adding newest mamba

build_images.py

@@ -0,0 +1,49 @@
+#!/usr/bin/env bash
+
+import glob
+import os
+import shutil
+import fileinput
+import datetime
+
+ymls = glob.glob("**/**/environment.yml", recursive=True)
+yamls = glob.glob("**/**/environment.yaml", recursive=True)
+
+yamls.extend(ymls)
+
+top_dir = os.getcwd()
+date_tag = datetime.datetime.now().strftime('%Y.%m.%d')
+
+build_images = []
+for env in yamls:
+    base_dir = os.path.dirname(env)
+    if os.path.exists(os.path.join(base_dir, ".skip-jupyter-repo2docker")):
+        print("Skipping: ", base_dir)
+        continue
+    print(f"Processing: {base_dir}")
+    dirs = base_dir.split("/")
+    version = dirs.pop()
+    name = dirs.pop()
+    if not os.path.exists(base_dir):
+        continue
+    os.chdir(base_dir)
+    image = f"dabbleofdevops/binder-{name}:{version}"
+    cmd = f"jupyter-repo2docker --no-run --image-name {image} ."
+    print(f"Running: {name}:{version}")
+
+    try:
+        os.system(
+            cmd
+        )
+    except Exception as e:
+        print(f"Error: {e}")
+        continue
+
+    print(f"Complete: {name}:{version}")
+    os.system(f"docker push {image}")
+    os.system(f"docker tag {image} {name}:{date_tag}")
+    os.system(f"docker push {name}:{date_tag}")
+    build_images.append(image)
+
+print("Complete")
+print(build_images)

easybuild/easyconfigs/alphafold/2.2.2/alphafold-2.2.2.eb

@@ -0,0 +1,25 @@
+easyblock = 'Conda'
+
+name = 'alphafold'
+version = '2.2.2'
+
+homepage = 'https://alphafold.ebi.ac.uk/'
+description = "AlphaFold Protein Structure Database"
+toolchain = SYSTEM
+
+builddependencies = [('Miniconda3', '4.12.0')]
+
+environment_file = "environment.yml"
+sources = ["%(namelower)s-%(version)s.yml", "install-%(namelower)s-%(version)s.sh", "%(namelower)s-%(version)s-requirements.txt"]
+sanity_check_commands = ['python --version']
+
+postinstallcmds = [
+"""
+export INSTALLDIR=%(installdir)s && \
+export BUILDDIR=%(builddir)s && \
+chmod 777 *sh && \
+bash ./install-%(namelower)s-%(version)s.sh
+"""
+]
+
+moduleclass = 'bio'

easybuild/easyconfigs/alphafold/alphafold-2.2.2.yml → easybuild/easyconfigs/alphafold/2.2.2/environment.yml

@@ -37,15 +37,11 @@ dependencies:
   - pdbfixer
   - python-graphviz
   - nglview
-  - dask
-  - dask-gateway-server-jobqueue
-  - dask-gateway
   - colorlog
   - typer
   - rich
   - pydantic
   - pip
   - pip:
       - funcy
-      - aws-pcluster-dask-gateway
       - https://github.com/deepmind/alphafold/archive/refs/tags/v2.2.2.tar.gz

easybuild/easyconfigs/amber/22/amber-22.eb.bak

@@ -0,0 +1,53 @@
+easyblock = 'Conda'
+
+name = 'Amber'
+local_amber_ver = 22
+local_ambertools_ver = 22
+# Patch levels from https://ambermd.org/AmberPatches.php and https://ambermd.org/ATPatches.php
+patchlevels = (3, 0)  # (AmberTools, Amber)
+version = '%s.%s' % (local_amber_ver, patchlevels[1])
+versionsuffix = '-AmberTools-%s.%s' % (local_ambertools_ver, patchlevels[0])
+
+homepage = 'https://ambermd.org/amber.html'
+description = """Amber (originally Assisted Model Building with Energy Refinement) is software for performing
+ molecular dynamics and structure prediction."""
+
+toolchain = SYSTEM
+#toolchain = {'name': 'foss', 'version': '2021b'}
+#toolchainopts = {'usempi': True, 'openmp': True}
+
+sources = [
+    '%%(name)s%s.tar.bz2' % local_amber_ver,
+    'AmberTools%s.tar.bz2' % local_ambertools_ver,
+]
+patches = [
+]
+checksums = [
+    '3c887ccbad690fc76ff0b120a3448eae023c08e76582aac07900d4a9708ebd16',  # Amber22.tar.bz2
+    '1571d4e0f7d45b2a71dce5999fa875aea8c90ee219eb218d7916bf30ea229121',  # AmberTools22.tar.bz2
+]
+
+builddependencies = [
+]
+
+dependencies = [
+]
+
+# All tests are expected to pass or be skipped
+#runtest = True
+
+#static = False
+
+sanity_check_commands = ['python --version']
+
+postinstallcmds = [
+"""
+export INSTALLDIR=%(installdir)s && \
+export BUILDDIR=%(builddir)s && \
+export PREFIX=%(prefix)s && \
+chmod 777 *sh && \
+bash ./install-%(namelower)s-%(version)s.sh
+"""
+]
+
+moduleclass = 'chem'

easybuild/easyconfigs/dask/2023.7.0/dask-2023.7.0.eb

@@ -0,0 +1,18 @@
+easyblock = 'Conda'
+
+name = 'dask'
+version = '2023.7.0'
+
+homepage = 'https://www.dask.org/'
+description = """Dask makes it easy to scale the Python libraries that you know and love like NumPy, pandas, and scikit-learn."""
+
+toolchain = SYSTEM
+
+builddependencies = [('Miniconda3', '4.12.0')]
+sources = ["%(namelower)s-%(version)s.yml"]
+environment_file = "environment.yml"
+
+sanity_check_commands = ['python --version']
+
+moduleclass = 'tools'
+

easybuild/easyconfigs/deepchem/jax-2.6.1/deepchem-jax-2.6.1.eb

@@ -0,0 +1,18 @@
+
+easyblock = 'Conda'
+
+name = 'deepchem-jax'
+version = '2.6.1'
+
+homepage = 'https://github.com/deepchem/deepchem'
+description = """DeepChem aims to provide a high quality open-source toolchain that democratizes the use of deep-learning in drug discovery, materials science, quantum chemistry, and biology."""
+
+toolchain = SYSTEM
+
+builddependencies = [('Miniconda3', '4.12.0')]
+sources = ["%(namelower)s-%(version)s.yml"]
+environment_file = "environment.yml"
+
+sanity_check_commands = ['python --version']
+
+moduleclass = 'bio'

easybuild/easyconfigs/deepchem/deepchem-jax-2.6.1.yml → easybuild/easyconfigs/deepchem/jax-2.6.1/environment.yml

@@ -5,8 +5,6 @@ channels:
   - defaults
 dependencies:
   - python=3.9
-  - ipython
-  - ipykernel
   - deepchem
   - pip
   - pip:

easybuild/easyconfigs/deepchem/tensorflow-2.6.1/deepchem-tensorflow-2.6.1.eb

@@ -0,0 +1,18 @@
+
+easyblock = 'Conda'
+
+name = 'deepchem-tensorflow'
+version = '2.6.1'
+
+homepage = 'https://github.com/deepchem/deepchem'
+description = """DeepChem aims to provide a high quality open-source toolchain that democratizes the use of deep-learning in drug discovery, materials science, quantum chemistry, and biology."""
+
+toolchain = SYSTEM
+
+builddependencies = [('Miniconda3', '4.12.0')]
+sources = ["%(namelower)s-%(version)s.yml"]
+environment_file = "environment.yml"
+
+sanity_check_commands = ['python --version']
+
+moduleclass = 'bio'

easybuild/easyconfigs/deepchem/torch-2.6.1/deepchem-torch-2.6.1.eb

@@ -0,0 +1,18 @@
+
+easyblock = 'Conda'
+
+name = 'deepchem-torch'
+version = '2.6.1'
+
+homepage = 'https://github.com/deepchem/deepchem'
+description = """DeepChem aims to provide a high quality open-source toolchain that democratizes the use of deep-learning in drug discovery, materials science, quantum chemistry, and biology."""
+
+toolchain = SYSTEM
+
+builddependencies = [('Miniconda3', '4.12.0')]
+sources = ["%(namelower)s-%(version)s.yml"]
+environment_file = "environment.yml"
+
+sanity_check_commands = ['python --version']
+
+moduleclass = 'bio'

easybuild/easyconfigs/deeplabcut/deeplabcut/2.3/deeplabcut-2.3.eb

@@ -0,0 +1,16 @@
+easyblock = 'Conda'
+
+name = 'deeplabcut'
+version = '2.3'
+
+homepage = 'http://deeplabcut.org/'
+description = "Official implementation of DeepLabCut: Markerless pose estimation of user-defined features with deep learning for all animals incl. humans"
+toolchain = SYSTEM
+
+builddependencies = [('Miniconda3', '4.12.0')]
+
+environment_file = "environment.yml"
+sources = ["%(namelower)s-%(version)s.yml"]
+sanity_check_commands = ['python --version']
+
+moduleclass = 'bio'

easybuild/easyconfigs/docking/1.0/docking-1.0.eb

@@ -0,0 +1,16 @@
+easyblock = 'Conda'
+
+name = 'docking'
+version = '1.0'
+
+homepage = 'https://openbabel.org/'
+description = "A chemical toolbox designed to speak the many languages of chemical data."
+toolchain = SYSTEM
+
+builddependencies = [('Miniconda3', '4.12.0')]
+
+environment_file = "environment.yml"
+sources = ["%(namelower)s-%(version)s.yml"]
+sanity_check_commands = ['python --version']
+
+moduleclass = 'chem'

easybuild/easyconfigs/easybuild/4.5.4/easybuild-4.5.4.eb

@@ -0,0 +1,18 @@
+
+easyblock = 'Conda'
+
+name = 'EasyBuild'
+version = '4.5.4'
+
+homepage = 'https://easybuild.io'
+description = """EasyBuild is a software build and installation framework that allows you to manage (scientific) software on High Performance Computing (HPC) systems in an efficient way."""
+
+toolchain = SYSTEM
+
+builddependencies = [('Miniconda3', '4.12.0')]
+sources = ["%(namelower)s-%(version)s.yml"]
+environment_file = "environment.yml"
+
+sanity_check_commands = ['python --version']
+
+moduleclass = 'tools'

easybuild/easyconfigs/foldseek/7.04e0ec8/apt.txt

@@ -0,0 +1,5 @@
+bzip2
+unzip
+tar
+rsync
+build-essential

easybuild/easyconfigs/foldseek-7.04e0ec8.yml → easybuild/easyconfigs/foldseek/7.04e0ec8/environment.yml

@@ -3,7 +3,7 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-- python=3.6
+#- python=3.6
 - pip
 - foldseek=7.04e0ec8
 - panel

easybuild/easyconfigs/foldseek/7.04e0ec8/foldseek-7.04e0ec8.eb

@@ -0,0 +1,18 @@
+easyblock = 'Conda'
+
+name = 'foldseek'
+version = '7.04e0ec8'
+
+homepage = 'https://github.com/steineggerlab/foldseek'
+description = """Foldseek enables fast and sensitive comparisons of large structure sets."""
+
+toolchain = SYSTEM
+
+builddependencies = [('Miniconda3', '4.12.0')]
+sources = ["%(namelower)s-%(version)s.yml"]
+environment_file = "environment.yml"
+
+sanity_check_commands = ['python --version']
+
+moduleclass = 'bio'
+

easybuild/easyconfigs/pangeo-notebook-2022.05.10/datascience-2022.05.10.eb → easybuild/easyconfigs/jupyterlab/2022.05.10/jupyterlab-2022.05.10.eb

@@ -1,18 +1,17 @@
+
 easyblock = 'Conda'
 
-name = 'datascience'
+name = 'jupyterlab'
 version = '2022.05.10'
 
 homepage = 'https://github.com/pangeo-data'
-description = """General Data Science Environment
-Jupyterlab : Pangeo 2022.05.10
-Sphinx, Myst Parser, NBSphinx, and other data science extensions"""
+description = "Jupyterlab : Pangeo 2022.05.10"
 toolchain = SYSTEM
 
-environment_file = "%(namelower)s-%(version)s.yml"
+environment_file = "environment.yml"
 sources = ["%(namelower)s-%(version)s.yml"]
 sanity_check_commands = ['python --version']
 
 builddependencies = [('Miniconda3', '4.12.0')]
 
-moduleclass = 'bio'
+moduleclass = 'bio'

easybuild/easyconfigs/jupyterlab/2023.07.10/jupyterlab-2023.07.10.eb

@@ -0,0 +1,17 @@
+
+easyblock = 'Conda'
+
+name = 'jupyterlab'
+version = '2023.07.10'
+
+homepage = 'https://github.com/pangeo-data'
+description = "Jupyterlab"
+toolchain = SYSTEM
+
+environment_file = "environment.yml"
+sources = ["%(namelower)s-%(version)s.yml"]
+sanity_check_commands = ['python --version']
+
+builddependencies = [('Miniconda3', '4.12.0')]
+
+moduleclass = 'bio'

easybuild/easyconfigs/jupyterlab/2023.09.17/jupyterlab-2023.09.17.eb

@@ -0,0 +1,17 @@
+
+easyblock = 'Conda'
+
+name = 'jupyterlab'
+version = '2023.09.17'
+
+homepage = 'https://github.com/pangeo-data'
+description = "Jupyterlab"
+toolchain = SYSTEM
+
+environment_file = "environment.yml"
+sources = ["%(namelower)s-%(version)s.yml"]
+sanity_check_commands = ['python --version']
+
+builddependencies = [('Miniconda3', '4.12.0')]
+
+moduleclass = 'bio'

easybuild/easyconfigs/mdanalysis/2.4.2/mdanalysis-2.4.2.eb

@@ -0,0 +1,16 @@
+easyblock = 'Conda'
+
+name = 'mdanalysis'
+version = '2.4.2'
+
+homepage = 'https://www.mdanalysis.org/'
+description = "A Python package for the handling and analysis of molecular simulations data."
+toolchain = SYSTEM
+
+builddependencies = [('Miniconda3', '4.12.0')]
+
+environment_file = "environment.yml"
+sources = ["%(namelower)s-%(version)s.yml"]
+sanity_check_commands = ['python --version']
+
+moduleclass = 'chem'