progress on #166 FragPipe

166_FragPipe/EasyPQP-0.1.40-foss-2022b.eb

@@ -0,0 +1,37 @@
+easyblock = 'PythonBundle'
+
+name = 'EasyPQP'
+version = '0.1.40'
+
+homepage = 'https://github.com/grosenberger/easypqp'
+description = """EasyPQP is a Python package that provides simplified and fast peptide query
+ parameter generation for OpenSWATH. It can process input from MSFragger or other database
+ search engines in pepXML format. """
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('Biopython', '1.81'),
+    ('matplotlib', '3.7.0'),
+    # ('numba', '0.56.4'),  # TODO
+    ('scikit-learn', '1.2.1'),
+]
+
+sanity_pip_check = True
+use_pip = True
+
+exts_list = [
+    ('%(namelower)s', version, {
+        'checksums': ['9ea5db3d58b7ed49972477240ab079e60cc42488bfccf508d2a74e2d7f357bc5'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/%(namelower)s'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["%(namelower)s --help"]
+
+moduleclass = 'tools'

166_FragPipe/FragPipe-20.0-Java-11.eb

@@ -0,0 +1,26 @@
+easyblock = 'Tarball'
+
+name = 'FragPipe'
+version = '20.0'
+versionsuffix = '-Java-%(javaver)s'
+
+homepage = 'https://fragpipe.nesvilab.org'
+description = """FragPipe is a Java Graphical User Interface (GUI) for a suite of computational
+ tools enabling comprehensive analysis of mass spectrometry-based proteomics data."""
+
+toolchain = SYSTEM
+
+source_urls = ['https://github.com/Nesvilab/%(name)s/releases/download/%(version)s/']
+sources = ['%(name)s-%(version)s.zip']
+checksums = ['0d77db85ae26c190a915823e1c68238f3a19533810734b008564b2a8d85d1bd6']
+
+dependencies = [('Java', '11')]
+
+sanity_check_paths = {
+    'files': ['bin/%(namelower)s', 'lib/%(namelower)s-%(version)s.jar'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["%(namelower)s -h | grep -q v%(version)s"]
+
+moduleclass = 'bio'

166_FragPipe/Philosopher-5.0.0-GCC-12.2.0.eb

@@ -0,0 +1,35 @@
+easyblock = 'MakeCp'
+
+name = 'Philosopher'
+version = '5.0.0'
+
+homepage = 'https://philosopher.nesvilab.org/'
+description = """Philosopher is a fast, easy-to-use, scalable, and versatile
+ data analysis software for mass spectrometry-based proteomics. Philosopher
+ is dependency-free and can analyze both traditional database searches and
+ open searches for post-translational modification (PTM) discovery."""
+
+toolchain = {'name': 'GCC', 'version': '12.2.0'}
+
+source_urls = ['https://github.com/Nesvilab/philosopher/archive/']
+sources = [{'download_filename': 'v%s.tar.gz' % version, 'filename': SOURCE_TAR_GZ}]
+checksums = ['0c6895c60c1c2543f7b0ad7f8baae4be39c9c519d6035c8fdd2ad8a2f83a99cc']
+
+builddependencies = [
+    ('Go', '1.21.2', '', SYSTEM),
+]
+
+buildopts = 'CC="$CC" CFLAGS="$CFLAGS"'
+
+files_to_copy = [
+    (['%(namelower)s'], 'bin'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/%(namelower)s'],
+    'dirs': []
+}
+
+sanity_check_commands = ['%(namelower)s --help']
+
+moduleclass = 'bio'

166_FragPipe/llvmlite-0.39.1_fix-LLVM-15.patch

@@ -0,0 +1,95 @@
+fix build on top of LLVM 14,
+like this: https://github.com/numba/llvmlite/issues/897
+diff -ruN llvmlite-0.39.1.orig/ffi/passmanagers.cpp llvmlite-0.39.1/ffi/passmanagers.cpp
+--- llvmlite-0.39.1.orig/ffi/passmanagers.cpp	2022-09-01 13:47:22.477959200 +0000
++++ llvmlite-0.39.1/ffi/passmanagers.cpp	2023-01-10 16:59:33.776510869 +0000
+@@ -8,6 +8,7 @@
+ #include "llvm/IR/DiagnosticInfo.h"
+ #include "llvm/IR/DiagnosticPrinter.h"
+ #include "llvm/IR/LegacyPassManager.h"
++#include "llvm/Pass.h"
+ #include "llvm/IR/Module.h"
+ #include "llvm/Support/FileSystem.h"
+ #include "llvm/Support/ToolOutputFile.h"
+@@ -17,9 +18,6 @@
+ #include "llvm-c/Transforms/IPO.h"
+ #include "llvm-c/Transforms/Scalar.h"
+ #include "llvm/IR/LegacyPassManager.h"
+-#if LLVM_VERSION_MAJOR > 11
+-#include "llvm/IR/RemarkStreamer.h"
+-#endif
+ #include "llvm/IR/LLVMRemarkStreamer.h"
+ #include "llvm/Remarks/RemarkStreamer.h"
+ #include "llvm/Transforms/IPO.h"
+diff -ruN llvmlite-0.39.1.orig/ffi/targets.cpp llvmlite-0.39.1/ffi/targets.cpp
+--- llvmlite-0.39.1.orig/ffi/targets.cpp	2022-09-01 13:47:22.449959300 +0000
++++ llvmlite-0.39.1/ffi/targets.cpp	2023-01-10 16:59:54.544810234 +0000
+@@ -6,7 +6,7 @@
+ #include "llvm/IR/LegacyPassManager.h"
+ #include "llvm/IR/Type.h"
+ #include "llvm/Support/Host.h"
+-#include "llvm/Support/TargetRegistry.h"
++#include "llvm/MC/TargetRegistry.h"
+ #include "llvm/Target/TargetMachine.h"
+
+ #include <cstdio>
+@@ -204,7 +204,6 @@
+         rm = Reloc::DynamicNoPIC;
+
+     TargetOptions opt;
+-    opt.PrintMachineCode = PrintMC;
+     opt.MCOptions.ABIName = ABIName;
+
+     bool jit = JIT;
+diff -ruN llvmlite-0.39.1.orig/ffi/value.cpp llvmlite-0.39.1/ffi/value.cpp
+--- llvmlite-0.39.1.orig/ffi/value.cpp	2022-09-01 13:47:22.449959300 +0000
++++ llvmlite-0.39.1/ffi/value.cpp	2023-01-10 16:59:09.616162588 +0000
+@@ -154,7 +154,7 @@
+     Argument *arg = unwrap<Argument>(A);
+     unsigned argno = arg->getArgNo();
+     AttributeSet attrs =
+-        arg->getParent()->getAttributes().getParamAttributes(argno);
++        arg->getParent()->getAttributes().getParamAttrs(argno);
+     return wrap(new AttributeSetIterator(attrs.begin(), attrs.end()));
+ }
+
+diff -ruN llvmlite-0.39.1.orig/llvmlite/tests/test_binding.py llvmlite-0.39.1/llvmlite/tests/test_binding.py
+--- llvmlite-0.39.1.orig/llvmlite/tests/test_binding.py	2022-09-01 13:47:22.481959000 +0000
++++ llvmlite-0.39.1/llvmlite/tests/test_binding.py	2023-01-10 17:00:04.868959051 +0000
+@@ -18,6 +18,16 @@
+ from llvmlite.tests import TestCase
+
+
++def clean_string_whitespace(x: str) -> str:
++    # Remove trailing whitespace from the end of each line
++    x = re.sub(r"\s+$", "", x, flags=re.MULTILINE)
++    # Remove intermediate blank lines
++    x = re.sub(r"\n\s*\n", r"\n", x, flags=re.MULTILINE)
++    # Remove extraneous whitespace from the beginning and end of the string
++    x = x.strip()
++    return x
++
++
+ # arvm7l needs extra ABI symbols to link successfully
+ if platform.machine() == 'armv7l':
+     llvm.load_library_permanently('libgcc_s.so.1')
+@@ -555,7 +565,10 @@
+         bd = ir.IRBuilder(fn.append_basic_block(name="<>!*''#"))
+         bd.ret(ir.Constant(ir.IntType(32), 12345))
+         asm = str(mod)
+-        self.assertEqual(asm, asm_nonalphanum_blocklabel)
++        self.assertEqual(
++            clean_string_whitespace(asm),
++            clean_string_whitespace(asm_nonalphanum_blocklabel)
++        )
+
+     def test_global_context(self):
+         gcontext1 = llvm.context.get_global_context()
+@@ -640,7 +653,7 @@
+     def test_version(self):
+         major, minor, patch = llvm.llvm_version_info
+         # one of these can be valid
+-        valid = [(11,)]
++        valid = [(11,), (12,), (13,), (14,), (15,)]
+         self.assertIn((major,), valid)
+         self.assertIn(patch, range(10))

166_FragPipe/numba-0.58.1-foss-2022b.eb

@@ -0,0 +1,54 @@
+easyblock = 'PythonBundle'
+
+name = 'numba'
+version = '0.58.1'
+
+homepage = 'https://numba.pydata.org/'
+description = """Numba is an Open Source NumPy-aware optimizing compiler for
+Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM
+compiler infrastructure to compile Python syntax to machine code."""
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+toolchainopts = {'pic': True}
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('SciPy-bundle', '2023.02'),
+    ('LLVM', '15.0.5'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+local_llvmlite_preinstallopts = "export LLVM_CONFIG=${EBROOTLLVM}/bin/llvm-config && "
+local_llvmlite_preinstallopts += "export LLVMLITE_SKIP_LLVM_VERSION_CHECK=1 && "
+
+exts_list = [
+    ('llvmlite', '0.39.1', {
+        'preinstallopts': local_llvmlite_preinstallopts,
+        'patches': ['llvmlite-0.39.1_fix-LLVM-15.patch'],
+        'checksums': [
+            {'llvmlite-0.39.1.tar.gz': 'b43abd7c82e805261c425d50335be9a6c4f84264e34d6d6e475207300005d572'},
+            {'llvmlite-0.39.1_fix-LLVM-15.patch': 'c30d9827da278ea27a75b7fa29648227a874e21219c95156608e64d4533b9c36'},
+        ],
+    }),
+    (name, version, {
+        'checksums': [
+            {'numba-0.58.1.tar.gz': '487ded0633efccd9ca3a46364b40006dbdaca0f95e99b8b83e778d1195ebcbaa'},
+        ],
+    }),
+]
+
+fix_python_shebang_for = ['bin/*']
+
+sanity_check_paths = {
+    'files': ['bin/numba', 'bin/pycc'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = [
+    "python -m llvmlite.tests",
+    "numba --help",
+]
+
+moduleclass = 'lang'