diff --git a/EM/crYOLO/build b/EM/crYOLO/build new file mode 100755 index 0000000..70072a6 --- /dev/null +++ b/EM/crYOLO/build @@ -0,0 +1,40 @@ +#!/usr/bin/env modbuild + +pbuild::add_to_group 'EM' +pbuild::prep() { + echo "prepping" + mkdir -p "$SRC_DIR" + curl -fsSLo "$SRC_DIR/miniconda.sh" 'https://repo.anaconda.com/miniconda/Miniconda2-latest-Linux-x86_64.sh' + curl -fsSLo "$SRC_DIR/cryoloBM.tgz" 'ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_BM_V1_1_1/cryoloBM-1.1.1.tar.gz' + curl -fsSLo "$SRC_DIR/cryolo.tgz" 'ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_V1_2_3/cryolo-1.2.3.tar.gz' + : +} + +pbuild::configure() { + : +} + +pbuild::compile() { + : +} + +pbuild::install() { + mkdir -p $PREFIX + + # Install conda + bash "$SRC_DIR/miniconda.sh" -b -p $PREFIX/conda + + # Create environment + $PREFIX/conda/bin/conda create -y --name crYOLO anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy + + # Activate + source $PREFIX/conda/bin/activate crYOLO + + # Install + pip install $SRC_DIR/cryolo.tgz + pip install $SRC_DIR/cryoloBM.tgz + + # Deactivate + source deactivate +} + diff --git a/EM/crYOLO/files/variants b/EM/crYOLO/files/variants new file mode 100644 index 0000000..942ddbb --- /dev/null +++ b/EM/crYOLO/files/variants @@ -0,0 +1,2 @@ +crYOLO/1.2.3 unstable cuda/9.0.176 + diff --git a/EM/crYOLO/modulefile b/EM/crYOLO/modulefile new file mode 100644 index 0000000..fbafb29 --- /dev/null +++ b/EM/crYOLO/modulefile @@ -0,0 +1,51 @@ +#%Module + +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-help " +CrYOLO is a fast and accurate particle picking procedure. It's based on +convolutional neural networks and utilizes the popular You Only Look Once +(YOLO) object detection system. + + * crYOLO makes picking fast – On a modern GPU it will pick your particles at + up to 6 micrographs per second. + * crYOLO makes picking smart – The network learns the context of particles + (e.g. not to pick particles on carbon or within ice contamination ) + * crYOLO makes training easy – You might use a general network model and skip + training completely. However, if the general model doesn't give you + satisfactory results or if you would like to improve them, you might want + to train a specialized model specific for your data set by selecting + particles (no selection of negative examples necessary) on a small number + of micrographs. +" + +# Check for supported shell types +set shelltype [module-info shelltype] +switch -- $shelltype { + "sh" { + } + default { + puts stderr "Shells of type '$shelltype' are NOT supported!" + } +} + +#puts stderr "Switching crYOLO mode to [module-info mode]" +#puts stdout "{ date; echo Switching crYOLO mode to [module-info mode] ; } >> /gpfs/home/bliven_s/cryolo_mod.log;\n" + + +switch [module-info mode] { + "load" { + #puts stderr "source $PREFIX/conda/bin/activate crYOLO" + puts stdout "source $PREFIX/conda/bin/activate crYOLO;\n" + } + "unload" - + "remove" { + #puts stderr "source deactivate" + puts stdout "source $PREFIX/conda/bin/deactivate;\n" + puts stdout {unset $(set|sed -rn 's/^(_?conda[a-z_]*).*$/\1/pI');} + } +} + diff --git a/Tools/datacatalog/README.md_template b/Tools/datacatalog/README.md_template new file mode 100644 index 0000000..77355fb --- /dev/null +++ b/Tools/datacatalog/README.md_template @@ -0,0 +1,21 @@ +# The Mellanox MXM communication library + +## Overview + +The Mellanox MXM communication library provides support for the Mellanox MXM interface for InfiniBand. + +## Installation + +For the module we use a RPM distributed by HP. + +1. Create new directory `/opt/psi/System/mxm/VERSION_merlin` +1. Download RPM from https://downloads.linux.hpe.com/sdr/repo/mlnx_ofed/RedHatEnterpriseServer/ +1. Unpack RPM with `rpm2cpio RPM | cpio -i --make-dirs` somewhere +1. copy all files from `opt/mellanox/mxm` to the module directory +1. adapt directories in `lib/pkg-config/mxm.pc` +1. add new variant to `files/variants` +1. run the build-script to install the modulefile and to set the release + + +> **Note:** The shared library `libmxm.so`provided by the RPMs for RHEL 6 cannot be used to compile other software. +They requiry GLIBC >= 2.14, but on RHEL 6 only 2.12 is installed! \ No newline at end of file diff --git a/Tools/datacatalog/build b/Tools/datacatalog/build new file mode 100755 index 0000000..02013a8 --- /dev/null +++ b/Tools/datacatalog/build @@ -0,0 +1,20 @@ +#!/usr/bin/env modbuild + +pbuild::prep() { + : +} + +pbuild::configure() { + : +} + +pbuild::compile() { + : +} + +pbuild::install() { + mkdir -p "$PREFIX/bin" + /usr/bin/curl -o "$PREFIX/bin/datasetIngestor" https://intranet.psi.ch/pub/Daas/WebHome/datasetIngestor + chmod +x "$PREFIX/bin/datasetIngestor" +} + diff --git a/Tools/datacatalog/files/variants.Linux b/Tools/datacatalog/files/variants.Linux new file mode 100644 index 0000000..ba32705 --- /dev/null +++ b/Tools/datacatalog/files/variants.Linux @@ -0,0 +1,3 @@ +datacatalog/1.1.15 removed +datacatalog/1.1.3 deprecated +datacatalog/1.1.4 stable diff --git a/Tools/datacatalog/modulefile b/Tools/datacatalog/modulefile new file mode 100644 index 0000000..fb6329c --- /dev/null +++ b/Tools/datacatalog/modulefile @@ -0,0 +1,11 @@ +#%Module1.0 + +module-whatis "SciCat datacatalog related tools" +module-url "https://melanie.gitpages.psi.ch/SciCatPages/" +module-license "GPL-V3" +module-maintainer "Stephan Egli " + +module-help " +Data catalog ingest and retrieve tools. +" +