end] -set flavour [lindex $useflags 0] -set env_to_activate [string tolower ${P}]-${version}-${flavour} - -#puts stderr "P/V: $P/$V" -#puts stderr "USEFLAG: [lindex $useflags 0]" -#puts stderr "$env_to_activate" switch [module-info mode] { "load" { # Relies on the anaconda module being loaded since we need to update the path - puts stdout "conda activate $env_to_activate;\n" + puts stdout "conda activate ${P}_${V};\n" } "unload" - "remove" {