diff --git a/139_AMICA/AMICA.eb b/139_AMICA/AMICA.eb new file mode 100644 index 00000000..033dde80 --- /dev/null +++ b/139_AMICA/AMICA.eb @@ -0,0 +1,39 @@ +easyblock = 'CmdCp' + +name = 'AMICA' +version = '2024.1.19' +local_commit = 'e0db55f07c8c410641cd5b0df5498a5a53129ce6' + +homepage = 'https://github.com/sccn/amica' +description = """Code for AMICA: Adaptive Mixture ICA with shared components""" + +toolchain = {'name': 'intel', 'version': '2023a'} +toolchainopts = {'openmp': True} +# https://github.com/sccn/amica/archive/e0db55f07c8c410641cd5b0df5498a5a53129ce6.zip +source_urls = ['https://github.com/sccn/amica/archive/'] +# source_urls = ['https://github.com/sccn/amica/wiki/Amica-Download/27dc1d87dbb608ddccb3cf46202a179b3a943f0c/'] +sources = ['%s.zip' % local_commit] +# sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] example +checksums = ['5c581f0edaa7d7ae7a8a2a993db22c4d211b38860a20099b0b4e9a0dc5fa6162'] + +# dependencies = [ +# ('Python', '3.11.3'), +# ('Meson', '1.1.1'), +# ('Ninja', '1.11.1'), +# ('CMake', '3.26.3'), +# ('SAMtools', '1.18'), +# ] + +# cmds_map = [('.*', "./compile")] +install_cmd = "mpif90 -static-intel -fpp -O3 -march=core-avx2 -heap-arrays -qopenmp -mkl -DMKL -o amica15ex funmod2.f90 amica17.f90" +test_cmd = "./amica17nsg ./amicadefs.param" +files_to_copy = [(['install/bin/*'], 'bin'), (['install/lib/*'], 'lib'), (['install/include/*'], 'include')] + +# sanity_check_paths = { +# 'files': ['bin/randseq', 'bin/indexlr', 'bin/mi_bf_generate'], +# 'dirs': [], +# } + +# sanity_check_commands = ['randseq --help', 'indexlr --help'] + +moduleclass = 'math' diff --git a/169_Bonito/Bonito-0.4.0-fosscuda-2020b.eb b/169_Bonito/Bonito1.eb similarity index 100% rename from 169_Bonito/Bonito-0.4.0-fosscuda-2020b.eb rename to 169_Bonito/Bonito1.eb diff --git a/169_Bonito/Bonito2.eb b/169_Bonito/Bonito2.eb new file mode 100644 index 00000000..f860d1f4 --- /dev/null +++ b/169_Bonito/Bonito2.eb @@ -0,0 +1,59 @@ +# author: Denis Kristak (INUITS) +easyblock = 'PythonBundle' + +name = 'Bonito' +version = '0.7.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/nanoporetech/bonito' +description = "Convolution Basecaller for Oxford Nanopore Reads" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('CUDA', '11.7.0', '', SYSTEM), + ('SciPy-bundle', '2022.05'), + ('PyTorch', '1.12.1', '-CUDA-%(cudaver)s'), + ('edlib', '1.3.9'), + ('ont-fast5-api', '4.1.1'), +] + +use_pip = True + +# strip out too strict version requirements for dependencies +local_bonito_preinstallopts = "sed -i 's/[><=]=.*//g' requirements.txt && " +# fix requirements for stuff we include as a proper dependency +local_bonito_preinstallopts += "sed -i 's/genomeworks-cuda-10-2/genomeworks/g' requirements.txt && " +local_bonito_preinstallopts += "sed -i 's/cupy-cuda102/cupy/g' requirements.txt && " +local_bonito_preinstallopts += "sed -i 's/numpy~=[0-9.]*/numpy/g' requirements.txt && " +local_bonito_preinstallopts += "sed -i 's/torch~=[0-9.]*/torch/g' requirements.txt && " +local_bonito_preinstallopts += "export PATH=%(installdir)s/bin/:$PATH && " + +exts_list = [ + ('fast-ctc-decode', '0.3.2', { + 'source_tmpl': 'fast_ctc_decode-0.3.5-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl', + 'unpack_sources': False, + }), + ('mappy', '2.24', { + }), + ('ont-bonito', version, { + 'modulename': 'bonito', + 'preinstallopts': local_bonito_preinstallopts, + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/bonito'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "bonito --help", + "bonito convert --help", + "bonito download --help", +] + +moduleclass = 'bio' diff --git a/169_Bonito/GenomeWorks-2021.02.2-fosscuda-2020b.eb b/169_Bonito/GenomeWorks-2021.02.2-fosscuda-2022a.eb similarity index 100% rename from 169_Bonito/GenomeWorks-2021.02.2-fosscuda-2020b.eb rename to 169_Bonito/GenomeWorks-2021.02.2-fosscuda-2022a.eb diff --git a/169_Bonito/bonito_install_locally_pip.txt b/169_Bonito/bonito_install_locally_pip.txt new file mode 100644 index 00000000..e39c9356 --- /dev/null +++ b/169_Bonito/bonito_install_locally_pip.txt @@ -0,0 +1,177 @@ +Defaulting to user installation because normal site-packages is not writeable +Collecting ont-bonito + Downloading ont-bonito-0.7.3.tar.gz (55 kB) + ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 55.7/55.7 kB 1.2 MB/s eta 0:00:00 + Preparing metadata (setup.py) ... done +Collecting mappy==2.24 (from ont-bonito) + Downloading mappy-2.24.tar.gz (140 kB) + ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 140.9/140.9 kB 5.4 MB/s eta 0:00:00 + Preparing metadata (setup.py) ... done +Collecting toml==0.10.2 (from ont-bonito) + Downloading toml-0.10.2-py2.py3-none-any.whl (16 kB) +Requirement already satisfied: tqdm<5,>4 in ./.local/lib/python3.10/site-packages (from ont-bonito) (4.65.0) +Requirement already satisfied: scipy==1.10.1 in ./.local/lib/python3.10/site-packages (from ont-bonito) (1.10.1) +Collecting numpy~=1.24.2 (from ont-bonito) + Downloading numpy-1.24.4-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.6 kB) +Collecting pysam==0.21.0 (from ont-bonito) + Downloading pysam-0.21.0-cp310-cp310-manylinux_2_24_x86_64.whl (20.0 MB) + ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 20.0/20.0 MB 17.8 MB/s eta 0:00:00 +Collecting parasail==1.3.4 (from ont-bonito) + Downloading parasail-1.3.4-py2.py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (15.6 MB) + ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 15.6/15.6 MB 7.3 MB/s eta 0:00:00 +Collecting pandas<2,>1 (from ont-bonito) + Downloading pandas-1.5.3-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.1 MB) + ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 12.1/12.1 MB 17.5 MB/s eta 0:00:00 +Collecting requests~=2.28.2 (from ont-bonito) + Downloading requests-2.28.2-py3-none-any.whl (62 kB) + ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.8/62.8 kB 17.2 MB/s eta 0:00:00 +Collecting ont-koi==0.3.0 (from ont-bonito) + Downloading ont_koi-0.3.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.7 MB) + ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.7/3.7 MB 4.6 MB/s eta 0:00:00 +Collecting ont-remora==2.1.3 (from ont-bonito) + Downloading ont-remora-2.1.3.tar.gz (95 kB) + ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 95.8/95.8 kB 4.9 MB/s eta 0:00:00 + Installing build dependencies ... done + Getting requirements to build wheel ... done + Installing backend dependencies ... done + Preparing metadata (pyproject.toml) ... done +Collecting ont-fast5-api==3.3.0 (from ont-bonito) + Downloading ont_fast5_api-3.3.0-py3-none-any.whl (2.0 MB) + ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.0/2.0 MB 12.2 MB/s eta 0:00:00 +Collecting pod5==0.2.0 (from ont-bonito) + Downloading pod5-0.2.0-py3-none-any.whl.metadata (20 kB) +Collecting fast-ctc-decode==0.3.5 (from ont-bonito) + Downloading fast_ctc_decode-0.3.5-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (622 kB) + ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 622.2/622.2 kB 11.5 MB/s eta 0:00:00 +Requirement already satisfied: python-dateutil==2.8.2 in ./.local/lib/python3.10/site-packages (from ont-bonito) (2.8.2) +Collecting edlib==1.3.9 (from ont-bonito) + Downloading edlib-1.3.9-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (363 kB) + ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 363.3/363.3 kB 12.6 MB/s eta 0:00:00 +Requirement already satisfied: torch~=2.0.0 in ./.local/lib/python3.10/site-packages (from ont-bonito) (2.0.1) +Collecting h5py>=2.8 (from ont-fast5-api==3.3.0->ont-bonito) + Downloading h5py-3.10.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.5 kB) +Requirement already satisfied: packaging in ./.local/lib/python3.10/site-packages (from ont-fast5-api==3.3.0->ont-bonito) (23.0) +Collecting progressbar33>=2.3.1 (from ont-fast5-api==3.3.0->ont-bonito) + Downloading progressbar33-2.4.tar.gz (10 kB) + Preparing metadata (setup.py) ... done +Requirement already satisfied: cffi in ./.local/lib/python3.10/site-packages (from ont-koi==0.3.0->ont-bonito) (1.15.1) +Requirement already satisfied: scikit-learn in ./.local/lib/python3.10/site-packages (from ont-remora==2.1.3->ont-bonito) (1.2.2) +Requirement already satisfied: tabulate in ./.local/lib/python3.10/site-packages (from ont-remora==2.1.3->ont-bonito) (0.9.0) +Collecting thop (from ont-remora==2.1.3->ont-bonito) + Downloading thop-0.1.1.post2209072238-py3-none-any.whl (15 kB) +Requirement already satisfied: matplotlib in ./.local/lib/python3.10/site-packages (from ont-remora==2.1.3->ont-bonito) (3.7.1) +Collecting seaborn (from ont-remora==2.1.3->ont-bonito) + Downloading seaborn-0.13.2-py3-none-any.whl.metadata (5.4 kB) +Collecting lib-pod5==0.2.0 (from pod5==0.2.0->ont-bonito) + Downloading lib_pod5-0.2.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (1.1 kB) +Collecting iso8601 (from pod5==0.2.0->ont-bonito) + Downloading iso8601-2.1.0-py3-none-any.whl.metadata (3.7 kB) +Requirement already satisfied: more-itertools in /usr/lib/python3/dist-packages (from pod5==0.2.0->ont-bonito) (8.10.0) +Collecting pyarrow~=11.0.0 (from pod5==0.2.0->ont-bonito) + Downloading pyarrow-11.0.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (34.9 MB) + ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 34.9/34.9 MB 14.5 MB/s eta 0:00:00 +Requirement already satisfied: pytz in /usr/lib/python3/dist-packages (from pod5==0.2.0->ont-bonito) (2022.1) +Collecting polars~=0.17.12 (from pod5==0.2.0->ont-bonito) + Downloading polars-0.17.15-cp37-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (14 kB) +Collecting h5py>=2.8 (from ont-fast5-api==3.3.0->ont-bonito) + Downloading h5py-3.8.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.6 MB) + 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(3.26.3) +Requirement already satisfied: lit in ./.local/lib/python3.10/site-packages (from triton==2.0.0->torch~=2.0.0->ont-bonito) (16.0.5) +Requirement already satisfied: pycparser in ./.local/lib/python3.10/site-packages (from cffi->ont-koi==0.3.0->ont-bonito) (2.21) +Requirement already satisfied: MarkupSafe>=2.0 in /usr/lib/python3/dist-packages (from jinja2->torch~=2.0.0->ont-bonito) (2.0.1) +Requirement already satisfied: contourpy>=1.0.1 in ./.local/lib/python3.10/site-packages (from matplotlib->ont-remora==2.1.3->ont-bonito) (1.0.7) +Requirement already satisfied: cycler>=0.10 in ./.local/lib/python3.10/site-packages (from matplotlib->ont-remora==2.1.3->ont-bonito) (0.11.0) +Requirement already satisfied: fonttools>=4.22.0 in ./.local/lib/python3.10/site-packages (from matplotlib->ont-remora==2.1.3->ont-bonito) (4.39.4) +Requirement already satisfied: kiwisolver>=1.0.1 in ./.local/lib/python3.10/site-packages (from matplotlib->ont-remora==2.1.3->ont-bonito) (1.4.4) 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0:00:00 +Downloading numpy-1.24.4-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (17.3 MB) + ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 17.3/17.3 MB 16.4 MB/s eta 0:00:00 +Downloading polars-0.17.15-cp37-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (18.2 MB) + ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 18.2/18.2 MB 15.8 MB/s eta 0:00:00 +Downloading urllib3-1.26.18-py2.py3-none-any.whl (143 kB) + ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 143.8/143.8 kB 15.6 MB/s eta 0:00:00 +Using cached Cython-3.0.8-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.6 MB) +Downloading iso8601-2.1.0-py3-none-any.whl (7.5 kB) +Downloading seaborn-0.13.2-py3-none-any.whl (294 kB) + ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 294.9/294.9 kB 29.4 MB/s eta 0:00:00 +Building wheels for collected packages: ont-bonito, mappy, ont-remora, progressbar33 + Building wheel for ont-bonito (setup.py) ... done + Created wheel for ont-bonito: filename=ont_bonito-0.7.3-py3-none-any.whl size=64132 sha256=96c89a4cb5fa6f97c52c482dd2fbec1e36f59da7f77e7f7f93526ff7b86f634c + Stored in directory: /home/paveltom/.cache/pip/wheels/8a/5f/79/e34f103da052f9b48e817d9860021d76d256ce634d3f4290d0 + Building wheel for mappy (setup.py) ... done + Created wheel for mappy: filename=mappy-2.24-cp310-cp310-linux_x86_64.whl size=645358 sha256=f2df0f9fec6c1f91b299152c32397d3783a67374522e9b21760c773b8c082650 + Stored in directory: /home/paveltom/.cache/pip/wheels/fa/d8/36/723f268198e0abc930b8ee18135c39f24871bbc66b633f9cd0 + Building wheel for ont-remora (pyproject.toml) ... done + Created wheel for ont-remora: filename=ont_remora-2.1.3-cp310-cp310-linux_x86_64.whl size=896793 sha256=0676d6b49b3fd8a74744f4ea71672a24634691b6c42c9f666b2bce217f475ee2 + Stored in directory: /home/paveltom/.cache/pip/wheels/71/37/66/5ccd42186fb05f861deb3ff19e9de4b0c6ac792d022e83e5ee + Building wheel for progressbar33 (setup.py) ... done + Created wheel for progressbar33: filename=progressbar33-2.4-py3-none-any.whl size=12143 sha256=453c1538e4bc0ec891b57905dec36da3d7a785e3ca3a56b82b031c343260249f + Stored in directory: /home/paveltom/.cache/pip/wheels/28/6d/b6/fd4b9b1489353528a2eea1200c98532fd60d535e22498d9e28 +Successfully built ont-bonito mappy ont-remora progressbar33 +Installing collected packages: progressbar33, mappy, fast-ctc-decode, edlib, urllib3, toml, polars, numpy, iso8601, cython, requests, pysam, pyarrow, parasail, pandas, ont-koi, lib-pod5, h5py, vbz-h5py-plugin, ont-fast5-api, seaborn, pod5, thop, ont-remora, ont-bonito + Attempting uninstall: urllib3 + Found existing installation: urllib3 2.0.4 + Uninstalling urllib3-2.0.4: + Successfully uninstalled urllib3-2.0.4 + Attempting uninstall: numpy + Found existing installation: numpy 1.23.3 + Uninstalling numpy-1.23.3: + Successfully uninstalled numpy-1.23.3 + Attempting uninstall: requests + Found existing installation: requests 2.31.0 + Uninstalling requests-2.31.0: + Successfully uninstalled requests-2.31.0 + Attempting uninstall: pandas + Found existing installation: pandas 2.0.1 + Uninstalling pandas-2.0.1: + Successfully uninstalled pandas-2.0.1 +ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. +locust 2.13.1 requires ConfigArgParse>=1.0, which is not installed. +locust 2.13.1 requires Flask-BasicAuth>=0.2.0, which is not installed. +locust 2.13.1 requires gevent>=20.12.1, which is not installed. +ffaves 0.0.1 requires multiprocess==0.70.12.2, which is not installed. +elody 0.0.16 requires requests>=2.31.0, but you have requests 2.28.2 which is incompatible. +poetry 1.2.2 requires platformdirs<3.0.0,>=2.5.2, but you have platformdirs 3.5.3 which is incompatible. +ffaves 0.0.1 requires numpy==1.20.3, but you have numpy 1.24.4 which is incompatible. +ffaves 0.0.1 requires scipy==1.7.3, but you have scipy 1.10.1 which is incompatible. +Successfully installed cython-3.0.8 edlib-1.3.9 fast-ctc-decode-0.3.5 h5py-3.8.0 iso8601-2.1.0 lib-pod5-0.2.0 mappy-2.24 numpy-1.24.4 ont-bonito-0.7.3 ont-fast5-api-3.3.0 ont-koi-0.3.0 ont-remora-2.1.3 pandas-1.5.3 parasail-1.3.4 pod5-0.2.0 polars-0.17.15 progressbar33-2.4 pyarrow-11.0.0 pysam-0.21.0 requests-2.28.2 seaborn-0.13.2 thop-0.1.1.post2209072238 toml-0.10.2 urllib3-1.26.18 vbz-h5py-plugin-1.0.1 diff --git a/169_Bonito/old_Bonito-0.4.0-fosscuda-2020b.eb b/169_Bonito/old_Bonito-0.4.0-fosscuda-2020b.eb new file mode 100644 index 00000000..59554e81 --- /dev/null +++ b/169_Bonito/old_Bonito-0.4.0-fosscuda-2020b.eb @@ -0,0 +1,126 @@ +# author: Denis Kristak (INUITS) +easyblock = 'PythonBundle' + +name = 'Bonito' +version = '0.4.0' + +homepage = 'https://github.com/nanoporetech/bonito' +description = "Convolution Basecaller for Oxford Nanopore Reads" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('PyTorch', '1.7.1'), + ('h5py', '3.1.0'), + ('Mako', '1.1.3'), + ('PyYAML', '5.3.1'), + ('python-parasail', '1.2.4'), + ('tqdm', '4.56.2'), + ('apex', '20210420'), + ('minimap2', '2.18'), + ('CuPy', '8.5.0'), + ('GenomeWorks', '2021.02.2'), + ('pyspoa', '0.0.8'), + ('ont-fast5-api', '3.3.0'), +] + +use_pip = True + +# strip out too strict version requirements for dependencies +local_bonito_preinstallopts = "sed -i 's/[><=]=.*//g' requirements.txt && " +# fix requirements for stuff we include as a proper dependency +local_bonito_preinstallopts += "sed -i 's/genomeworks-cuda-10-2/genomeworks/g' requirements.txt && " +local_bonito_preinstallopts += "sed -i 's/cupy-cuda102/cupy/g' requirements.txt && " +local_bonito_preinstallopts += "sed -i 's/numpy~=[0-9.]*/numpy/g' requirements.txt && " +local_bonito_preinstallopts += "sed -i 's/torch~=[0-9.]*/torch/g' requirements.txt && " +local_bonito_preinstallopts += "export PATH=%(installdir)s/bin/:$PATH && " + +exts_list = [ + ('python-editor', '1.0.4', { + 'modulename': 'editor', + 'checksums': ['51fda6bcc5ddbbb7063b2af7509e43bd84bfc32a4ff71349ec7847713882327b'], + }), + ('alembic', '1.6.4', { + 'checksums': ['becb572c6701c90ca249f97fc1ae231468cc9516df367a350901eeb9310a8d43'], + }), + ('cmd2', '1.5.0', { + 'checksums': ['701a8c9975c4abc45e5d13906ab149f959f812869106347323a3f89ac0e82a62'], + }), + ('prettytable', '2.1.0', { + 'checksums': ['5882ed9092b391bb8f6e91f59bcdbd748924ff556bb7c634089d5519be87baa0'], + }), + ('cliff', '3.7.0', { + 'preinstallopts': "sed -i'' 's/cmd2.*/cmd2/g' requirements.txt && ", + 'checksums': ['389c81960de13f05daf1cbd546f33199e86c518ba4266c79ec7a153a280980ea'], + }), + ('colorlog', '5.0.1', { + 'checksums': ['f17c013a06962b02f4449ee07cfdbe6b287df29efc2c9a1515b4a376f4e588ea'], + }), + ('greenlet', '1.1.0', { + 'checksums': ['c87df8ae3f01ffb4483c796fe1b15232ce2b219f0b18126948616224d3f658ee'], + }), + ('SQLAlchemy', '1.4.15', { + 'checksums': ['0ff100c75cd175f35f4d24375a0b3d82461f5b1af5fc8d112ef0e5ceea8049e6'], + }), + ('cmaes', '0.8.2', { + 'checksums': ['1c04ba23ded925ef13b96f42cfbd667a905ea5b80754c750e6448b9fcda96a5d'], + }), + ('optuna', '2.7.0', { + 'checksums': ['eb1595108ec444e840deb0037351074144fecb7a4eff6870fc11569ab782cfc6'], + }), + ('colorama', '0.4.4', { + 'checksums': ['5941b2b48a20143d2267e95b1c2a7603ce057ee39fd88e7329b0c292aa16869b'], + }), + ('pyperclip', '1.8.2', { + 'checksums': ['105254a8b04934f0bc84e9c24eb360a591aaf6535c9def5f29d92af107a9bf57'], + }), + ('importlib_metadata', '4.0.1', { + 'checksums': ['8c501196e49fb9df5df43833bdb1e4328f64847763ec8a50703148b73784d581'], + }), + ('stevedore', '3.3.0', { + 'checksums': ['3a5bbd0652bf552748871eaa73a4a8dc2899786bc497a2aa1fcb4dcdb0debeee'], + }), + ('fast-ctc-decode', '0.3.0', { + 'source_tmpl': 'fast_ctc_decode-%(version)s-cp38-cp38-manylinux2010_x86_64.whl', + 'unpack_sources': False, + 'checksums': ['623d83f8de5e02199a09bfe0160a1e477f0db8d4ab612b26a7e42c2a335b378c'], + }), + ('mappy', '2.18', { + 'checksums': ['18fffdb4b831cc3f5399b919b0942c640bf9a943ca22102ac446f53af3b905a8'], + }), + ('seqdist', '0.0.3', { + 'preinstallopts': "sed -i 's/cupy-cuda102//g' settings.ini && sed -i 's/[<>=]=[0-9].*//g' settings.ini && ", + 'checksums': ['bdbbea6ebba1c6dd6698d46e23ba7858f93a7cdf0c7cbc2ea66660291acb044f'], + }), + ('crf-beam', '0.0.1a0', { + 'modulename': 'kbeam', + 'sources': ['crf_beam-%(version)s-cp38-cp38-manylinux1_x86_64.whl'], + 'unpack_sources': False, + 'checksums': ['0cba80ff4d7f90595f498921cf904736e3bce558dba80de5611874d89e72312e'], + }), + ('networkx', '2.5.1', { + 'checksums': ['109cd585cac41297f71103c3c42ac6ef7379f29788eb54cb751be5a663bb235a'], + }), + ('ont-bonito', version, { + 'modulename': 'bonito', + 'preinstallopts': local_bonito_preinstallopts, + 'checksums': ['429310d56e2d7dabd91a9a9c972504a0aa2b6d6469563b14d4aae30adfe9a87e'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/bonito'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "bonito --help", + "bonito convert --help", + "bonito download --help", +] + +moduleclass = 'bio' diff --git a/271_phyluce/phyluce-1.7.3-foss-2023a.eb b/271_phyluce/phyluce-1.7.3-foss-2023a.eb index 06621496..aa242327 100644 --- a/271_phyluce/phyluce-1.7.3-foss-2023a.eb +++ b/271_phyluce/phyluce-1.7.3-foss-2023a.eb @@ -48,16 +48,18 @@ exts_list = [ '%(name)s-%(version)s_removal-Bio-Alphabet.patch', ], 'checksums': [ - '931fd512730bb101266b27728576df00277858d256e1ab30d64b474588362e11', # v1.7.3.tar.gz - '543daee90e1422a7a43c304d6f33e5f16411cc7b85c522b847388feff8cc402a', # phyluce-1.7.3_fix-config-paths.patch - 'f6c5237552fde5a3bf24105781a9001ee5e87bbd825015fc1aa6b5c6a147e171', # phyluce-1.7.3_removal-Bio-Alphabet.patch + # v1.7.3.tar.gz + '931fd512730bb101266b27728576df00277858d256e1ab30d64b474588362e11', + # phyluce-1.7.3_fix-config-paths.patch + '543daee90e1422a7a43c304d6f33e5f16411cc7b85c522b847388feff8cc402a', + # phyluce-1.7.3_removal-Bio-Alphabet.patch + 'f6c5237552fde5a3bf24105781a9001ee5e87bbd825015fc1aa6b5c6a147e171', ], }), ] use_pip = True sanity_pip_check = True -download_dep_fail = True sanity_check_paths = { 'files': [], diff --git a/278_FFAVES/FFAVES.eb b/278_FFAVES/FFAVES.eb index 9c2b57e0..10782f1c 100644 --- a/278_FFAVES/FFAVES.eb +++ b/278_FFAVES/FFAVES.eb @@ -41,9 +41,9 @@ exts_list = [ }), ] -# sanity_check_paths = { -# 'files': ['bin/%s' % x for x in ['ffaves.py', 'get_gprof', 'get_objgraph', 'undill']], -# 'dirs': ['lib/python%(pyshortver)s/site-packages/'], -# } +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['ffaves.py', 'get_gprof', 'get_objgraph', 'undill']], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} moduleclass = 'bio'