Updated CMake

Updated cactus
Added igraph
Updated SignalP
Updated umap-learn

easyconfigs/c/CMake/CMake-3.29.5-IGB-gcc-8.2.0.eb

@@ -0,0 +1,31 @@
+easyblock = 'ConfigureMake'
+
+name = 'CMake'
+version = '3.29.5'
+
+homepage = 'http://www.cmake.org'
+description = """CMake, the cross-platform, open-source build system.
+ CMake is a family of tools designed to build, test and package software."""
+
+toolchain = {'name': 'IGB-gcc', 'version': '8.2.0'}
+
+source_urls = ['https:/Kitware/CMake/releases/download/v%(version)s/']
+sources = [SOURCELOWER_TAR_GZ]
+
+configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES'
+
+dependencies = [
+ ('ncurses', '6.1'),
+ # OS dependency should be preferred if the os version is more recent then this version,
+ # it's nice to have an up to date openssl for security reasons
+ # ('OpenSSL', '1.0.2j'),
+]
+
+osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')]
+
+sanity_check_paths = {
+ 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']],
+ 'dirs': [],
+}
+
+moduleclass = 'devel'

easyconfigs/c/cactus/cactus-2.8.2.eb

@@ -0,0 +1,26 @@
+easyblock = 'Tarball'
+
+name = 'cactus'
+version = '2.8.2'
+
+homepage = 'https:/ComparativeGenomicsToolkit/cactus'
+description = """Cactus is a reference-free whole-genome alignment program, as well as a pangenome graph construction toolkit."""
+
+toolchain = SYSTEM
+
+sources = ['cactus-bin-v%(version)s.tar.gz']
+source_urls = ['https:/ComparativeGenomicsToolkit/cactus/releases/download/v%(version)s/']
+
+dependencies = [
+]
+
+keepsymlinks = True
+
+sanity_check_paths = {
+ 'files': ['bin/cactus_analyseAssembly'],
+ 'dirs': [],
+}
+
+modextrapaths = {}
+
+moduleclass = 'bio'

easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.12-IGB-gcc-8.2.0-Python-3.7.2.eb

@@ -15,6 +15,7 @@ source_urls = [PYPI_LOWER_SOURCE]
 dependencies = [
  ('Python', '3.7.2'),
  ('Biopython','1.76','-Python-%(pyver)s'),
+ ('DIAMOND','2.0.15'),
 ]
 
 
@@ -47,5 +48,5 @@ sanity_check_paths = {
  'dirs': [],
 }
 
-postinstallcmds = ['mkdir %(installdir)s/lib/python%(pyshortver)s/site-packages/data
+postinstallcmds = ['mkdir %(installdir)s/lib/python%(pyshortver)s/site-packages/data']
 moduleclass = 'bio'

easyconfigs/i/igraph/igraph-0.10.12-IGB-gcc-8.2.0.eb

@@ -0,0 +1,37 @@
+easyblock = 'CMakeMake'
+
+name = 'igraph'
+version = '0.10.12'
+
+homepage = 'https://igraph.org'
+description = """igraph is a library for creating and manipulating graphs. You can look at it in two ways: first, igraph contains the implementation of quite a lot of graph algorithms."""
+
+toolchain = {'name': 'IGB-gcc', 'version': '8.2.0'}
+toolchainopts = {'pic': True}
+
+sources = ['igraph-%(version)s.tar.gz']
+source_urls = ['https:/igraph/igraph/releases/download/%(version)s/']
+
+builddependencies = [('CMake', '3.29.5')]
+
+
+dependencies = [
+ ('libxml2','2.9.7'),
+]
+
+separate_build_dir = True
+
+configopts = ["-DBUILD_SHARED_LIBS=OFF", "-DBUILD_SHARED_LIBS=ON", "-DIGRAPH_OPENMP_SUPPORT=ON","-DIGRAPH_ENABLE_TLS=ON"]
+
+sanity_check_paths = {
+ 'files': ['include/igraph/igraph.h'] + ['lib/libigraph.%s' % x for x in ['a', SHLIB_EXT]],
+ 'dirs': [],
+}
+
+modextrapaths = {
+}
+
+
+moduleclass = 'bio'
+
+

easyconfigs/i/igraph/igraph-0.11.5-IGB-gcc-8.2.0-Python-3.10.1.eb

@@ -0,0 +1,45 @@
+easyblock = 'PythonPackage'
+
+name = 'igraph'
+version = '0.11.5'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://python.igraph.org/en/stable/'
+description = """Python interface of igraph, a fast and open source C library to manipulate and analyze graphs (aka networks). It can be used to:"""
+
+toolchain = {'name': 'IGB-gcc', 'version': '8.2.0'}
+
+sources = ['igraph-%(version)s-cp39-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl']
+source_urls = [PYPI_LOWER_SOURCE]
+
+dependencies = [
+ ('Python', '3.10.1'),
+]
+
+
+exts_default_options = {
+ 'source_urls': [PYPI_SOURCE],
+ 'sanity_pip_check': True,
+}
+
+exts_defaultclass = "PythonPackage"
+exts_list = [
+ ('texttable','1.7.0', {
+ 'source_tmpl': 'texttable-%(version)s-py2.py3-none-any.whl'
+ }),
+ ('leidenalg','0.10.2',
+]
+
+use_pip = True
+sanity_pip_check = True
+unpack_sources = False
+#use_pip_for_deps = True
+
+exts_filter = ('python -c "import %(ext_name)s"', "")
+
+sanity_check_paths = {
+ 'files': [],
+ 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'],
+}
+
+moduleclass = 'bio'

easyconfigs/l/leidenalg/leidenalg-0.10.2-IGB-gcc-8.2.0-Python-3.10.1.eb

@@ -0,0 +1,41 @@
+easyblock = 'PythonPackage'
+
+name = 'leidenalg'
+version = '0.10.2'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://pypi.org/project/leidenalg/'
+description = """This package implements the Leiden algorithm in C++ and exposes it to python. It relies on (python-)igraph for it to function."""
+
+toolchain = {'name': 'IGB-gcc', 'version': '8.2.0'}
+
+sources = ['leidenalg-%(version)s-cp38-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl']
+source_urls = [PYPI_LOWER_SOURCE]
+
+dependencies = [
+ ('Python', '3.10.1'),
+ ('igraph','0.11.5','-Python-%(pyver)s'),
+]
+
+
+exts_default_options = {
+ 'source_urls': [PYPI_SOURCE],
+ 'sanity_pip_check': True,
+}
+
+exts_defaultclass = "PythonPackage"
+exts_list = []
+
+use_pip = True
+sanity_pip_check = True
+unpack_sources = False
+#use_pip_for_deps = True
+
+exts_filter = ('python -c "import %(ext_name)s"', "")
+
+sanity_check_paths = {
+ 'files': [],
+ 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'],
+}
+
+moduleclass = 'bio'

easyconfigs/m/Mayo/Mayo-2024-IGB-gcc-8.2.0.eb

@@ -10,8 +10,17 @@ toolchain = {'name': 'IGB-gcc', 'version': '8.2.0'}
 
 dependencies = [
  ('Python','3.10.1'),
- ('PyTorch','1.12.1','-Python-%(pyver)s'),
+ #('PyTorch','1.12.1','-Python-%(pyver)s'),
+ ('PyTorch','1.13.1','-Python-%(pyver)s'),
  ('transformers','4.40.2','-Python-%(pyver)s'),
+ ('seqkit','2.6.1','',True),
+ ('hifiasm','0.19.6'),
+ ('Bandage','0.8.1','',True),
+ ('gfatools','0.5'),
+ ('scanpy','1.10.1','-Python-%(pyver)s'),
+ ('igraph','0.11.5','-Python-%(pyver)s'),
+ ('leidenalg','0.10.2','-Python-%(pyver)s'),
+ ('R','4.4.0'),
 ]
 
 modextrapaths = {}

easyconfigs/r/R/R-4.4.0-IGB-gcc-8.2.0.eb

@@ -46,6 +46,7 @@ dependencies = [
  ('GDAL','3.9.0'),
  ('GEOS','3.8.0'),
  ('GMP','6.1.2'),
+ ('GSL','2.5'),
 
 ]
 

easyconfigs/s/SignalP/SignalP-6.0h-IGB-gcc-8.2.0-Python-3.10.1.eb

@@ -39,4 +39,6 @@ sanity_check_paths = {
  'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'],
 }
 
+postinstallcmds = ['cp -fR %(builddir)s/signalp6_fast/signalp-6-package/models/* %(installdir)s/lib/python%(pyshortver)s/site-packages/%(namelower)s/model_weights']
+
 moduleclass = 'bio'

easyconfigs/s/scanpy/scanpy-1.10.1-IGB-gcc-8.2.0-Python-3.10.1.eb

@@ -0,0 +1,71 @@
+easyblock = 'PythonPackage'
+
+name = 'scanpy'
+version = '1.10.1'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://scverse.org/'
+description = """Scanpy is a scalable toolkit for analyzing single-cell gene expression data built jointly with anndata."""
+
+toolchain = {'name': 'IGB-gcc', 'version': '8.2.0'}
+
+sources = ['scanpy-%(version)s-py3-none-any.whl']
+source_urls = [PYPI_LOWER_SOURCE]
+
+dependencies = [
+ ('Python', '3.10.1'),
+ ('numba','0.59.0','-Python-%(pyver)s'),
+ ('umap-learn','0.5.6','-Python-%(pyver)s'),
+]
+
+
+exts_default_options = {
+ 'source_urls': [PYPI_SOURCE],
+ 'sanity_pip_check': True,
+}
+
+exts_defaultclass = "PythonPackage"
+exts_list = [
+ ('array-api-compat','1.7.1', {
+ 'source_tmpl': 'array_api_compat-%(version)s-py3-none-any.whl'
+ }),
+ ('anndata','0.10.7',{
+ 'source_tmpl': 'anndata-%(version)s-py3-none-any.whl'
+ }),
+ ('legacy-api-wrap','1.4', {
+ 'source_tmpl': 'legacy_api_wrap-%(version)s-py3-none-any.whl'
+ }),
+ ('natsort','8.4.0',{
+ 'source_tmpl': 'natsort-%(version)s-py3-none-any.whl'
+ }),
+ ('seaborn','0.13.2',{
+ 'source_tmpl': 'seaborn-%(version)s-py3-none-any.whl'
+ }),
+ ('stdlib-list','0.10.0', {
+ 'source_tmpl': 'stdlib_list-%(version)s-py3-none-any.whl'
+ }),
+ ('session-info','1.0.0', {
+ 'source_tmpl': 'session_info-%(version)s.tar.gz'
+ }),
+ ('mudata','0.2.3', {
+ 'source_tmpl': 'mudata-%(version)s-py3-none-any.whl'
+ }),
+ ('muon','0.1.6', {
+ 'source_tmpl': 'muon-%(version)s-py3-none-any.whl'
+ }),
+
+]
+
+use_pip = True
+sanity_pip_check = True
+unpack_sources = False
+#use_pip_for_deps = True
+
+exts_filter = ('python -c "import %(ext_name)s"', "")
+
+sanity_check_paths = {
+ 'files': [],
+ 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'],
+}
+
+moduleclass = 'bio'