{bio} [foss/2021b] chrombpnet 0.1.7

easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2021b.eb

@@ -29,7 +29,7 @@ dependencies = [
     ('zlib', '1.2.11'),
     ('Boost', '1.77.0'),
     ('GSL', '2.7'),
-    ('SAMtools', '1.14'),
+    ('SAMtools', '1.15.1'),
     ('HTSlib', '1.14'),  # also provides tabix
     ('BCFtools', '1.14'),
     ('lpsolve', '5.5.2.11'),

easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.6-foss-2021b.eb

@@ -19,7 +19,7 @@ dependencies = [
     ('AUGUSTUS', '3.4.0'),
     ('GeneMark-ET', '4.71'),
     ('BamTools', '2.5.2'),
-    ('SAMtools', '1.14'),
+    ('SAMtools', '1.15.1'),
     ('GenomeThreader', '1.7.3', '-Linux_x86_64-64bit', SYSTEM),
     ('spaln', '2.4.12'),
     ('Exonerate', '2.4.0'),

easybuild/easyconfigs/b/Bismark/Bismark-0.23.1-foss-2021b.eb

@@ -25,7 +25,7 @@ checksums = ['2ceb620cfc3f1c869f4bda656ab01c242f1da7ec01615b0d23b28c702147a337']
 dependencies = [
     ('Perl', '5.34.0'),
     ('Bowtie2', '2.4.4'),
-    ('SAMtools', '1.14'),
+    ('SAMtools', '1.15.1'),
 ]
 
 sanity_check_commands = ['bismark --help']

easybuild/easyconfigs/b/bokeh/bokeh-2.4.2-foss-2021b.eb

@@ -18,8 +18,8 @@ dependencies = [
 use_pip = True
 
 exts_list = [
-    ('tornado', '6.1', {
-        'checksums': ['33c6e81d7bd55b468d2e793517c909b139960b6c790a60b7991b9b6b76fb9791'],
+    ('tornado', '6.2', {
+        'checksums': ['9b630419bde84ec666bfd7ea0a4cb2a8a651c2d5cccdbdd1972a0c859dfc3c13'],
     }),
     (name, version, {
         'checksums': ['f0a4b53364ed3b7eb936c5cb1a4f4132369e394c7ae0a8ef420459410958033d'],

easybuild/easyconfigs/c/Cufflinks/Cufflinks-20190706-GCC-11.2.0.eb

@@ -18,7 +18,7 @@ checksums = ['444c632083a473fe4fd99ff189cef5bbd95daee0912e8eefe79534bf225fbcb6']
 builddependencies = [
     ('Eigen', '3.3.9'),
     ('Autotools', '20210726'),
-    ('SAMtools', '1.14'),
+    ('SAMtools', '1.15.1'),
     ('Boost', '1.75.0'),
 ]
 

easybuild/easyconfigs/c/cffi/cffi-1.14.5-GCCcore-11.2.0.eb

@@ -0,0 +1,38 @@
+easyblock = "PythonBundle"
+
+name = 'cffi'
+version = '1.14.5'
+
+homepage = 'https://cffi.readthedocs.io/en/latest/'
+description = """C Foreign Function Interface for Python. Interact with almost any C code from
+Python, based on C-like declarations that you can often copy-paste from header
+files or documentation.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '11.2.0'}
+toolchainopts = {'pic': True}
+
+builddependencies = [
+    ('binutils', '2.37'),
+]
+
+dependencies = [
+    ('Python', '3.9.6'),
+]
+
+exts_default_options = {
+    'download_dep_fail': True,
+    'sanity_pip_check': True,
+    'use_pip': True,
+}
+
+exts_list = [
+    ('pycparser', '2.20', {
+        'checksums': ['2d475327684562c3a96cc71adf7dc8c4f0565175cf86b6d7a404ff4c771f15f0'],
+    }),
+    (name, version, {
+        'checksums': ['fd78e5fee591709f32ef6edb9a015b4aa1a5022598e36227500c8f4e02328d9c'],
+    }),
+]
+
+moduleclass = 'tools'

easybuild/easyconfigs/c/chrombpnet/chrombpnet-0.1.7-foss-2021b.eb

@@ -0,0 +1,73 @@
+easyblock = 'PythonBundle'
+
+name = 'chrombpnet'
+version = '0.1.7'
+
+homepage = 'https://github.com/kundajelab/chrombpnet'
+description = """ ChromBPNet is a fully convolutional neural network that uses dilated convolutions with residual
+connections to enable large receptive fields with efficient parameterization.
+It also performs automatic assay bias correction. """
+
+toolchain = {'name': 'foss', 'version': '2021b'}
+
+dependencies = [
+    ('SAMtools', '1.15.1'),
+    ('BEDTools', '2.30.0'),
+    ('Kent_tools', '422'),
+    ('pyBigWig', '0.3.18'),
+    ('MEME', '5.4.1'),
+    ('Python', '3.9.6'),
+    ('h5py', '3.6.0'),
+    ('pyfaidx', '0.7.0'),
+    ('deepdish', '0.3.7'),
+    ('matplotlib', '3.4.3'),
+    ('modisco', '0.5.16.0'),
+    ('modisco-lite', '2.0.7'),
+    ('scikit-learn', '1.0.1'),
+    ('TensorFlow', '2.8.4'),
+    ('tensorflow-probability', '0.16.0'),
+    ('protobuf-python', '3.17.3'),
+    ('tqdm', '4.62.3'),
+    ('kundajelab-shap', '1'),
+    ('SciPy-bundle', '2021.10'),  # for numpy=1.21.3, pandas=1.3.4  and scipy=1.7.1
+    ('WeasyPrint', '52.5'),
+]
+
+use_pip = True
+
+# Loosen unnecessarily strict version dependencies
+local_preinstallopts = "sed -i 's|pyfaidx==|pyfaidx>=|g' requirements.txt && "
+local_preinstallopts += "sed -i 's|scikit-learn>=1.1.2|scikit-learn>=1.0.0|g' requirements.txt && "
+local_preinstallopts += "sed -i 's|tensorflow==|tensorflow>=|g' requirements.txt && "
+local_preinstallopts += "sed -i 's|tensorflow-probability==|tensorflow-probability>=|g' requirements.txt && "
+local_preinstallopts += "sed -i 's|protobuf==3.20|protobuf>=3.17.0|g' requirements.txt && "
+local_preinstallopts += "sed -i 's|tqdm==|tqdm>=|g' requirements.txt && "
+local_preinstallopts += "sed -i 's|numpy==1.23.4|numpy>=1.21.0|g' requirements.txt && "
+
+exts_list = [
+    ('matplotlib-venn', '0.11.6', {
+        'checksums': ['d209a9845bb3a54c4247f1ef3f745e4819660ecc9208137097d2a51281f2a478'],
+    }),
+    ('tensorflow-estimator', '2.8.0', {
+        'source_tmpl': 'tensorflow_estimator-%(version)s-py2.py3-none-any.whl',
+        'checksums': ['bee8e0520c60ae7eaf6ca8cb46c5a9f4b45725531380db8fbe38fcb48478b6bb'],
+    }),
+    ('deeplift', '0.6.13.0', {
+        'checksums': ['354ac5a00630b2df0856e8c948262e38c7eb83a719f71d6b5bf8ec4b064cb432'],
+    }),
+    (name, version, {
+        'preinstallopts': local_preinstallopts,
+        'checksums': ['e5fae544d8e533d770c72313b9902097ffd32ef66d5962e90546c3cd9ecce759'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/chrombpnet'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["chrombpnet --help"]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'

easybuild/easyconfigs/c/coverage/coverage-6.4-GCCcore-11.2.0.eb

@@ -0,0 +1,35 @@
+easyblock = 'PythonPackage'
+
+name = 'coverage'
+version = '6.4'
+
+homepage = 'https://coverage.readthedocs.io'
+description = """ Coverage.py is a tool for measuring code coverage of Python programs.
+ It monitors your program, noting which parts of the code have been executed,
+ then analyzes the source to identify code that could have been executed but was not. """
+
+toolchain = {'name': 'GCCcore', 'version': '11.2.0'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['727dafd7f67a6e1cad808dc884bd9c5a2f6ef1f8f6d2f22b37b96cb0080d4f49']
+
+builddependencies = [
+    ('binutils', '2.37'),
+]
+
+dependencies = [
+    ('Python', '3.9.6'),
+]
+
+use_pip = True
+sanity_pip_check = True
+download_dep_fail = True
+
+sanity_check_paths = {
+    'files': ['bin/coverage%s' % x for x in ['', '3', '-%(pyshortver)s']],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'],
+}
+
+sanity_check_commands = ["coverage --help"]
+
+moduleclass = 'tools'

easybuild/easyconfigs/d/DROP/DROP-1.1.1-foss-2021b-R-4.1.2.eb

@@ -21,7 +21,7 @@ dependencies = [
     ('snakemake', '6.10.0'),
     ('wget', '1.21.2'),
     ('HTSlib', '1.14'),  # for tabix
-    ('SAMtools', '1.14'),
+    ('SAMtools', '1.15.1'),
     ('BCFtools', '1.14'),
     ('Pandoc', '2.13', '', SYSTEM),
 ]

easybuild/easyconfigs/d/deepdish/deepdish-0.3.7-foss-2021b.eb

@@ -0,0 +1,32 @@
+easyblock = 'PythonPackage'
+
+name = 'deepdish'
+version = '0.3.7'
+
+homepage = 'https://github.com/uchicago-cs/deepdish'
+description = """Flexible HDF5 saving/loading and other
+data science tools from the University of Chicago."""
+
+toolchain = {'name': 'foss', 'version': '2021b'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['6aff3abef693cec34438f183f29d1a2d9862aba27bb959d4f24d56e007e41ff3']
+
+builddependencies = [
+    ('binutils', '2.37'),
+]
+
+dependencies = [
+    ('Python', '3.9.6'),
+    ('SciPy-bundle', '2021.10'),
+    ('scikit-image', '0.19.1'),
+    ('PyTables', '3.6.1'),
+]
+
+preinstallopts = """python setup.py build && """
+
+use_pip = True
+sanity_pip_check = True
+download_dep_fail = True
+
+moduleclass = 'data'

easybuild/easyconfigs/d/dm-reverb/dm-reverb-0.7.0-foss-2021b.eb

@@ -25,7 +25,7 @@ builddependencies = [
 
 dependencies = [
     ('Python', '3.9.6'),
-    ('TensorFlow', '2.7.1'),
+    ('TensorFlow', '2.8.4'),
     ('Abseil', '20210324.2'),
     ('dm-tree', '0.1.6'),
     ('gRPC', '1.44.0'),

easybuild/easyconfigs/f/finder/finder-1.1.0-foss-2021b.eb

@@ -26,7 +26,7 @@ checksums = [
 
 dependencies = [
     ('STAR', '2.7.9a'),
-    ('SAMtools', '1.14'),
+    ('SAMtools', '1.15.1'),
     ('BEDTools', '2.30.0'),
     ('AUGUSTUS', '3.4.0'),
     ('BRAKER', '2.1.6'),

easybuild/easyconfigs/f/funannotate/funannotate-1.8.13-foss-2021b.eb

@@ -44,7 +44,7 @@ dependencies = [
     ('Proteinortho', '6.2.3'),
     ('Kent_tools', '422'),  # provides pslCDnaFilter
     ('Salmon', '1.4.0'),
-    ('SAMtools', '1.14'),
+    ('SAMtools', '1.15.1'),
     ('SignalP', '6.0g', '-fast'),
     ('SNAP', '2.0.1'),
     ('StringTie', '2.2.1'),

easybuild/easyconfigs/g/GAPPadder/GAPPadder-20170601-foss-2021b-Python-2.7.18.eb

@@ -20,7 +20,7 @@ dependencies = [
     ('KMC', '3.2.1', versionsuffix),
     ('Velvet', '1.2.10', '-mt-kmer_191'),
     ('BWA', '0.7.17'),
-    ('SAMtools', '1.14'),
+    ('SAMtools', '1.15.1'),
     ('BamTools', '2.5.2'),
 ]
 

easybuild/easyconfigs/g/GRIDSS/GRIDSS-2.13.2-foss-2021b-Java-11.eb

@@ -31,7 +31,7 @@ dependencies = [
     ('Java', '11', '', SYSTEM),
     ('picard', '2.25.1', versionsuffix, SYSTEM),
     ('R', '4.1.2'),
-    ('SAMtools', '1.14'),
+    ('SAMtools', '1.15.1'),
     ('BWA', '0.7.17'),
 ]
 

easybuild/easyconfigs/h/hdf5plugin/hdf5plugin-3.2.0-foss-2021b.eb

@@ -0,0 +1,34 @@
+easyblock = 'PythonPackage'
+
+name = 'hdf5plugin'
+version = '3.2.0'
+
+homepage = "https://github.com/silx-kit/hdf5plugin"
+description = """hdf5plugin provides HDF5 compression filters
+(namely: Blosc, Blosc2, BitShuffle, BZip2, FciDecomp, LZ4, SZ,
+SZ3, Zfp, ZStd) and makes them usable from h5py."""
+
+toolchain = {'name': 'foss', 'version': '2021b'}
+
+builddependencies = [
+    ('binutils', '2.37'),
+]
+
+dependencies = [
+    ('h5py', '3.6.0'),
+    ('py-cpuinfo', '9.0.0'),
+    ('Python', '3.9.6'),
+]
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['8900ab06df2a20f88c9c56ecf45a99655e08ba4d730706f8798b4ea2158b291a']
+
+download_dep_fail = True
+sanity_pip_check = True
+use_pip = True
+
+modextrapaths = {
+    'HDF5_PLUGIN_PATH': 'lib/python%(pyshortver)s/site-packages/hdf5plugin/plugins',
+}
+
+moduleclass = 'data'

easybuild/easyconfigs/i/Iris/Iris-1.0.5-GCC-11.2.0-Java-15.eb

@@ -18,7 +18,7 @@ dependencies = [
     ('Java', '15', '', SYSTEM),
     ('minimap2', '2.22'),
     ('HTSlib', '1.14'),
-    ('SAMtools', '1.14'),
+    ('SAMtools', '1.15.1'),
     ('Racon', '1.5.0'),
 ]