From a09d9d64c5e03757705d3711493a67d2632eeece Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 26 Jan 2024 19:52:37 +0100 Subject: [PATCH 01/12] progress on #166 FragPipe --- 166_FragPipe/IonQuant-1.9.8-Java-11.eb | 9 ++++++++- 166_FragPipe/MSFragger-3.8-Java-11.eb | 3 --- 2 files changed, 8 insertions(+), 4 deletions(-) diff --git a/166_FragPipe/IonQuant-1.9.8-Java-11.eb b/166_FragPipe/IonQuant-1.9.8-Java-11.eb index 5cb376df..a37f306f 100644 --- a/166_FragPipe/IonQuant-1.9.8-Java-11.eb +++ b/166_FragPipe/IonQuant-1.9.8-Java-11.eb @@ -18,11 +18,18 @@ checksums = ['98010f55d53c3fce786538da2976e1caaf688b29649d32e66ead8ba24a0db754'] dependencies = [('Java', '11')] -modextrapaths = {'PATH': ['']} +postinstallcmds = [ + "mkdir -p %(installdir)s/bin", + "echo '#!/bin/sh' > %(installdir)s/bin/%(namelower)s", + "echo 'java -jar %(installdir)s/%(name)s-%(version)s.jar $@' >> %(installdir)s/bin/%(namelower)s", + "chmod a+rx %(installdir)s/bin/%(namelower)s", +] sanity_check_paths = { 'files': ['%(name)s-%(version)s.jar'], 'dirs': [], } +sanity_check_commands = ["%(namelower)s | grep '^Usage'"] + moduleclass = 'bio' diff --git a/166_FragPipe/MSFragger-3.8-Java-11.eb b/166_FragPipe/MSFragger-3.8-Java-11.eb index ddd1b60a..d1963eae 100644 --- a/166_FragPipe/MSFragger-3.8-Java-11.eb +++ b/166_FragPipe/MSFragger-3.8-Java-11.eb @@ -27,14 +27,11 @@ postinstallcmds = [ "chmod a+rx %(installdir)s/bin/%(namelower)s", ] -# modextrapaths = {'CLASSPATH': ''} - sanity_check_paths = { 'files': ['%(name)s-%(version)s.jar'], 'dirs': [], } -# sanity_check_commands = ['java -jar %(name)s-%(version)s.jar --help'] sanity_check_commands = ['%(namelower)s --help'] moduleclass = 'bio' From 53a438512d97ad22673ca1e408dff915ed296376 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 26 Jan 2024 19:52:57 +0100 Subject: [PATCH 02/12] progress on #236 NGSpeciesID --- .../NGSpeciesID-0.3.0-foss-2023a.eb | 43 +++++++++++++++++++ 236_NGSpeciesID/edlib-1.2.7-GCC-12.3.0.eb | 2 +- 236_NGSpeciesID/medaka-1.11.3-foss-2023a.eb | 5 ++- 3 files changed, 47 insertions(+), 3 deletions(-) create mode 100644 236_NGSpeciesID/NGSpeciesID-0.3.0-foss-2023a.eb diff --git a/236_NGSpeciesID/NGSpeciesID-0.3.0-foss-2023a.eb b/236_NGSpeciesID/NGSpeciesID-0.3.0-foss-2023a.eb new file mode 100644 index 00000000..b9a14fc1 --- /dev/null +++ b/236_NGSpeciesID/NGSpeciesID-0.3.0-foss-2023a.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonPackage' + +name = 'NGSpeciesID' +version = '0.3.0' + +homepage = 'https://github.com/ksahlin/NGSpeciesID' +description = "NGSpeciesID is a tool for clustering and consensus forming of targeted ONT reads." + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['71663ce280220d4e692cc6c3aea44f91e40b3143ed09a9462bdf2feb1d94aa9f'] + +dependencies = [ + ('Python', '3.11.3'), + ('python-parasail', '1.3.4'), + ('edlib', '1.2.7'), # TODO change version to python-1.3.9 + ('medaka', '1.11.3'), + ('spoa', '4.1.0'), + ('Racon', '1.5.0'), + ('minimap2', '2.26'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +# no proper namespace for NGSpeciesID +options = {'modulename': 'modules.consensus'} + +# parasail requirements are too strict +preinstallopts = "sed -i 's/parasail==/parasail>=/g' setup.py && " + +sanity_check_paths = { + 'files': ['bin/NGSpeciesID'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["NGSpeciesID --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/236_NGSpeciesID/edlib-1.2.7-GCC-12.3.0.eb b/236_NGSpeciesID/edlib-1.2.7-GCC-12.3.0.eb index 8535acf8..9e0c95d8 100644 --- a/236_NGSpeciesID/edlib-1.2.7-GCC-12.3.0.eb +++ b/236_NGSpeciesID/edlib-1.2.7-GCC-12.3.0.eb @@ -1,7 +1,7 @@ easyblock = 'PythonBundle' name = 'edlib' -version = '1.2.7' +version = '1.2.7' # TODO change version to python-1.3.9 homepage = 'https://martinsos.github.io/edlib' description = "Lightweight, super fast library for sequence alignment using edit (Levenshtein) distance." diff --git a/236_NGSpeciesID/medaka-1.11.3-foss-2023a.eb b/236_NGSpeciesID/medaka-1.11.3-foss-2023a.eb index 86267451..7defdab4 100644 --- a/236_NGSpeciesID/medaka-1.11.3-foss-2023a.eb +++ b/236_NGSpeciesID/medaka-1.11.3-foss-2023a.eb @@ -32,7 +32,7 @@ dependencies = [ ('minimap2', _minimap_ver), ('HTSlib', '1.18'), # for tabix, bgzip ('Racon', '1.5.0'), - ('edlib', '1.2.7'), + ('edlib', '1.2.7'), # TODO change version to python-1.3.9 ('pyspoa', '0.2.1'), ('python-parasail', '1.3.4'), ('ont-fast5-api', '4.1.2'), @@ -54,7 +54,8 @@ exts_list = [ (name, version, { 'checksums': ['940568212d152f573270967b02f6e841561cc43138b6aa15783c371457fef7b9'], # Some requirements are too strict. - 'preinstallopts': "sed -i 's/tensorflow.*/tensorflow/g;s/cffi==/cffi>=/g' requirements.txt && ", + 'preinstallopts': "sed -i 's/tensorflow.*/tensorflow/g;s/cffi==/cffi>=/g' requirements.txt && " + + "sed -i 's/8, 9, 10/8, 9, 10, 11/g' setup.py && sed -i 's/,<3.11//g' setup.py && ", }), ] From c20d4a7d035f7b38e6e8a1b25b8f3f8ddbea484d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 26 Jan 2024 19:53:35 +0100 Subject: [PATCH 03/12] progress on #248 MONAI --- 248_MONAI/MONAI-1.3.0-foss-2023a.eb | 86 +++++++++++++++++++++++++++++ 1 file changed, 86 insertions(+) create mode 100644 248_MONAI/MONAI-1.3.0-foss-2023a.eb diff --git a/248_MONAI/MONAI-1.3.0-foss-2023a.eb b/248_MONAI/MONAI-1.3.0-foss-2023a.eb new file mode 100644 index 00000000..6b5a6e95 --- /dev/null +++ b/248_MONAI/MONAI-1.3.0-foss-2023a.eb @@ -0,0 +1,86 @@ +easyblock = 'PythonBundle' + +name = 'MONAI' +version = '1.3.0' + +homepage = 'https://monai.io/' +description = """ +MONAI is a PyTorch-based, open-source framework for deep learning in healthcare +imaging, part of PyTorch Ecosystem. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +github_account = 'Project-MONAI' + +dependencies = [ + ('Python', '3.11.3'), + ('PyTorch', '2.1.2'), # TODO 2.1.2 + ('PyTorch-Ignite', '0.4.12'), # TODO + ('einops', '0.7.0'), + ('ITK', '5.3.0'), + ('NiBabel', '5.2.0'), + ('scikit-image', '0.22.0'), + ('tensorboard', '2.10.0'), # TODO + ('torchvision', '0.13.1'), # TODO + ('tqdm', '4.66.1'), + ('Pillow', '10.0.0'), + ('openslide-python', '1.3.1'), + ('BeautifulSoup', '4.12.2'), +] + +# install MONAI with list of 'extras', which require additional dependencies +local_pip_extras = "nibabel,skimage,pillow,tensorboard,gdown,ignite,torchvision,itk,tqdm,lmdb,psutil,openslide,fire" + +# avoid using hatchling as build backend (since installing it for this old Python version is a nightmare) +local_preinstallopts_termcolor = ' '.join([ + r"""sed -i -e 's/^build-backend = .*/build-backend = "setuptools.build_meta"/g' """, + r"""-e 's/^requires = \[/requires = \["setuptools"/g' """, + r"""-e '/"hatch/d' """, + # replace dynamic version with hardcoded version + r"""-e '/"version"/d' """, + r"""-e 's/^readme = .*/version = "%(version)s"/g' """, + r"pyproject.toml && ", +]) + +exts_list = [ + ('gdown', '4.7.1', { + 'checksums': ['347f23769679aaf7efa73e5655270fcda8ca56be65eb84a4a21d143989541045'], + }), + ('lmdb', '1.4.1', { + 'checksums': ['1f4c76af24e907593487c904ef5eba1993beb38ed385af82adb25a858f2d658d'], + }), + ('termcolor', '2.3.0', { + 'checksums': ['b5b08f68937f138fe92f6c089b99f1e2da0ae56c52b78bf7075fd95420fd9a5a'], + 'preinstallopts': local_preinstallopts_termcolor, + }), + ('fire', '0.5.0', { + 'checksums': ['a6b0d49e98c8963910021f92bba66f65ab440da2982b78eb1bbf95a0a34aacc6'], + }), + (name, version, { + 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['67e0f55678faad4bd38b1ea69d5de94586b20b551b8ad745415623a8b6c1c5e2'], + 'preinstallopts': "BUILD_MONAI=1", + 'use_pip_extras': local_pip_extras, + }), +] + +use_pip = True + +sanity_pip_check = True + +# 'pip check' does not verify whether all optional dependencies required to support 'extras' +# are actually available, so we do it here via an import check; +# Pillow is a special case, since there we need to use 'import PIL' +sanity_check_commands = [ + "python -c 'import monai; monai.config.print_config()'", + "python -c 'import PIL'", # for Pillow required dependency +] + ["python -c 'import %s'" % x for x in local_pip_extras.split(',') if x != 'pillow'] + +sanity_check_paths = { + 'files': ['lib/python%%(pyshortver)s/site-packages/%%(namelower)s/_C.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' From 5fa6c6447475ae393365d5aa1e092c118135fa12 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 29 Jan 2024 16:10:12 +0100 Subject: [PATCH 04/12] #71 and #235 progress --- 235_singleM/error_log.txt | 174 +++++++++++++++++++ 235_singleM/polars_cargopython.eb | 26 ++- 71_GRASP_suite/GRASPsuite-2022.7.4-system.eb | 12 +- 3 files changed, 200 insertions(+), 12 deletions(-) diff --git a/235_singleM/error_log.txt b/235_singleM/error_log.txt index 90aabb20..53f09c66 100644 --- a/235_singleM/error_log.txt +++ b/235_singleM/error_log.txt @@ -1,3 +1,177 @@ +Polars build - problem with Mask bitmask +ERROR: +error[E0599]: no function or associated item named `from_bitmask` found for struct `Mask` in the current scope + --> crates/polars-arrow/src/bitmap/bitmask.rs:152:19 + | + 152 | Mask::from_bitmask(mask >> byte_shift) + | ^^^^^^^^^^^^ function or associated item not found in `Mask<_, _>` + | + --> crates/polars-arrow/src/bitmap/bitmask.rs:152:19 + | + 152 | Mask::from_bitmask(mask >> byte_shift) + | ^^^^^^^^^^^^ function or associated item not found in `Mask<_, _>` + | + note: if you're trying to build a new `Mask<_, _>` consider using one of the following associated functions: + Mask::::splat + Mask::::from_array + Mask::::from_int_unchecked + Mask::::from_int + --> /tmp/vsc47063/easybuild/build/Rust/1.75.0/GCCcore-12.3.0/rustc-1.75.0-src/library/core/src/../../portable-simd/crates/core_simd/src/masks.rs:122:5 + = help: items from traits can only be used if the trait is in scope + help: the following trait is implemented but not in scope; perhaps add a `use` for it: + | + 1 + use std::simd::ToBitMask; + | + help: there is an associated function with a similar name + | + 152 | Mask::from_int(mask >> byte_shift) + | ~~~~~~~~ + + error[E0599]: no function or associated item named `from_bitmask` found for struct `Mask` in the current scope + --> crates/polars-arrow/src/bitmap/bitmask.rs:159:19 + | + 159 | Mask::from_bitmask(shifted) + Mask::::from_int_unchecked + Mask::::from_int + --> /tmp/vsc47063/easybuild/build/Rust/1.75.0/GCCcore-12.3.0/rustc-1.75.0-src/library/core/src/../../portable-simd/crates/core_simd/src/masks.rs:122:5 + = help: items from traits can only be used if the trait is in scope + help: the following trait is implemented but not in scope; perhaps add a `use` for it: + | + 1 + use std::simd::ToBitMask; + | + help: there is an associated function with a similar name + | + 159 | Mask::from_int(shifted) + | ~~~~~~~~ + + error[E0599]: no function or associated item named `from_bitmask` found for struct `Mask` in the current scope + --> crates/polars-arrow/src/bitmap/bitmask.rs:161:19 + | + 161 | Mask::from_bitmask(0u64) + | ^^^^^^^^^^^^ function or associated item not found in `Mask<_, _>` + | + note: if you're trying to build a new `Mask<_, _>` consider using one of the following associated functions: + Mask::::splat + Mask::::from_array + Mask::::from_int_unchecked + Mask::::from_int + --> /tmp/vsc47063/easybuild/build/Rust/1.75.0/GCCcore-12.3.0/rustc-1.75.0-src/library/core/src/../../portable-simd/crates/core_simd/src/masks.rs:122:5 + = help: items from traits can only be used if the trait is in scope + help: the following trait is implemented but not in scope; perhaps add a `use` for it: + | + 1 + use std::simd::ToBitMask; + | + help: there is an associated function with a similar name + | + 161 | Mask::from_int(0u64) + | ~~~~~~~~ + + error[E0599]: no function or associated item named `from_bitmask` found for struct `Mask` in the current scope + --> crates/polars-arrow/src/legacy/kernels/agg_mean.rs:95:43 + | + 95 | let mask = Mask::::from_bitmask(validity_chunk as u64); + | ^^^^^^^^^^^^ function or associated item not found in `Mask` + | + = help: items from traits can only be used if the trait is in scope + help: the following trait is implemented but not in scope; perhaps add a `use` for it: + | + 1 + use std::simd::ToBitMask; + | + help: there is an associated function with a similar name + | + 95 | let mask = Mask::::from_int(validity_chunk as u64); + | ~~~~~~~~ + + For more information about this error, try `rustc --explain E0599`. + error: could not compile `polars-arrow` (lib) due to 4 previous errors + warning: build failed, waiting for other jobs to finish... + maturin failed + Caused by: Failed to build a native library through cargo + Caused by: Cargo build finished with "exit status: 101": `env -u CARGO PYO3_ENVIRONMENT_SIGNATURE="cpython-3.11-64bit" PYO3_PYTHON="/apps/gent/RHEL8/cascadelake-ib/software/ +e-12.3.0/bin/python" PYTHON_SYS_EXECUTABLE="/apps/gent/RHEL8/cascadelake-ib/software/Python/3.11.3-GCCcore-12.3.0/bin/python" "cargo" "rustc" "--message-format" "json-render-diagnos +th" "/tmp/vsc47063/easybuild/build/polars/0.20.4/foss-2023a/polars/polars-0.20.4/py-polars/Cargo.toml" "--release" "--lib"` + Error: command ['maturin', 'pep517', 'build-wheel', '-i', '/apps/gent/RHEL8/cascadelake-ib/software/Python/3.11.3-GCCcore-12.3.0/bin/python', '--compatibility', 'off'] returne +us 1 + [end of output] + + note: This error originates from a subprocess, and is likely not a problem with pip. + ERROR: Failed building wheel for polars +Failed to build polars +ERROR: Could not build wheels for polars, which is required to install pyproject.toml-based projects + +#################################################################### +Polar build -> problem with cmake: +ERROR: +== 2024-01-22 17:36:52,265 run.py:247 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.11.3-GCCcore-12.3.0/bin/python -m pip install --prefix=/scratch/geasybuild/RHEL8/cascadelake-ampere-ib/software/polars/0.20.4-foss-2023a --no-deps --ignore-installed --no-index --no-build-isolation + . 01-22 17:37:37,595 build_log.py:171 ERROR EasyBuild crashed with an error (at easybuild/easybuild-framework/easybuild/base/exceptions.py:126 in + __init__): cmd " /apelake-ib/software/Python/3.11.3-GCCcore-12.3.0/bin/python -m pip install --prefix=/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/so-foss-2023a --no-deps --ignore-installed --no-index --no-build-isolation ." exited with exit code 1 and output: + Processing /tmp/vsc47063/easybuild/build/polars/0.20.4/foss-2023a/polars/polars-0.20.4 + Preparing metadata (pyproject.toml): started + Preparing metadata (pyproject.toml): finished with status 'done' + Building wheels for collected packages: polars + Building wheel for polars (pyproject.toml): started + Building wheel for polars (pyproject.toml): finished with status 'error' + error: subprocess-exited-with-error + + Building wheel for polars (pyproject.toml) did not run successfully. + exit code: 1 + > [230 lines of output] + Running `maturin pep517 build-wheel -i /apps/gent/RHEL8/cascadelake-ib/software/Python/3.11.3-GCCcore-12.3.0/bin/python --compatibility off` + Building a mixed python/rust project + Found pyo3 bindings with abi3 support for Python 3.8 + Not using a specific python interpreter + Compiling libc v0.2.151 + Compiling proc-macro2 v1.0.74 + ... + Compiling libz-ng-sys v1.1.12 + Compiling xxhash-rust v0.8.8 + Compiling itoap v1.0.1 + Compiling alloc-no-stdlib v2.0.4 + error: failed to run custom build command for `libz-ng-sys v1.1.12` + + Caused by: + process didn't exit successfully: `/tmp/vsc47063/easybuild/build/polars/0.20.4/foss-2023a/polars/polars-0.20.4/target/release/build/libz-ng-sys- + ld-script-build_zng` (exit status: 101) + --- stdout + CMAKE_TOOLCHAIN_FILE_x86_64-unknown-linux-gnu = None + CMAKE_TOOLCHAIN_FILE_x86_64_unknown_linux_gnu = None + HOST_CMAKE_TOOLCHAIN_FILE = None + CMAKE_TOOLCHAIN_FILE = None + CMAKE_GENERATOR_x86_64-unknown-linux-gnu = None + CMAKE_GENERATOR_x86_64_unknown_linux_gnu = None + HOST_CMAKE_GENERATOR = None + CMAKE_GENERATOR = None + CMAKE_PREFIX_PATH_x86_64-unknown-linux-gnu = None + CMAKE_PREFIX_PATH_x86_64_unknown_linux_gnu = None + HOST_CMAKE_PREFIX_PATH = None + CMAKE_PREFIX_PATH = Some("/apps...) + CMAKE_x86_64-unknown-linux-gnu = None + CMAKE_x86_64_unknown_linux_gnu = None + HOST_CMAKE = None + CMAKE = None + running: cd "/tmp/vsc47063/easybuild/build/polars/0.20.4/foss-2023a/polars/polars-0.20.4/target/release/build/libz-ng-sys-659b643918b75119/out/build" && CMAKE_PREFIHEL8/... + --- stderr + thread 'main' panicked at /tmp/vsc47063/easybuild/build/polars/0.20.4/foss-2023a/cmake-0.1.50/src/lib.rs:1098:5: + + failed to execute command: No such file or directory (os error 2) + is `cmake` not installed? + + build script failed, must exit now + note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace + warning: build failed, waiting for other jobs to finish... + maturin failed + Caused by: Failed to build a native library through cargo + Caused by: Cargo build finished with "exit status: 101": `env -u CARGO PYO3_ENVIRONMENT_SIGNATURE="cpython-3.11-64bit" PYO3_PYTHON="/apps/gent/R + software/Python/3.11.3-GCCcore-12.3.0/bin/python" PYTHON_SYS_EXECUTABLE="/apps/gent/RHEL8/cascadelake-ib/software/Python/3.11.3-GCCcore-12.3.0/bin/pytho + --message-format" "json-render-diagnostics" "--manifest-path" "/tmp/vsc47063/easybuild/build/polars/0.20.4/foss-2023a/polars/polars-0.20.4/py-polars/Car + "--lib"` + Error: command ['maturin', 'pep517', 'build-wheel', '-i', '/apps/gent/RHEL8/cascadelake-ib/software/Python/3.11.3-GCCcore-12.3.0/bin/python', '--c + ] returned non-zero exit status 1 + [end of output] + + note: This error originates from a subprocess, and is likely not a problem with pip. + ERROR: Failed building wheel for polars +############################################################################# Polar build -> bad maturin or cargo? ERROR: == 2024-01-18 19:00:19,731 build_log.py:171 ERROR EasyBuild crashed with an error (at easybuild/easybuild-framework/easybuild/base/exceptions.py:126 in __init__): cmd " /apps/gent/RHftware/Python/3.11.3-GCCcore-12.3.0/bin/python -m pip install --prefix=/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/polars/0.20.4s --ignore-installed --no-index --no-build-isolation ." exited with exit code 1 and output: diff --git a/235_singleM/polars_cargopython.eb b/235_singleM/polars_cargopython.eb index a2ba6c1b..862c9dd6 100644 --- a/235_singleM/polars_cargopython.eb +++ b/235_singleM/polars_cargopython.eb @@ -1,7 +1,7 @@ easyblock = "CargoPythonBundle" name = 'polars' -version = '0.20.4' +version = '0.20.6' homepage = 'https://pola.rs/' description = """Lightning-fast DataFrame library for Rust and Python.""" @@ -10,10 +10,11 @@ toolchain = {'name': 'foss', 'version': '2023a'} #done toolchainopts = {'pic': True} builddependencies = [ - ('Rust', '1.75.0'), #done + ('Rust', '1.75.0'),#done ] dependencies = [ + # ('Rust', '1.75.0'), ('Python', '3.11.3'), #done ('Arrow', '14.0.1'), #done ('SciPy-bundle', '2023.07'), #done @@ -21,15 +22,16 @@ dependencies = [ ('maturin', '1.4.0', '-Rust-1.75.0'), #done # ('setuptools-rust', '1.6.0'), #done ('poetry', '1.5.1'), #done + ('CMake', '3.26.3'), #done ] +# installopts = 'rustup update -- nightly' +prebuildopts = 'rustup update -- nightly && ' + exts_list = [ ('plot', '0.6.5', { 'checksums': ['453e93798cd21f6a1bfc1fe248237334d6f8a71fea02fd6b9d483476202d1cc2'], }), - # ('deltalake', '0.15.1', { - # 'checksums': ['77ca8e239297c7db99ae0dd4c13097550f4dca64d6b6f9bd493d9084fdf25fb3'], - # }), ('xlsx2csv', '0.8.2', { 'checksums': ['cdd272c82f8b32f1cee76aeaef87b2ee3549661fddf90f7ecf2310967a16fc84'], }), @@ -38,7 +40,7 @@ exts_list = [ 'checksums': ['9403902685b3423cba786db01a36f36efef90ae3d429e45b74dadb4ae9e328dc'], }), (name, version, { - 'checksums': ['21a90aa0c7401c80fc814b4db371dced780df6bd5ac81a329307e796b5821190'], + 'checksums': ['b53553308bc7e2b4f841b18f1949b61ed7f2cf155c5c64712298efa5af67a997'], }), ] @@ -50,6 +52,10 @@ exts_list = [ # 'sanity_pip_check': True, # 'installopts': '', # } + + # ('deltalake', '0.15.1', { + # 'checksums': ['77ca8e239297c7db99ae0dd4c13097550f4dca64d6b6f9bd493d9084fdf25fb3'], + # }), # ('setuptools', '65.6.3', { # 'checksums': ['a7620757bf984b58deaf32fc8a4577a9bbc0850cf92c20e1ce41c38c19e5fb75'], # }), @@ -131,6 +137,8 @@ crates = [ ('bincode', '1.3.3'), ('bitflags', '1.3.2'), ('bitflags', '2.4.1'), + # ('bitmap', '3.1.3'), + # ('bitmask', '0.5.0'), ('block-buffer', '0.10.4'), ('brotli', '3.4.0'), ('brotli-decompressor', '2.5.1'), @@ -227,7 +235,7 @@ crates = [ ('git2', '0.18.1'), ('glob', '0.3.1'), ('group', '0.12.1'), - ('h2', '0.3.22'), + ('h2', '0.3.24'), ('half', '1.8.2'), ('half', '2.3.1'), ('halfbrown', '0.2.4'), @@ -312,7 +320,7 @@ crates = [ ('num_cpus', '1.16.0'), ('numpy', '0.20.0'), ('object', '0.32.2'), - ('object_store', '0.8.0'), + ('object_store', '0.9.0'), ('once_cell', '1.19.0'), ('oorandom', '11.1.3'), ('openssl-probe', '0.1.5'), @@ -387,6 +395,8 @@ crates = [ ('rustls', '0.21.10'), ('rustls-native-certs', '0.6.3'), ('rustls-pemfile', '1.0.4'), + ('rustls-pemfile', '2.0.0'), + ('rustls-pki-types', '1.1.0'), ('rustls-webpki', '0.101.7'), ('rustversion', '1.0.14'), ('ryu', '1.0.16'), diff --git a/71_GRASP_suite/GRASPsuite-2022.7.4-system.eb b/71_GRASP_suite/GRASPsuite-2022.7.4-system.eb index cbbaa4f6..0e5afae6 100644 --- a/71_GRASP_suite/GRASPsuite-2022.7.4-system.eb +++ b/71_GRASP_suite/GRASPsuite-2022.7.4-system.eb @@ -4,14 +4,18 @@ name = 'GRASP-suite' version = '2022.7.4' versionsuffix = '-Java-%(javaver)s' -homepage = 'https://bodenlab.github.io/GRASP-suite/' +homepage = 'https://github.com/bodenlab/GRASP-suite/' + description = """GRASP-suite is a collection of tools and tutorials to perform and analyse ancestral sequence reconstruction.""" toolchain = SYSTEM source_urls = ['https://bodenlab.github.io/GRASP-suite/project/graspcmd/archive/'] -sources = ['bnkit.jar'] +sources = [{ + "download_filename": "bnkit.jar", + "filename": "%(name)s-%(version)s.jar", +}] checksums = ['7ee4cbc9f23857c8c7cf3e6bd0dde962d9a244974d955aac92212b5b5e29a385'] dependencies = [('Java', '17')] @@ -19,14 +23,14 @@ dependencies = [('Java', '17')] postinstallcmds = [ "mkdir -p %(installdir)s/bin", "echo '#!/bin/sh' > %(installdir)s/bin/grasp", - "echo 'java -jar -Xmx16g %(installdir)s/bnkit.jar $@' >> %(installdir)s/bin/grasp", + "echo 'java -jar -Xmx16g %(installdir)s/%(name)s-%(version)s.jar $@' >> %(installdir)s/bin/grasp", "chmod a+rx %(installdir)s/bin/grasp" ] sanity_check_commands = ["grasp -h"] sanity_check_paths = { - 'files': ['bin/grasp', 'bnkit.jar'], + 'files': ['bin/grasp', '%(name)s-%(version)s.jar'], 'dirs': [], } From e4cee874892fb9faa8d765a91e3a89c04a6a39d6 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 29 Jan 2024 18:22:09 +0100 Subject: [PATCH 05/12] Progress on #271 --- 271_phyluce/ABySS-2.3.7-foss-2023a.eb | 29 +++++++++++++++++++++++++ 271_phyluce/btllib.eb | 31 +++++++++++++++++++++++++++ 271_phyluce/phyluce.eb | 3 +++ 3 files changed, 63 insertions(+) create mode 100644 271_phyluce/ABySS-2.3.7-foss-2023a.eb create mode 100644 271_phyluce/btllib.eb diff --git a/271_phyluce/ABySS-2.3.7-foss-2023a.eb b/271_phyluce/ABySS-2.3.7-foss-2023a.eb new file mode 100644 index 00000000..7c258f24 --- /dev/null +++ b/271_phyluce/ABySS-2.3.7-foss-2023a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'ABySS' +version = '2.3.7' + +homepage = 'https://www.bcgsc.ca/platform/bioinfo/software/abyss' +description = """Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler""" + +toolchain = {'name': 'foss', 'version': '2023a'} +# toolchainopts = {'usempi': True, 'cstd': 'c++11'} + +source_urls = ['http://github.com/bcgsc/abyss/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ba37780e79ec3aa359b6003e383caef13479a87f4d0022af01b86398f9ffca1f'] + +dependencies = [ + ('Boost', '1.82.0'), + ('sparsehash', '2.0.4'), + ('SQLite', '3.42.0'), +] + +configopts = 'CXXFLAGS="$CXXFLAGS -Wno-error=deprecated-copy"' + +sanity_check_paths = { + 'files': ["bin/ABYSS", "bin/ABYSS-P"], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/271_phyluce/btllib.eb b/271_phyluce/btllib.eb new file mode 100644 index 00000000..aee2776b --- /dev/null +++ b/271_phyluce/btllib.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' +# easyblock = 'CmdCp' + +name = 'btllib' +version = '1.7.0' + +homepage = 'https://github.com/bcgsc/btllib' +description = """Bioinformatics Technology Lab common code library""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True, 'cstd': 'c++17'} + +source_urls = ['https://github.com/bcgsc/btllib/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['ad8f26cf6187a000fe6cc7a61fa625567f029bca9bb0271d695347627a014059'] + +dependencies = [ + ('Python', '3.11.3'), + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), + ('CMake', '3.26.3'), +] + +# configopts = 'CXXFLAGS="$CXXFLAGS"' + +# sanity_check_paths = { +# 'files': ["bin/ABYSS", "bin/ABYSS-P"], +# 'dirs': [] +# } + +moduleclass = 'bio' diff --git a/271_phyluce/phyluce.eb b/271_phyluce/phyluce.eb index 3869ad16..3d26fc1f 100644 --- a/271_phyluce/phyluce.eb +++ b/271_phyluce/phyluce.eb @@ -80,8 +80,11 @@ sanity_check_commands = ["%s --help" % x for x in [ "phyluce_assembly_get_fastq_lengths", "phyluce_assembly_get_match_counts", "phyluce_assembly_match_contigs_to_barcodes", + "phyluce_genetrees_get_mean_bootrep_support", + "phyluce_genetrees_generate_multilocus_bootstrap_count", "phyluce_genetrees_rename_tree_leaves", "phyluce_genetrees_sort_multilocus_bootstraps", + "phyluce_genetrees_get_tree_counts", "phyluce_ncbi_chunk_fasta_for_ncbi", # "phyluce_ncbi_example-prep.conf", # "phyluce_ncbi_prep_uce_align_files_for_ncbi", # Bio.Alphabet import IUPAC error From 6937d25c14c0763b3b2fd66f49b6def668f3be31 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Tue, 30 Jan 2024 11:37:32 +0100 Subject: [PATCH 06/12] #271 btllib with CmdCP --- 271_phyluce/btllib_cmdcp.eb | 42 +++++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 271_phyluce/btllib_cmdcp.eb diff --git a/271_phyluce/btllib_cmdcp.eb b/271_phyluce/btllib_cmdcp.eb new file mode 100644 index 00000000..c3f9a192 --- /dev/null +++ b/271_phyluce/btllib_cmdcp.eb @@ -0,0 +1,42 @@ +# easyblock = 'PythonPackage' +easyblock = 'CmdCp' + +name = 'btllib' +version = '1.7.0' + +homepage = 'https://github.com/bcgsc/btllib' +description = """Bioinformatics Technology Lab common code library""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'openmp': True, 'cstd': 'c++17'} + +source_urls = ['https://github.com/bcgsc/btllib/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['ad8f26cf6187a000fe6cc7a61fa625567f029bca9bb0271d695347627a014059'] + +dependencies = [ + ('Python', '3.11.3'), + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), + ('CMake', '3.26.3'), +] + +cmds_map = [('.*', "./compile")] + +files_to_copy = [(['btllib'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/btllib'], + 'dirs': [], +} + +# sanity_check_commands = ['FastTree 2>&1 | grep "FastTree Version %(version)s"'] + +# configopts = 'CXXFLAGS="$CXXFLAGS"' + +# sanity_check_paths = { +# 'files': ["bin/ABYSS", "bin/ABYSS-P"], +# 'dirs': [] +# } + +moduleclass = 'bio' From 856cd391db344e65a250a863c3f7b3eb494f853e Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Tue, 30 Jan 2024 12:56:05 +0100 Subject: [PATCH 07/12] #271 btllib progress --- 271_phyluce/btllib_cmdcp.eb | 18 +++++++++++++++--- 1 file changed, 15 insertions(+), 3 deletions(-) diff --git a/271_phyluce/btllib_cmdcp.eb b/271_phyluce/btllib_cmdcp.eb index c3f9a192..d2afa17e 100644 --- a/271_phyluce/btllib_cmdcp.eb +++ b/271_phyluce/btllib_cmdcp.eb @@ -10,9 +10,21 @@ description = """Bioinformatics Technology Lab common code library""" toolchain = {'name': 'GCCcore', 'version': '12.3.0'} toolchainopts = {'openmp': True, 'cstd': 'c++17'} -source_urls = ['https://github.com/bcgsc/btllib/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['ad8f26cf6187a000fe6cc7a61fa625567f029bca9bb0271d695347627a014059'] +# source_urls = ['https://github.com/bcgsc/btllib/archive/'] +# sources = ['v%(version)s.tar.gz'] +# checksums = ['ad8f26cf6187a000fe6cc7a61fa625567f029bca9bb0271d695347627a014059'] + +sources = [{ + 'filename': '%(name)s-%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/bcgsc', + 'repo_name': 'btllib', + 'tag': 'v%(version)s', + 'recursive': True, + 'keep_git_dir': True, + } +}] +checksums = ['62936bf7b136c1628736d5b69ba9b7f738417fa19802e4e5e36c2bf35e7aa9fa'] dependencies = [ ('Python', '3.11.3'), From daa9dc348369fdf0bac5c0e3a597971b72f8de0e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 30 Jan 2024 15:02:28 +0100 Subject: [PATCH 08/12] progress on #166 FragPipe --- 166_FragPipe/IonQuant-1.9.8-Java-11.eb | 2 ++ 166_FragPipe/MSFragger-3.8-Java-11.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/166_FragPipe/IonQuant-1.9.8-Java-11.eb b/166_FragPipe/IonQuant-1.9.8-Java-11.eb index a37f306f..f776bee0 100644 --- a/166_FragPipe/IonQuant-1.9.8-Java-11.eb +++ b/166_FragPipe/IonQuant-1.9.8-Java-11.eb @@ -16,6 +16,8 @@ toolchain = SYSTEM sources = ['%(name)s-%(version)s.zip'] checksums = ['98010f55d53c3fce786538da2976e1caaf688b29649d32e66ead8ba24a0db754'] +download_instructions = 'Manual download required, see https://msfragger.arsci.com/ionquant/' + dependencies = [('Java', '11')] postinstallcmds = [ diff --git a/166_FragPipe/MSFragger-3.8-Java-11.eb b/166_FragPipe/MSFragger-3.8-Java-11.eb index d1963eae..a6063f0a 100644 --- a/166_FragPipe/MSFragger-3.8-Java-11.eb +++ b/166_FragPipe/MSFragger-3.8-Java-11.eb @@ -18,6 +18,8 @@ toolchain = SYSTEM sources = ['%(name)s-%(version)s.zip'] checksums = ['526684890d1f8d7e37b49d9957a58c9880e66172dabbc517b87a5cd957d47b0a'] +download_instructions = 'Manual download required, see http://msfragger-upgrader.nesvilab.org/upgrader/' + dependencies = [('Java', '11')] postinstallcmds = [ From 8eb029b490a061d72b80031eb381f2ac1ad7c48a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 30 Jan 2024 15:03:13 +0100 Subject: [PATCH 09/12] progress on #236 NGSpeciesID --- 236_NGSpeciesID/edlib-1.2.7-GCC-12.3.0.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/236_NGSpeciesID/edlib-1.2.7-GCC-12.3.0.eb b/236_NGSpeciesID/edlib-1.2.7-GCC-12.3.0.eb index 9e0c95d8..16c47468 100644 --- a/236_NGSpeciesID/edlib-1.2.7-GCC-12.3.0.eb +++ b/236_NGSpeciesID/edlib-1.2.7-GCC-12.3.0.eb @@ -23,11 +23,10 @@ exts_list = [ (name, version, { 'source_urls': ['https://github.com/Martinsos/edlib/archive/'], 'source_tmpl': 'v%(version)s.tar.gz', + # TODO comment 'preinstallopts': 'cd bindings/python && make && python -m cogapp -d -o README.rst README-tmpl.rst && ', 'checksums': ['8767bc1b04a1a67282d57662e5702c4908996e96b1753b5520921ff189974621'], }), ] moduleclass = 'bio' - -# TODO edlib.bycython.cpp:198:12: fatal error: longintrepr.h: No such file or directory From 7b1ed4d4daa97b640a147be5446427ae9ff64d03 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 30 Jan 2024 15:04:29 +0100 Subject: [PATCH 10/12] progress on #248 MONAI --- 248_MONAI/MONAI-1.3.0-foss-2023a.eb | 4 +- 248_MONAI/PyTorch-Ignite-0.4.13-foss-2023a.eb | 29 ++++++++ 248_MONAI/tensorboard-2.10.0-foss-2022a.eb | 73 +++++++++++++++++++ 248_MONAI/torchvision-0.16.2-foss-2023a.eb | 25 +++++++ 4 files changed, 129 insertions(+), 2 deletions(-) create mode 100644 248_MONAI/PyTorch-Ignite-0.4.13-foss-2023a.eb create mode 100644 248_MONAI/tensorboard-2.10.0-foss-2022a.eb create mode 100644 248_MONAI/torchvision-0.16.2-foss-2023a.eb diff --git a/248_MONAI/MONAI-1.3.0-foss-2023a.eb b/248_MONAI/MONAI-1.3.0-foss-2023a.eb index 6b5a6e95..756c3a9b 100644 --- a/248_MONAI/MONAI-1.3.0-foss-2023a.eb +++ b/248_MONAI/MONAI-1.3.0-foss-2023a.eb @@ -15,8 +15,8 @@ github_account = 'Project-MONAI' dependencies = [ ('Python', '3.11.3'), - ('PyTorch', '2.1.2'), # TODO 2.1.2 - ('PyTorch-Ignite', '0.4.12'), # TODO + ('PyTorch', '2.1.2'), + ('PyTorch-Ignite', '0.4.12'), ('einops', '0.7.0'), ('ITK', '5.3.0'), ('NiBabel', '5.2.0'), diff --git a/248_MONAI/PyTorch-Ignite-0.4.13-foss-2023a.eb b/248_MONAI/PyTorch-Ignite-0.4.13-foss-2023a.eb new file mode 100644 index 00000000..91ff3887 --- /dev/null +++ b/248_MONAI/PyTorch-Ignite-0.4.13-foss-2023a.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonBundle' + +name = 'PyTorch-Ignite' +version = '0.4.13' + +homepage = 'https://pytorch-ignite.ai/' +description = """ +Ignite is a high-level library to help with training and evaluating neural +networks in PyTorch flexibly and transparently.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('PyTorch', '2.1.2'), +] + +exts_list = [ + ('%(namelower)s', version, { + 'source_tmpl': 'pytorch_ignite-%(version)s-py3-none-any.whl', + 'checksums': ['b17959072af98b1494de603305588a81e22911a122a3ee444d88fc71153778f5'], + 'modulename': 'ignite', + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/248_MONAI/tensorboard-2.10.0-foss-2022a.eb b/248_MONAI/tensorboard-2.10.0-foss-2022a.eb new file mode 100644 index 00000000..4cf2f36f --- /dev/null +++ b/248_MONAI/tensorboard-2.10.0-foss-2022a.eb @@ -0,0 +1,73 @@ +easyblock = 'PythonBundle' + +name = 'tensorboard' +version = '2.10.0' + +homepage = 'https://github.com/tensorflow/tensorboard' +description = """TensorBoard is a suite of web applications for inspecting and understanding your TensorFlow runs +and graphs.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('protobuf-python', '3.19.4'), +] + +exts_list = [ + ('absl-py', '1.2.0', { + 'modulename': 'absl', + 'checksums': ['f568809938c49abbda89826223c992b630afd23c638160ad7840cfe347710d97'], + }), + ('cachetools', '5.2.0', { + 'checksums': ['6a94c6402995a99c3970cc7e4884bb60b4a8639938157eeed436098bf9831757'], + }), + ('pyasn1-modules', '0.2.8', { + 'checksums': ['905f84c712230b2c592c19470d3ca8d552de726050d1d1716282a1f6146be65e'], + }), + ('rsa', '4.9', { + 'checksums': ['e38464a49c6c85d7f1351b0126661487a7e0a14a50f1675ec50eb34d4f20ef21'], + }), + ('google-auth', '2.11.1', { + 'modulename': 'google.auth', + 'checksums': ['516e6623038b81430dd062a1a25ecd24f173d7c15cdf4e48a9e78bc87e97aeec'], + }), + ('oauthlib', '3.2.1', { + 'checksums': ['1565237372795bf6ee3e5aba5e2a85bd5a65d0e2aa5c628b9a97b7d7a0da3721'], + }), + ('requests-oauthlib', '1.3.1', { + 'checksums': ['75beac4a47881eeb94d5ea5d6ad31ef88856affe2332b9aafb52c6452ccf0d7a'], + }), + ('google-auth-oauthlib', '0.4.6', { + 'checksums': ['a90a072f6993f2c327067bf65270046384cda5a8ecb20b94ea9a687f1f233a7a'], + }), + ('grpcio', '1.49.1', { + 'modulename': 'grpc', + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", + 'checksums': ['d4725fc9ec8e8822906ae26bb26f5546891aa7fbc3443de970cc556d43a5c99f'], + }), + ('Markdown', '3.4.1', { + 'checksums': ['3b809086bb6efad416156e00a0da66fe47618a5d6918dd688f53f40c8e4cfeff'], + }), + ('tensorboard_data_server', '0.6.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['809fe9887682d35c1f7d1f54f0f40f98bb1f771b14265b453ca051e2ce58fca7'], + }), + ('tensorboard_plugin_wit', '1.8.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['ff26bdd583d155aa951ee3b152b3d0cffae8005dc697f72b44a8e8c2a77a8cbe'], + }), + ('Werkzeug', '2.2.2', { + 'checksums': ['7ea2d48322cc7c0f8b3a215ed73eabd7b5d75d0b50e31ab006286ccff9e00b8f'], + }), + (name, version, { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['76c91a5e8959cd2208cc32cb17a0cb002badabb66a06ac2af02a7810f49a59e3'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/248_MONAI/torchvision-0.16.2-foss-2023a.eb b/248_MONAI/torchvision-0.16.2-foss-2023a.eb new file mode 100644 index 00000000..7a2b2889 --- /dev/null +++ b/248_MONAI/torchvision-0.16.2-foss-2023a.eb @@ -0,0 +1,25 @@ +name = 'torchvision' +version = '0.16.2' + +homepage = 'https://github.com/pytorch/vision' +description = " Datasets, Transforms and Models specific to Computer Vision" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/pytorch/vision/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['8c1f2951e98d8ada6e5a468f179af4be9f56d2ebc3ab057af873da61669806d7'] + +builddependencies = [ + ('CMake', '3.26.3'), + # ('Python-bundle-PyPI', '2023.06'), + # ('Ninja', '1.11.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Pillow-SIMD', '9.5.0'), + ('PyTorch', '2.1.2'), +] + +moduleclass = 'vis' From 22b0c93fac4166d4f8483bf3779697864f1242ae Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 31 Jan 2024 12:51:26 +0100 Subject: [PATCH 11/12] #271 progress btllib abyss --- 271_phyluce/ABySS-2.3.7-foss-2023a.eb | 1 + ...ib_cmdcp.eb => btllib-1.7.0-GCC-12.3.0.eb} | 25 +++++---------- 271_phyluce/btllib.eb | 31 ------------------- 3 files changed, 8 insertions(+), 49 deletions(-) rename 271_phyluce/{btllib_cmdcp.eb => btllib-1.7.0-GCC-12.3.0.eb} (53%) delete mode 100644 271_phyluce/btllib.eb diff --git a/271_phyluce/ABySS-2.3.7-foss-2023a.eb b/271_phyluce/ABySS-2.3.7-foss-2023a.eb index 7c258f24..f76dec72 100644 --- a/271_phyluce/ABySS-2.3.7-foss-2023a.eb +++ b/271_phyluce/ABySS-2.3.7-foss-2023a.eb @@ -17,6 +17,7 @@ dependencies = [ ('Boost', '1.82.0'), ('sparsehash', '2.0.4'), ('SQLite', '3.42.0'), + ('btllib', '1.7.0'), ] configopts = 'CXXFLAGS="$CXXFLAGS -Wno-error=deprecated-copy"' diff --git a/271_phyluce/btllib_cmdcp.eb b/271_phyluce/btllib-1.7.0-GCC-12.3.0.eb similarity index 53% rename from 271_phyluce/btllib_cmdcp.eb rename to 271_phyluce/btllib-1.7.0-GCC-12.3.0.eb index d2afa17e..448b9f16 100644 --- a/271_phyluce/btllib_cmdcp.eb +++ b/271_phyluce/btllib-1.7.0-GCC-12.3.0.eb @@ -1,4 +1,3 @@ -# easyblock = 'PythonPackage' easyblock = 'CmdCp' name = 'btllib' @@ -7,12 +6,8 @@ version = '1.7.0' homepage = 'https://github.com/bcgsc/btllib' description = """Bioinformatics Technology Lab common code library""" -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} -toolchainopts = {'openmp': True, 'cstd': 'c++17'} - -# source_urls = ['https://github.com/bcgsc/btllib/archive/'] -# sources = ['v%(version)s.tar.gz'] -# checksums = ['ad8f26cf6187a000fe6cc7a61fa625567f029bca9bb0271d695347627a014059'] +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'openmp': True} sources = [{ 'filename': '%(name)s-%(version)s.tar.gz', @@ -31,24 +26,18 @@ dependencies = [ ('Meson', '1.1.1'), ('Ninja', '1.11.1'), ('CMake', '3.26.3'), + ('SAMtools', '1.18'), ] cmds_map = [('.*', "./compile")] -files_to_copy = [(['btllib'], 'bin')] +files_to_copy = [(['install/bin/*'], 'bin'), (['install/lib/*'], 'lib'), (['install/include/*'], 'include'),] sanity_check_paths = { - 'files': ['bin/btllib'], + 'files': ['bin/randseq', 'bin/indexlr', 'bin/mi_bf_generate' ], 'dirs': [], } -# sanity_check_commands = ['FastTree 2>&1 | grep "FastTree Version %(version)s"'] - -# configopts = 'CXXFLAGS="$CXXFLAGS"' - -# sanity_check_paths = { -# 'files': ["bin/ABYSS", "bin/ABYSS-P"], -# 'dirs': [] -# } +sanity_check_commands = ['randseq --help', 'indexlr --help'] -moduleclass = 'bio' +moduleclass = 'lang' diff --git a/271_phyluce/btllib.eb b/271_phyluce/btllib.eb deleted file mode 100644 index aee2776b..00000000 --- a/271_phyluce/btllib.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'PythonPackage' -# easyblock = 'CmdCp' - -name = 'btllib' -version = '1.7.0' - -homepage = 'https://github.com/bcgsc/btllib' -description = """Bioinformatics Technology Lab common code library""" - -toolchain = {'name': 'foss', 'version': '2023a'} -toolchainopts = {'usempi': True, 'cstd': 'c++17'} - -source_urls = ['https://github.com/bcgsc/btllib/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['ad8f26cf6187a000fe6cc7a61fa625567f029bca9bb0271d695347627a014059'] - -dependencies = [ - ('Python', '3.11.3'), - ('Meson', '1.1.1'), - ('Ninja', '1.11.1'), - ('CMake', '3.26.3'), -] - -# configopts = 'CXXFLAGS="$CXXFLAGS"' - -# sanity_check_paths = { -# 'files': ["bin/ABYSS", "bin/ABYSS-P"], -# 'dirs': [] -# } - -moduleclass = 'bio' From 8ca74233057e71af107e8c7c4542c2fefa42f17b Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 31 Jan 2024 14:36:48 +0100 Subject: [PATCH 12/12] #271 working ABySS --- 271_phyluce/ABySS-2.3.7-foss-2023a.eb | 13 +++++++--- 271_phyluce/error_log.txt | 36 +++++++++++++++++++++++++++ 2 files changed, 46 insertions(+), 3 deletions(-) create mode 100644 271_phyluce/error_log.txt diff --git a/271_phyluce/ABySS-2.3.7-foss-2023a.eb b/271_phyluce/ABySS-2.3.7-foss-2023a.eb index f76dec72..d454923a 100644 --- a/271_phyluce/ABySS-2.3.7-foss-2023a.eb +++ b/271_phyluce/ABySS-2.3.7-foss-2023a.eb @@ -7,24 +7,31 @@ homepage = 'https://www.bcgsc.ca/platform/bioinfo/software/abyss' description = """Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler""" toolchain = {'name': 'foss', 'version': '2023a'} -# toolchainopts = {'usempi': True, 'cstd': 'c++11'} +toolchainopts = {'usempi': True, 'cstd': 'c++17'} +# toolchainopts = {'usempi': True} source_urls = ['http://github.com/bcgsc/abyss/releases/download/%(version)s/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['ba37780e79ec3aa359b6003e383caef13479a87f4d0022af01b86398f9ffca1f'] dependencies = [ + ('Autoconf', '2.71'), + ('Automake', '1.16.5'), ('Boost', '1.82.0'), ('sparsehash', '2.0.4'), - ('SQLite', '3.42.0'), + ('OpenMPI', '4.1.5'), + # ('SQLite', '3.42.0'), ('btllib', '1.7.0'), ] -configopts = 'CXXFLAGS="$CXXFLAGS -Wno-error=deprecated-copy"' +preconfigopts = "./autogen.sh && " +configopts = 'CXXFLAGS="$CXXFLAGS -Wno-error"' sanity_check_paths = { 'files': ["bin/ABYSS", "bin/ABYSS-P"], 'dirs': [] } +sanity_check_commands = ['ABYSS --help'] + moduleclass = 'bio' diff --git a/271_phyluce/error_log.txt b/271_phyluce/error_log.txt new file mode 100644 index 00000000..5a5b942a --- /dev/null +++ b/271_phyluce/error_log.txt @@ -0,0 +1,36 @@ +Error during run Abyss: +ERROR_1: +mpicxx -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/tmp/vsc47063/easybuild/build/ABySS/2.3.7/foss-2023a/abyss-2.3.7 -I/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-amper-12.3.0/include -I/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/OpenMPI/4.1.5-GCC-12.3.0/include -I/scratch/gent/vo/001/gelake-ampere-ib/software/sparsehash/2.0.4-GCCcore-12.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/Boost/1.82.0-GCC-12.3.0/include -I/scratch/gRHEL8/cascadelake-ampere-ib/software/FFTW.MPI/3.3.10-gompi-2023a/include -I/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.3.1-GCC-12.3.0/include -ib/software/FlexiBLAS/3.3.1-GCC-12.3.0/include/flexiblas -isystem/tmp/vsc47063/easybuild/build/ABySS/2.3.7/foss-2023a/abyss-2.3.7/boost_1_56_0 -Wall -Wedeclarations -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -O2 -ftree-vectorize -march=native -fno-math-errno -Wno-error=deprect_a-RUtils.Tpo .deps/libralgorithmsshort_a-RUtils.Po +mv -f .deps/libralgorithmsshort_a-RUtils.Tpo .deps/libralgorithmsshort_a-RUtils.Po +In file included from /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/btllib/1.7.0-GCC-12.3.0/include/btllib/nthash.hpp:12, + from /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/btllib/1.7.0-GCC-12.3.0/include/btllib/bloom_filter.hpp:4, + from BloomFilters.h:4, + from RAlgorithmsShort.h:4, + from RResolverShort.cpp:7: +/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/btllib/1.7.0-GCC-12.3.0/include/btllib/hashing_internals.hpp:554:11: error: +ilable with -std=c++17 or -std=gnu++17 [-Werror=c++17-extensions] + 554 | constexpr inline uint64_t AA_SEED_A = 0xf56d6192468323df; + | ^~~~~~ +/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/btllib/1.7.0-GCC-12.3.0/include/btllib/hashing_internals.hpp:555:11: error: +ilable with -std=c++17 or -std=gnu++17 [-Werror=c++17-extensions] + 555 | constexpr inline uint64_t AA_SEED_C = 0x9b0b2fd724e1e1d2; + | ^~~~~~ +/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/btllib/1.7.0-GCC-12.3.0/include/btllib/hashing_internals.hpp:556:11: error: +ilable with -std=c++17 or -std=gnu++17 [-Werror=c++17-extensions] + 556 | constexpr inline uint64_t AA_SEED_D = 0xe8c583296b03c7af; +..... +mv -f .deps/libralgorithmsshort_a-SequenceTree.Tpo .deps/libralgorithmsshort_a-SequenceTree.Po +cc1plus: all warnings being treated as errors +make[2]: *** [Makefile:555: abyss_rresolver_short-RResolverShort.o] Error 1 +make[2]: *** Waiting for unfinished jobs.... +cc1plus: all warnings being treated as errors +make[2]: *** [Makefile:499: libralgorithmsshort_a-BloomFilters.o] Error 1 +mv -f .deps/abyss_rresolver_short-Contigs.Tpo .deps/abyss_rresolver_short-Contigs.Po +mv -f .deps/libralgorithmsshort_a-Contigs.Tpo .deps/libralgorithmsshort_a-Contigs.Po +cc1plus: all warnings being treated as errors +make[2]: *** [Makefile:485: libralgorithmsshort_a-RAlgorithmsShort.o] Error 1 +make[2]: Leaving directory '/tmp/vsc47063/easybuild/build/ABySS/2.3.7/foss-2023a/abyss-2.3.7/RResolver' +make[1]: *** [Makefile:488: all-recursive] Error 1 +make[1]: Leaving directory '/tmp/vsc47063/easybuild/build/ABySS/2.3.7/foss-2023a/abyss-2.3.7' +make: *** [Makefile:408: all] Error 2 + (at easybuild/easybuild-framework/easybuild/tools/run.py:682 in parse_cmd_output) \ No newline at end of file