Merge branch 'wip' of github.com:vscentrum/vsc-software-stack into wip

vscentrum · Jan 31, 2024 · f0788f9 · f0788f9
2 parents 38a4279 + 8ca7423
commit f0788f9
Show file tree

Hide file tree

Showing 16 changed files with 592 additions and 21 deletions.
diff --git a/166_FragPipe/IonQuant-1.9.8-Java-11.eb b/166_FragPipe/IonQuant-1.9.8-Java-11.eb
@@ -16,13 +16,22 @@ toolchain = SYSTEM
 sources = ['%(name)s-%(version)s.zip']
 checksums = ['98010f55d53c3fce786538da2976e1caaf688b29649d32e66ead8ba24a0db754']
 
+download_instructions = 'Manual download required, see https://msfragger.arsci.com/ionquant/'
+
 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
@@ -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 = [
@@ -27,14 +29,11 @@ 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'
diff --git 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::<T, LANES>::splat
+            Mask::<T, LANES>::from_array
+            Mask::<T, LANES>::from_int_unchecked
+            Mask::<T, LANES>::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::<T, LANES>::from_int_unchecked
+            Mask::<T, LANES>::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::<T, LANES>::splat
+            Mask::<T, LANES>::from_array
+            Mask::<T, LANES>::from_int_unchecked
+            Mask::<T, LANES>::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::<i8, LANES>::from_bitmask(validity_chunk as u64);
+         |                                           ^^^^^^^^^^^^ function or associated item not found in `Mask<i8, 8>`
+         |
+         = 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::<i8, LANES>::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
@@ -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."""
@@ -10,26 +10,28 @@ 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
     ('matplotlib', '3.7.2'), #done
     ('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/236_NGSpeciesID/NGSpeciesID-0.3.0-foss-2023a.eb 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
@@ -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."
@@ -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