Merge branch 'cistem' into 'master'

Add cisTEM modulefile

See merge request Pmodules/buildblocks!155

EM/cisTEM/README

@@ -0,0 +1,16 @@
+# CisTEM
+
+## Installation
+
+1. Download binaries from https://cistem.org/
+2. Update files/variants
+3. Run `./build <version>` to create directories
+4. Move all executables to /opt/psi/EM/cisTEM/$VERSION/bin
+5. Copy/link files:
+
+    cisTEM_preallocate
+    cisTEM_preallocate132 -> cisTEM_preallocate
+    cisTEM_preallocate44 -> cisTEM_preallocate
+    default_run_profiles.txt -> ../settings/settings.txt
+
+6. Fix permissions: chmod 755 /opt/psi/EM/cisTEM/$VERSION/bin/*

EM/cisTEM/build

@@ -0,0 +1,22 @@
+#!/usr/bin/env modbuild
+
+# Binary distribution with manual installation. See README.md
+
+pbuild::add_to_group 'EM'
+
+pbuild::prep() {
+    :
+}
+
+pbuild::configure() {
+    :
+}
+
+pbuild::compile() {
+    :
+}
+
+pbuild::install() {
+    :
+}
+

EM/cisTEM/cisTEM_preallocate

@@ -0,0 +1,22 @@
+#!/bin/bash
+# Launch script for running cisTEM with the 'preallocated_44cpu' profile
+
+# Default arguments
+args=()
+if [[ ! "${@}" =~ -t|--time ]]; then
+    args+=(--time=08:00:00)
+fi
+if [[ ! "${@}" =~ -p|--partition ]]; then
+    args+=(--partition=daily)
+fi
+if [[ ! "${@}" =~ -n|--ntasks ]]; then
+    # Take number of tasks from the script name
+    DEFAULT_TASKS="$(echo "$0"|sed -rn 's/.*[^0-9]([0-9]+$)/\1/p')"
+    args+=(--ntasks="${DEFAULT_TASKS:-44}")
+fi
+if [[ ! "${@}" =~ -c|--cpus-per-task ]]; then
+    args+=(--cpus-per-task=2)
+fi
+
+exec interactive "${args[@]}" "$@"
+

EM/cisTEM/files/settings/2018-06-30_settings.sh

@@ -0,0 +1,17 @@
+number_of_profiles=2
+profile_0_name="slurm_128"
+profile_0_manager_command="nohup /afs/psi.ch/sys/psi.merlin/EM/cisTEM/1.0.0/cistem-1.0.0-beta/$command"
+profile_0_gui_address=""
+profile_0_controller_address=""
+profile_0_number_of_run_commands=1
+profile_0_command_0_command_to_run="sbatch /afs/psi.ch/sys/psi.merlin/EM/cisTEM/1.0.0/cistem-1.0.0-beta/slurm.sh $command"
+profile_0_command_0_number_of_copies=128
+profile_0_command_0_delay_time_in_ms=10
+profile_1_name="slurm_32"
+profile_1_manager_command="nohup /afs/psi.ch/sys/psi.merlin/EM/cisTEM/1.0.0/cistem-1.0.0-beta/$command"
+profile_1_gui_address=""
+profile_1_controller_address=""
+profile_1_number_of_run_commands=1
+profile_1_command_0_command_to_run="sbatch /afs/psi.ch/sys/psi.merlin/EM/cisTEM/1.0.0/cistem-1.0.0-beta/slurm.sh $command"
+profile_1_command_0_number_of_copies=32
+profile_1_command_0_delay_time_in_ms=10

EM/cisTEM/files/settings/2019-11-04_settings.txt

@@ -0,0 +1,33 @@
+number_of_profiles=4
+profile_0_name="preallocated 44cpu"
+profile_0_manager_command="/opt/psi/EM/cisTEM/1.0.0/cistem-1.0.0-beta/preallocated.sh $command"
+profile_0_gui_address=""
+profile_0_controller_address=""
+profile_0_number_of_run_commands=1
+profile_0_command_0_command_to_run="/opt/psi/EM/cisTEM/1.0.0/cistem-1.0.0-beta/preallocated.sh $command"
+profile_0_command_0_number_of_copies=43
+profile_0_command_0_delay_time_in_ms=10
+profile_1_name="preallocated 132cpu"
+profile_1_manager_command="/opt/psi/EM/cisTEM/1.0.0/cistem-1.0.0-beta/preallocated.sh $command"
+profile_1_gui_address=""
+profile_1_controller_address=""
+profile_1_number_of_run_commands=1
+profile_1_command_0_command_to_run="/opt/psi/EM/cisTEM/1.0.0/cistem-1.0.0-beta/preallocated.sh $command"
+profile_1_command_0_number_of_copies=131
+profile_1_command_0_delay_time_in_ms=10
+profile_2_name="allocate 44cpu"
+profile_2_manager_command="sbatch --ntasks=44 --job-name=cisTEM --partition=daily --cpus-per-task=2 /opt/psi/EM/cisTEM/1.0.0/cistem-1.0.0-beta/slurm.sh $command"
+profile_2_gui_address=""
+profile_2_controller_address=""
+profile_2_number_of_run_commands=1
+profile_2_command_0_command_to_run="srun -n 1 -c 2 $command"
+profile_2_command_0_number_of_copies=43
+profile_2_command_0_delay_time_in_ms=10
+profile_3_name="allocate 132cpu"
+profile_3_manager_command="sbatch --ntasks=132 --job-name=cisTEM --partition=daily --cpus-per-task=2 /opt/psi/EM/cisTEM/1.0.0/cistem-1.0.0-beta/slurm.sh $command"
+profile_3_gui_address=""
+profile_3_controller_address=""
+profile_3_number_of_run_commands=1
+profile_3_command_0_command_to_run="srun -n 1 -c 2 $command"
+profile_3_command_0_number_of_copies=131
+profile_3_command_0_delay_time_in_ms=10

EM/cisTEM/files/settings/settings.txt

@@ -0,0 +1 @@
+2019-11-04_settings.txt

EM/cisTEM/files/variants

@@ -0,0 +1 @@
+cistem/1.0.0	stable

EM/cisTEM/modulefile

@@ -0,0 +1,12 @@
+#%Module1.0
+
+module-whatis           "cisTEM is user-friendly software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them."
+module-url              "https://cistem.org"
+module-license          "3-clause BSD <http://license.janelia.org/license/janelia_license_1_2.html>"
+module-maintainer       "Spencer Bliven <spencer.bliven@psi.ch>"
+
+module-help     "
+cisTEM is user-friendly software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them. It was developed by Tim Grant, Alexis Rohou and Nikolaus Grigorieff and comprises a number of tools to process image data including movies, micrographs and stacks of single-particle images, implementing a complete “pipeline” of processing steps to obtain high-resolution single-particle reconstructions. 
+"
+
+prepend-path    PATH            $PREFIX/cistem-1.0.0-beta

EM/cisTEM/preallocated.sh

@@ -0,0 +1,9 @@
+#!/bin/bash
+# Wrapper for the 'preallocated' default profiles
+# usage in cistem profile: preallocated.sh $command
+set -e
+
+# Ensure we actually allocated resources
+: "${SLURM_NODELIST:?Error: No nodes preallocated! See https://intranet.psi.ch/BIO/ComputingCisTEM}"
+
+srun -N 1 -n 1 -c 2 --exclusive $@