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{bio}[foss/2023a] FLAIR 2.0 w/R 4.3.2 #21239

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@fizwit fizwit commented Aug 21, 2024

(created using eb --new-pr)

@fizwit fizwit changed the title update/rewrite FLAIR {bio}[foss/2023a] FLAIR 2.0 w/R 4.3.2 Jan 22, 2025
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Updated software FLAIR-2.0-foss-2023a.eb

Diff against FLAIR-1.5.1-20200630-foss-2019b-Python-3.7.4.eb

easybuild/easyconfigs/f/FLAIR/FLAIR-1.5.1-20200630-foss-2019b-Python-3.7.4.eb

diff --git a/easybuild/easyconfigs/f/FLAIR/FLAIR-1.5.1-20200630-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/f/FLAIR/FLAIR-2.0-foss-2023a.eb
index d23aaa2728..1914e2544c 100644
--- a/easybuild/easyconfigs/f/FLAIR/FLAIR-1.5.1-20200630-foss-2019b-Python-3.7.4.eb
+++ b/easybuild/easyconfigs/f/FLAIR/FLAIR-2.0-foss-2023a.eb
@@ -1,80 +1,71 @@
 # Author: Pavel Grochal (INUITS)
 # License: GPLv2
 
-easyblock = 'Tarball'
+easyblock = 'PythonBundle'
 
 name = 'FLAIR'
-version = '1.5.1-20200630'
-local_commit = '0f71b5f'
-versionsuffix = '-Python-%(pyver)s'
+version = '2.0'
+local_commit = '1f45ac4'
 
 homepage = 'https://github.com/BrooksLabUCSC/flair'
-description = """FLAIR (Full-Length Alternative Isoform analysis of RNA) 
-for the correction, isoform definition, and alternative splicing analysis of noisy reads. 
+description = """FLAIR (Full-Length Alternative Isoform analysis of RNA)
+for the correction, isoform definition, and alternative splicing analysis of noisy reads.
 FLAIR has primarily been used for nanopore cDNA, native RNA, and PacBio sequencing reads."""
 
-toolchain = {'name': 'foss', 'version': '2019b'}
-
-# https://github.com/BrooksLabUCSC/flair
-github_account = 'BrooksLabUCSC'
-source_urls = [GITHUB_LOWER_SOURCE]
-sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}]
-patches = ['FLAIR-%(version)s_fix-pandas2ri.py2rpy.patch']
-checksums = [
-    'fb621b7c4613cd691cbb844ee5d354f2e3076b28f2bbe347f305d4033a3a07b5',  # FLAIR-1.5.1-20200630.tar.gz
-    # FLAIR-1.5.1-20200630_fix-pandas2ri.py2rpy.patch
-    '3babe0aeae9fd308512ed82efefcdd82f5087983c2545009946c011fd1d4389d',
-]
+toolchain = {'name': 'foss', 'version': '2023a'}
 
 dependencies = [
-    ('Python', '3.7.4'),
-    ('R', '3.6.2'),  # provides ggplot2, qqman
-    ('SciPy-bundle', '2019.10', versionsuffix),  # provides numpy, pandas
-    ('rpy2', '3.2.6', versionsuffix),
-    ('tqdm', '4.41.1'),
-    ('SAMtools', '1.10'),
-    ('BEDTools', '2.29.2'),
-    ('pybedtools', '0.8.1'),
-    ('minimap2', '2.17'),
-    ('Pysam', '0.15.3'),
-    ('R-bundle-Bioconductor', '3.10'),  # provides DESeq2, DRIMSeq, stageR
-    ('matplotlib', '3.1.1', versionsuffix),
-    ('Seaborn', '0.10.0', versionsuffix),
-    ('Kent_tools', '401'),  # required for bedPartition command
+    ('Python', '3.11.3'),
+    ('R', '4.3.2'),  # provides ggplot2, qqman
+    ('SciPy-bundle', '2023.07'),  # provides numpy, pandas
+    ('Cython', '3.0.8'),
+    ('rpy2', '3.5.15'),
+    ('tqdm', '4.66.1'),
+    ('SAMtools', '1.18'),
+    ('BEDTools', '2.31.0'),
+    ('pybedtools', '0.9.1'),
+    ('minimap2', '2.26'),
+    ('Pysam', '0.22.0'),
+    ('R-bundle-Bioconductor', '3.18', '-R-%(rver)s'),  # provides DESeq2, DRIMSeq, stageR
+    ('matplotlib', '3.7.2'),
+    ('Seaborn', '0.13.2'),
+    ('Kent_tools', '468'),  # required for bedPartition command
 ]
 
-exts_defaultclass = 'PythonPackage'
-exts_default_options = {
-    'source_urls': [PYPI_LOWER_SOURCE],
-    'source_tmpl': SOURCE_TAR_GZ,
-    'download_dep_fail': True,
-    'use_pip': True,
-}
-exts_filter = ("python -c 'import %(ext_name)s'", '')
+use_pip = True
+sanity_pip_check = True
+
 exts_list = [
-    ('ncls', '0.0.53', {
-        'checksums': ['a1b927c8b4898f3071e502bb9bf42ceb5bcbc39910035bd1c1a987dc02061993'],
+    ('mappy', '2.24', {
+        'checksums': ['35a2fb73ef14173283d5abb31e7a318429e0330c3be95851df38dd83d4ff9af9'],
+    }),
+    ('pipettor', '1.0.0', {
+        'checksums': ['637113cae20c9b295277929d4bd0e4832d74564eb393e90a0beeb7c8ad3b0a84'],
     }),
-    ('kerneltree', '0.0.5', {
-        'checksums': ['27d9d8dda1b72657ae2f9edc87881e92dbea2d6da469b7c06e33271ffcb72f37'],
+    ('ncls', '0.0.68', {
+        'checksums': ['81aaa5abb123bb21797ed2f8ef921e20222db14a3ecbc61ccf447532f2b7ba93'],
+    }),
+    (name, version, {
+        'modulename': 'flair',
+        'source_urls': ['https://github.com/BrooksLabUCSC/flair/archive/'],
+        'sources': [{'download_filename': "%s.tar.gz" % local_commit, 'filename': '%(name)s-%(version)s.tar.gz'}],
+        'checksums': ['25804d558c77315d5d6c4e9549cf1749c75213fc4bf53680113fa4c2389043ec'],
     }),
 ]
 
+local_python_scripts = ['count_sam_transcripts']
 postinstallcmds = [
-    'ln -s %(installdir)s/%(namelower)s.py %(installdir)s/bin/%(namelower)s.py',
-    'chmod +x %(installdir)s/bin/*',
+    "ln -s %%(installdir)s/lib/python%%(pyshortver)s/site-packages/%%(namelower)s/%s.py  %%(installdir)s/bin/%s",
+    "chmod +x %%(installdir)s/bin/%s" % "count_sam_transcripts",
 ]
-
-fix_python_shebang_for = ['bin/*.py', '%(namelower)s.py']
-modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
+modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages/%(namelower)s']}
 
 sanity_check_paths = {
-    'files': ['bin/%(namelower)s.py', 'bin/ssPrep.py'],
+    'files': [],
     'dirs': ['lib/python%(pyshortver)s/site-packages'],
 }
-local_subcommands = ['align', 'correct', 'collapse', 'quantify', 'diffExp', 'diffSplice']
-sanity_check_commands = ["%%(namelower)s.py %s --help" % c for c in local_subcommands] + [
-    "ssPrep.py --help",
-]
+
+local_subcommands = ['align', 'correct', 'collapse', 'quantify']
+sanity_check_commands = ["%%(namelower)s %s --help" % c for c in local_subcommands] + ["%(namelower)s --version"]
 
 moduleclass = 'bio'
Diff against FLAIR-1.5-foss-2019b-Python-3.7.4.eb

easybuild/easyconfigs/f/FLAIR/FLAIR-1.5-foss-2019b-Python-3.7.4.eb

diff --git a/easybuild/easyconfigs/f/FLAIR/FLAIR-1.5-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/f/FLAIR/FLAIR-2.0-foss-2023a.eb
index d2f5792ecd..1914e2544c 100644
--- a/easybuild/easyconfigs/f/FLAIR/FLAIR-1.5-foss-2019b-Python-3.7.4.eb
+++ b/easybuild/easyconfigs/f/FLAIR/FLAIR-2.0-foss-2023a.eb
@@ -1,74 +1,71 @@
 # Author: Pavel Grochal (INUITS)
 # License: GPLv2
 
-easyblock = 'Tarball'
+easyblock = 'PythonBundle'
 
 name = 'FLAIR'
-version = '1.5'
-versionsuffix = '-Python-%(pyver)s'
+version = '2.0'
+local_commit = '1f45ac4'
 
 homepage = 'https://github.com/BrooksLabUCSC/flair'
-description = """FLAIR (Full-Length Alternative Isoform analysis of RNA) 
-for the correction, isoform definition, and alternative splicing analysis of noisy reads. 
+description = """FLAIR (Full-Length Alternative Isoform analysis of RNA)
+for the correction, isoform definition, and alternative splicing analysis of noisy reads.
 FLAIR has primarily been used for nanopore cDNA, native RNA, and PacBio sequencing reads."""
 
-toolchain = {'name': 'foss', 'version': '2019b'}
-
-# https://github.com/BrooksLabUCSC/flair
-github_account = 'BrooksLabUCSC'
-source_urls = [GITHUB_LOWER_SOURCE]
-sources = ["v%(version)s.tar.gz"]
-checksums = ['3631b45b356a44676415f3e0930c8f0eacb869ba7def61ea65194e667dfb9b00']
+toolchain = {'name': 'foss', 'version': '2023a'}
 
 dependencies = [
-    ('Python', '3.7.4'),
-    ('R', '3.6.2'),  # provides ggplot2, qqman
-    ('SciPy-bundle', '2019.10', versionsuffix),  # provides numpy, pandas
-    ('rpy2', '3.2.6', versionsuffix),
-    ('tqdm', '4.41.1'),
-    ('SAMtools', '1.10'),
-    ('BEDTools', '2.29.2'),
-    ('pybedtools', '0.8.1'),
-    ('minimap2', '2.17'),
-    ('Pysam', '0.15.3'),
-    ('R-bundle-Bioconductor', '3.10'),  # provides DESeq2, DRIMSeq, stageR
-    ('matplotlib', '3.1.1', versionsuffix),
-    ('Seaborn', '0.10.0', versionsuffix),
-    ('Kent_tools', '401'),  # required for bedPartition command
+    ('Python', '3.11.3'),
+    ('R', '4.3.2'),  # provides ggplot2, qqman
+    ('SciPy-bundle', '2023.07'),  # provides numpy, pandas
+    ('Cython', '3.0.8'),
+    ('rpy2', '3.5.15'),
+    ('tqdm', '4.66.1'),
+    ('SAMtools', '1.18'),
+    ('BEDTools', '2.31.0'),
+    ('pybedtools', '0.9.1'),
+    ('minimap2', '2.26'),
+    ('Pysam', '0.22.0'),
+    ('R-bundle-Bioconductor', '3.18', '-R-%(rver)s'),  # provides DESeq2, DRIMSeq, stageR
+    ('matplotlib', '3.7.2'),
+    ('Seaborn', '0.13.2'),
+    ('Kent_tools', '468'),  # required for bedPartition command
 ]
 
-exts_defaultclass = 'PythonPackage'
-exts_default_options = {
-    'source_urls': [PYPI_LOWER_SOURCE],
-    'source_tmpl': SOURCE_TAR_GZ,
-    'download_dep_fail': True,
-    'use_pip': True,
-}
-exts_filter = ("python -c 'import %(ext_name)s'", '')
+use_pip = True
+sanity_pip_check = True
+
 exts_list = [
-    ('ncls', '0.0.53', {
-        'checksums': ['a1b927c8b4898f3071e502bb9bf42ceb5bcbc39910035bd1c1a987dc02061993'],
+    ('mappy', '2.24', {
+        'checksums': ['35a2fb73ef14173283d5abb31e7a318429e0330c3be95851df38dd83d4ff9af9'],
+    }),
+    ('pipettor', '1.0.0', {
+        'checksums': ['637113cae20c9b295277929d4bd0e4832d74564eb393e90a0beeb7c8ad3b0a84'],
     }),
-    ('kerneltree', '0.0.5', {
-        'checksums': ['27d9d8dda1b72657ae2f9edc87881e92dbea2d6da469b7c06e33271ffcb72f37'],
+    ('ncls', '0.0.68', {
+        'checksums': ['81aaa5abb123bb21797ed2f8ef921e20222db14a3ecbc61ccf447532f2b7ba93'],
+    }),
+    (name, version, {
+        'modulename': 'flair',
+        'source_urls': ['https://github.com/BrooksLabUCSC/flair/archive/'],
+        'sources': [{'download_filename': "%s.tar.gz" % local_commit, 'filename': '%(name)s-%(version)s.tar.gz'}],
+        'checksums': ['25804d558c77315d5d6c4e9549cf1749c75213fc4bf53680113fa4c2389043ec'],
     }),
 ]
 
+local_python_scripts = ['count_sam_transcripts']
 postinstallcmds = [
-    'ln -s %(installdir)s/%(namelower)s.py %(installdir)s/bin/%(namelower)s.py',
-    'chmod +x %(installdir)s/bin/*',
+    "ln -s %%(installdir)s/lib/python%%(pyshortver)s/site-packages/%%(namelower)s/%s.py  %%(installdir)s/bin/%s",
+    "chmod +x %%(installdir)s/bin/%s" % "count_sam_transcripts",
 ]
-
-fix_python_shebang_for = ['bin/*.py', '%(namelower)s.py']
-modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
+modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages/%(namelower)s']}
 
 sanity_check_paths = {
-    'files': ['bin/%(namelower)s.py', 'bin/ssPrep.py'],
+    'files': [],
     'dirs': ['lib/python%(pyshortver)s/site-packages'],
 }
-local_subcommands = ['align', 'correct', 'collapse', 'quantify', 'diffExp', 'diffSplice']
-sanity_check_commands = ["%%(namelower)s.py %s --help" % c for c in local_subcommands] + [
-    "ssPrep.py --help",
-]
+
+local_subcommands = ['align', 'correct', 'collapse', 'quantify']
+sanity_check_commands = ["%%(namelower)s %s --help" % c for c in local_subcommands] + ["%(namelower)s --version"]
 
 moduleclass = 'bio'

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