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25 changes: 25 additions & 0 deletions
25
easybuild/easyconfigs/a/Arrow/Arrow-8.0.0_fix-BaseExtensionType-arrow-ext-methods.patch
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,25 @@ | ||
| fix for: | ||
| AttributeError: 'pyarrow.lib.BaseExtensionType' object has no attribute '__arrow_ext_class__' | ||
| see https://github.com/apache/arrow/pull/33802 | ||
| diff -u python/pyarrow/types.pxi.orig python/pyarrow/types.pxi | ||
| --- python/pyarrow/types.pxi.orig 2022-05-03 18:59:12.000000000 +0200 | ||
| +++ python/pyarrow/types.pxi 2024-01-09 13:15:20.313755064 +0100 | ||
| @@ -760,6 +836,18 @@ | ||
| DataType.init(self, type) | ||
| self.ext_type = <const CExtensionType*> type.get() | ||
|
|
||
| + def __arrow_ext_class__(self): | ||
| + """ | ||
| + The associated array extension class | ||
| + """ | ||
| + return ExtensionArray | ||
| + | ||
| + def __arrow_ext_scalar_class__(self): | ||
| + """ | ||
| + The associated scalar class | ||
| + """ | ||
| + return ExtensionScalar | ||
| + | ||
| @property | ||
| def extension_name(self): | ||
| """ |
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23 changes: 23 additions & 0 deletions
23
easybuild/easyconfigs/a/autopep8/autopep8-2.0.4-foss-2022a.eb
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,23 @@ | ||
| easyblock = 'PythonPackage' | ||
|
|
||
| name = 'autopep8' | ||
| version = '2.0.4' | ||
|
|
||
| homepage = "https://github.com/hhatto/autopep8" | ||
| description = """A tool that automatically formats Python code to conform to the PEP 8 style guide.""" | ||
|
|
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| toolchain = {'name': 'foss', 'version': '2022a'} | ||
|
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||
| sources = [SOURCE_TAR_GZ] | ||
| checksums = ['2913064abd97b3419d1cc83ea71f042cb821f87e45b9c88cad5ad3c4ea87fe0c'] | ||
|
|
||
| dependencies = [ | ||
| ('Python', '3.10.4'), | ||
| ('pycodestyle', '2.11.1'), | ||
| ] | ||
|
|
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| download_dep_fail = True | ||
| use_pip = True | ||
| sanity_pip_check = True | ||
|
|
||
| moduleclass = 'lib' |
67 changes: 67 additions & 0 deletions
67
easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,67 @@ | ||
| easyblock = 'PythonPackage' | ||
|
|
||
| name = 'BiG-SCAPE' | ||
| version = '1.1.5' | ||
|
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| homepage = 'https://bigscape-corason.secondarymetabolites.org/index.html' | ||
| description = """BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters | ||
| (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene | ||
| cluster families, and exploring gene cluster diversity linked to enzyme phylogenies.""" | ||
|
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| toolchain = {'name': 'foss', 'version': '2022a'} | ||
|
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| github_account = 'medema-group' | ||
| source_urls = [GITHUB_SOURCE] | ||
| sources = ['v%(version)s.tar.gz'] | ||
| patches = [ | ||
| '%(name)s-%(version)s_use_env_var_to_find-MIBiG-files.patch', | ||
| '%(name)s-%(version)s_use_env_var_for_domain_files.patch', | ||
| '%(name)s-%(version)s_use_env_var_for_html.patch', | ||
| '%(name)s-%(version)s_use_correct_name_for_FastTree.patch', | ||
| ] | ||
| checksums = [ | ||
| {'v1.1.5.tar.gz': 'ec7cebbec8f83f4187c80e02ecbb37411a1898a2b83bb80088810f1600528ec7'}, | ||
| {'BiG-SCAPE-1.1.5_use_env_var_to_find-MIBiG-files.patch': | ||
| 'f0602208765a2686a324a27ff6073aac01c230b6a81a00656269fd89c97cf370'}, | ||
| {'BiG-SCAPE-1.1.5_use_env_var_for_domain_files.patch': | ||
| '51337f22b2619ed38969f4ead5f7ce2f2df884f272793b47fb46d77e9c5e2aa2'}, | ||
| {'BiG-SCAPE-1.1.5_use_env_var_for_html.patch': '540be22396ab982c2aeaaed4ce5acdb8ccb8ce2b31d36bc69d37be7a29c7c42a'}, | ||
| {'BiG-SCAPE-1.1.5_use_correct_name_for_FastTree.patch': | ||
| 'e1572e4134c6163a3927ac32bd2a39b7f87cf01109f7913b3c55126e2381a771'}, | ||
| ] | ||
|
|
||
| dependencies = [ | ||
| ('Python', '3.10.4'), | ||
| ('SciPy-bundle', '2022.05'), | ||
| ('Biopython', '1.79'), | ||
| ('scikit-learn', '1.1.2'), | ||
| ('networkx', '2.8.4'), | ||
| ('HMMER', '3.3.2'), | ||
| ('FastTree', '2.1.11'), | ||
| ] | ||
|
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||
| use_pip = True | ||
| download_dep_fail = True | ||
| sanity_pip_check = True | ||
|
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| options = {'modulename': False} | ||
|
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| sanity_check_commands = [ | ||
| 'bigscape.py --help', | ||
| ] | ||
|
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| modextravars = { | ||
| 'BIG_SCAPE_HTML_PATH': '%(installdir)s/lib/python%(pyshortver)s/site-packages/BiG-SCAPE', | ||
| } | ||
|
|
||
| modloadmsg = "%(name)s needs processed Pfam database to work properly.\n" | ||
| modloadmsg += "For this, download the latest 'Pfam-A.hmm.gz' file from the Pfam website " | ||
| modloadmsg += "(http://ftp.ebi.ac.uk/pub/databases/Pfam/releases/), " | ||
| modloadmsg += "uncompress it and process it using the `hmmpress` command.\n" | ||
| modloadmsg += "For data files, like the domains_color_file.tsv and domain_includelist.txt, " | ||
| modloadmsg += "one can set the environment variable BIG_SCAPE_DATA_PATH, if that is not set " | ||
| modloadmsg += "it will use the directory where the bigscape command is started from.\n" | ||
| modloadmsg += "One can copy the domains_color_file.tsv from " | ||
| modloadmsg += "%(installdir)s/lib/python%(pyshortver)s/site-packages/BiG-SCAPE/domains_color_file.tsv\n" | ||
|
|
||
| moduleclass = 'bio' |
15 changes: 15 additions & 0 deletions
15
easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5_use_correct_name_for_FastTree.patch
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,15 @@ | ||
| FastTree binary is not lowercase. | ||
|
|
||
| Åke Sandgren, 2023-11-13 | ||
| diff -ru BiG-SCAPE-1.1.5.orig/bigscape.py BiG-SCAPE-1.1.5/bigscape.py | ||
| --- BiG-SCAPE-1.1.5.orig/bigscape.py 2022-11-14 17:04:47.000000000 +0100 | ||
| +++ BiG-SCAPE-1.1.5/bigscape.py 2023-11-13 07:52:23.064042200 +0100 | ||
| @@ -1644,7 +1644,7 @@ | ||
| # make tree | ||
| newick_file_path = os.path.join(gcf_trees_path, "GCF_c{:4.2f}_{:05d}.newick".format(cutoff,exemplar_idx)) | ||
| with open(newick_file_path, "w") as newick_file: | ||
| - command = ["fasttree", "-nopr", "-quiet", alignment_file_path] | ||
| + command = ["FastTree", "-nopr", "-quiet", alignment_file_path] | ||
| p = subprocess.Popen(command, stdout=newick_file, shell=False) | ||
| p.wait() # only with process has terminated will the file be ready | ||
|
|
37 changes: 37 additions & 0 deletions
37
easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5_use_env_var_for_domain_files.patch
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,37 @@ | ||
| Don't use domains_color_file.tsv and domain_includelist.txt from the install tree. | ||
| Use env var or current dir. | ||
|
|
||
| Åke Sandgren, 2023-11-02 | ||
| diff -ru BiG-SCAPE-1.1.5.orig/ArrowerSVG.py BiG-SCAPE-1.1.5/ArrowerSVG.py | ||
| --- BiG-SCAPE-1.1.5.orig/ArrowerSVG.py 2022-11-14 17:04:47.000000000 +0100 | ||
| +++ BiG-SCAPE-1.1.5/ArrowerSVG.py 2023-11-02 15:48:51.313247855 +0100 | ||
| @@ -27,7 +27,7 @@ | ||
| gene_contour_thickness = 2 # thickness grows outwards | ||
| stripe_thickness = 3 | ||
|
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| -domains_color_file = os.path.join(os.path.dirname(os.path.realpath(__file__)), "domains_color_file.tsv") | ||
| +domains_color_file = os.path.join(os.getenv('BIG_SCAPE_DATA_PATH', os.getcwd()), "domains_color_file.tsv") | ||
|
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| def read_color_domains_file(): | ||
| diff -ru BiG-SCAPE-1.1.5.orig/bigscape.py BiG-SCAPE-1.1.5/bigscape.py | ||
| --- BiG-SCAPE-1.1.5.orig/bigscape.py 2022-11-14 17:04:47.000000000 +0100 | ||
| +++ BiG-SCAPE-1.1.5/bigscape.py 2023-11-02 15:48:02.929621562 +0100 | ||
| @@ -2235,7 +2235,7 @@ | ||
| # Get domain_includelist | ||
| has_includelist = False | ||
| if options.domain_includelist: | ||
| - bigscape_path = os.path.dirname(os.path.realpath(__file__)) | ||
| + bigscape_path = os.getenv('BIG_SCAPE_DATA_PATH', os.getcwd()) | ||
| if os.path.isfile(os.path.join(bigscape_path,"domain_includelist.txt")): | ||
| domain_includelist = set() | ||
| for line in open(os.path.join(bigscape_path,"domain_includelist.txt"), "r"): | ||
| @@ -2850,7 +2852,7 @@ | ||
| if not os.path.isfile(pfams_js_file): | ||
| with open(pfams_js_file, "w") as pfams_js: | ||
| pfam_json = {} | ||
| - pfam_colors = generatePfamColorsMatrix(os.path.join(os.path.dirname(os.path.realpath(__file__)), "domains_color_file.tsv")) | ||
| + pfam_colors = generatePfamColorsMatrix(os.path.join(os.getenv('BIG_SCAPE_DATA_PATH', os.getcwd()), "domains_color_file.tsv")) | ||
| for pfam_code in pfam_info: | ||
| pfam_obj = {} | ||
| if pfam_code in pfam_colors: |
33 changes: 33 additions & 0 deletions
33
easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5_use_env_var_for_html.patch
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,33 @@ | ||
| Use EB specific env var to locate html_template | ||
|
|
||
| Åke Sandgren, 20231106 | ||
| diff -ru BiG-SCAPE-1.1.5.orig/bigscape.py BiG-SCAPE-1.1.5/bigscape.py | ||
| --- BiG-SCAPE-1.1.5.orig/bigscape.py 2022-11-14 17:04:47.000000000 +0100 | ||
| +++ BiG-SCAPE-1.1.5/bigscape.py 2023-11-06 11:20:46.410872382 +0100 | ||
| @@ -1881,7 +1881,7 @@ | ||
| with open(os.path.join(module_html_path, "bs_data.js"), "w") as bs_data_js: | ||
| bs_data_js.write("var bs_data={};\n".format(json.dumps(bs_data, indent=4, separators=(',', ':'), sort_keys=True))) | ||
| bs_data_js.write("dataLoaded('bs_data');\n") | ||
| - shutil.copy(os.path.join(os.path.dirname(os.path.realpath(__file__)), "html_template", "index_html"), os.path.join(module_html_path, "index.html")) | ||
| + shutil.copy(os.path.join(os.getenv('BIG_SCAPE_HTML_PATH'), "html_template", "index_html"), os.path.join(module_html_path, "index.html")) | ||
|
|
||
| ## Write bgc_networks.js | ||
| with open(os.path.join(module_html_path, "bs_networks.js"), "w") as bs_networks_js: | ||
| @@ -2832,7 +2834,7 @@ | ||
| create_directory(network_files_folder, "Network Files", False) | ||
|
|
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| # copy html templates | ||
| - dir_util.copy_tree(os.path.join(os.path.dirname(os.path.realpath(__file__)), "html_template", "output"), output_folder) | ||
| + dir_util.copy_tree(os.path.join(os.getenv('BIG_SCAPE_HTML_PATH'), "html_template", "output"), output_folder) | ||
|
|
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| # make a new run folder in the html output & copy the overview_html | ||
| network_html_folder = os.path.join(output_folder, "html_content", "networks", run_name) | ||
| @@ -2841,7 +2843,7 @@ | ||
| for cutoff in cutoff_list: | ||
| network_html_folder_cutoff = "{}_c{:.2f}".format(network_html_folder, cutoff) | ||
| create_directory(network_html_folder_cutoff, "Network HTML Files", False) | ||
| - shutil.copy(os.path.join(os.path.dirname(os.path.realpath(__file__)), "html_template", "overview_html"), os.path.join(network_html_folder_cutoff, "overview.html")) | ||
| + shutil.copy(os.path.join(os.getenv('BIG_SCAPE_HTML_PATH'), "html_template", "overview_html"), os.path.join(network_html_folder_cutoff, "overview.html")) | ||
| rundata_networks_per_run[network_html_folder_cutoff] = [] | ||
| html_subs_per_run[network_html_folder_cutoff] = [] | ||
|
|
16 changes: 16 additions & 0 deletions
16
easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5_use_env_var_to_find-MIBiG-files.patch
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,16 @@ | ||
| Use MIBIG_PATH env var to locate MIBiG files instead of hardocded path | ||
| that isn't right in the first place. | ||
|
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||
| Åke Sandgren, 20231027 | ||
| diff -ru BiG-SCAPE-1.1.5.orig/bigscape.py BiG-SCAPE-1.1.5/bigscape.py | ||
| --- BiG-SCAPE-1.1.5.orig/bigscape.py 2022-11-14 17:04:47.000000000 +0100 | ||
| +++ BiG-SCAPE-1.1.5/bigscape.py 2023-10-27 14:15:41.385679191 +0200 | ||
| @@ -2336,6 +2336,8 @@ | ||
|
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| print("\n Trying to read bundled MIBiG BGCs as reference") | ||
| mibig_path = os.path.join(os.path.dirname(os.path.realpath(__file__)),"Annotated_MIBiG_reference") | ||
| + # Use environment variable as first choice | ||
| + mibig_path = os.getenv('MIBIG_PATH', mibig_path) | ||
| bgcs_path = os.path.join(mibig_path,mibig_zipfile_numbgcs[1]) | ||
|
|
||
| # try to see if the zip file has already been decompressed |
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