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Merge pull request #21733 from maxim-masterov/prsice_2024a
{bio}[GCCcore/13.3.0] PRSice v2.3.5- Loading branch information
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easybuild/easyconfigs/p/PRSice/PRSice-2.3.5-GCCcore-13.3.0.eb
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|---|---|---|
| @@ -0,0 +1,44 @@ | ||
| # Contribution from the NIHR Biomedical Research Centre | ||
| # Guy's and St Thomas' NHS Foundation Trust and King's College London | ||
| # uploaded by J. Sassmannshausen | ||
|
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| easyblock = 'CMakeMakeCp' | ||
|
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| name = 'PRSice' | ||
| version = '2.3.5' | ||
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| homepage = 'https://choishingwan.github.io/PRSice/' | ||
| description = """PRSice (pronounced 'precise') is a Polygenic Risk | ||
| Score software for calculating, applying, evaluating and | ||
| plotting the results of polygenic risk scores (PRS) analyses.""" | ||
|
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| toolchain = {'name': 'GCCcore', 'version': '13.3.0'} | ||
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| source_urls = ['https://github.com/choishingwan/%(name)s/archive/'] | ||
| sources = ['%(version)s.tar.gz'] | ||
| patches = ['PRSice-2.3.5_remove_sysctl.patch'] | ||
| checksums = [ | ||
| '0a7e649ddebe4e969cd8400c5ad977a7b900be4f5c920a84483cb8930367354d', # 2.3.5.tar.gz | ||
| 'ab8286e8a0700ea163f552de66458e409c396e06b57c9adfff3b7f63083f7798', # PRSice-2.3.5_remove_sysctl.patch | ||
| ] | ||
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| builddependencies = [ | ||
| ('CMake', '3.29.3'), | ||
| ('binutils', '2.42'), | ||
| ('Eigen', '3.4.0'), | ||
| ] | ||
|
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| files_to_copy = [ | ||
| (['bin/%(name)s'], 'bin'), | ||
| 'README.md', | ||
| 'LICENSE', | ||
| ] | ||
|
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| sanity_check_paths = { | ||
| 'files': ['bin/%(name)s'], | ||
| 'dirs': [], | ||
| } | ||
|
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| sanity_check_commands = ['%(name)s --help'] | ||
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| moduleclass = 'bio' |
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easybuild/easyconfigs/p/PRSice/PRSice-2.3.5_remove_sysctl.patch
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| @@ -0,0 +1,194 @@ | ||
| # What: sysctl.h is removed in glibc v2.32. This patch is based on the following commits | ||
| # from https://github.com/choishingwan/PRSice: | ||
| # f285b243856b857a461d9a2b27e1f2f0ac25216e | ||
| # 53641c11750a7e0bdd06a925fbf28c1e3978ee72 | ||
| # Also see issue https://github.com/choishingwan/PRSice/issues/338 and PR https://github.com/choishingwan/PRSice/pull/243 | ||
| # Author: maxim-masterov (SURF) | ||
|
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||
| diff -Nru PRSice-2.3.5.orig/inc/misc.hpp PRSice-2.3.5/inc/misc.hpp | ||
| --- PRSice-2.3.5.orig/inc/misc.hpp 2024-10-23 18:13:58.539539000 +0200 | ||
| +++ PRSice-2.3.5/inc/misc.hpp 2024-10-23 18:14:29.383991502 +0200 | ||
| @@ -38,7 +38,6 @@ | ||
| #include <mach/mach_init.h> | ||
| #include <mach/mach_types.h> | ||
| #include <mach/vm_statistics.h> | ||
| -#include <sys/sysctl.h> | ||
| #elif defined _WIN32 | ||
| #include <windows.h> | ||
| // psapi must go after windows, or will generate error | ||
| @@ -48,7 +47,6 @@ | ||
| #include "stdlib.h" | ||
| #include "string.h" | ||
| #include <sys/param.h> | ||
| -#include <sys/sysctl.h> | ||
| #include <sys/types.h> | ||
| #include <unistd.h> | ||
| #endif | ||
| @@ -86,9 +84,6 @@ | ||
| #include <sys/param.h> | ||
| #include <sys/types.h> | ||
| #include <unistd.h> | ||
| -#if defined(BSD) | ||
| -#include <sys/sysctl.h> | ||
| -#endif | ||
|
|
||
| #else | ||
| #error "Unable to define getMemorySize( ) for an unknown OS." | ||
| @@ -170,73 +165,7 @@ | ||
| // TODO: Delete this, doesn't seems to give robust answer | ||
| inline size_t current_ram_usage() { return 0; } | ||
| // TODO: Delete this, doesn't seems to give robust answer | ||
| -inline size_t total_ram_available() | ||
| -{ | ||
| -#ifdef __APPLE__ | ||
| - int32_t mib[2]; | ||
| - size_t sztmp; | ||
| -#endif | ||
| - unsigned char* bigstack_ua = nullptr; // ua = unaligned | ||
| - int64_t llxx; | ||
| - intptr_t default_alloc_mb; | ||
| - intptr_t malloc_size_mb = 0; | ||
| -#ifdef __APPLE__ | ||
| - mib[0] = CTL_HW; | ||
| - mib[1] = HW_MEMSIZE; | ||
| - llxx = 0; | ||
| - | ||
| - sztmp = sizeof(int64_t); | ||
| - sysctl(mib, 2, &llxx, &sztmp, nullptr, 0); | ||
| - llxx /= 1048576; | ||
| -#else | ||
| -#ifdef _WIN32 | ||
| - MEMORYSTATUSEX memstatus; | ||
| - memstatus.dwLength = sizeof(memstatus); | ||
| - GlobalMemoryStatusEx(&memstatus); | ||
| - llxx = memstatus.ullTotalPhys / 1048576; | ||
| -#else | ||
| - llxx = ((uint64_t) sysconf(_SC_PHYS_PAGES)) | ||
| - * ((size_t) sysconf(_SC_PAGESIZE)) / 1048576; | ||
| -#endif | ||
| -#endif | ||
| - if (!llxx) { default_alloc_mb = BIGSTACK_DEFAULT_MB; } | ||
| - else if (llxx < (BIGSTACK_MIN_MB * 2)) | ||
| - { | ||
| - default_alloc_mb = BIGSTACK_MIN_MB; | ||
| - } | ||
| - else | ||
| - { | ||
| - default_alloc_mb = llxx / 2; | ||
| - } | ||
| - if (!malloc_size_mb) { malloc_size_mb = default_alloc_mb; } | ||
| - else if (malloc_size_mb < BIGSTACK_MIN_MB) | ||
| - { | ||
| - malloc_size_mb = BIGSTACK_MIN_MB; | ||
| - } | ||
| - std::string message = ""; | ||
| -#ifndef __LP64__ | ||
| - if (malloc_size_mb > 2047) { malloc_size_mb = 2047; } | ||
| -#endif | ||
| - bigstack_ua = | ||
| - (unsigned char*) malloc(malloc_size_mb * 1048576 * sizeof(char)); | ||
| - // if fail, return nullptr which will then get into the while loop | ||
| - while (!bigstack_ua) | ||
| - { | ||
| - malloc_size_mb = (malloc_size_mb * 3) / 4; | ||
| - if (malloc_size_mb < BIGSTACK_MIN_MB) | ||
| - { malloc_size_mb = BIGSTACK_MIN_MB; } | ||
| - bigstack_ua = | ||
| - (unsigned char*) malloc(malloc_size_mb * 1048576 * sizeof(char)); | ||
| - if (bigstack_ua) {} | ||
| - else if (malloc_size_mb == BIGSTACK_MIN_MB) | ||
| - { | ||
| - throw std::runtime_error("Failed to allocate required memory"); | ||
| - } | ||
| - } | ||
| - free(bigstack_ua); | ||
| - bigstack_ua = nullptr; | ||
| - return malloc_size_mb * 1024 * 1024; | ||
| -} | ||
| + | ||
| // function from John D.Cook | ||
| // https://www.johndcook.com/blog/standard_deviation/ | ||
| class RunningStat | ||
| @@ -1398,82 +1327,5 @@ | ||
| return (size_t) 0L; /* Unsupported. */ | ||
| #endif | ||
| } | ||
| - | ||
| - | ||
| -/** | ||
| - * Returns the size of physical memory (RAM) in bytes. | ||
| - */ | ||
| -inline size_t getMemorySize() | ||
| -{ | ||
| -#if defined(_WIN32) && (defined(__CYGWIN__) || defined(__CYGWIN32__)) | ||
| - /* Cygwin under Windows. ------------------------------------ */ | ||
| - /* New 64-bit MEMORYSTATUSEX isn't available. Use old 32.bit */ | ||
| - MEMORYSTATUS status; | ||
| - status.dwLength = sizeof(status); | ||
| - GlobalMemoryStatus(&status); | ||
| - return (size_t) status.dwTotalPhys; | ||
| - | ||
| -#elif defined(_WIN32) | ||
| - /* Windows. ------------------------------------------------- */ | ||
| - /* Use new 64-bit MEMORYSTATUSEX, not old 32-bit MEMORYSTATUS */ | ||
| - MEMORYSTATUSEX status; | ||
| - status.dwLength = sizeof(status); | ||
| - GlobalMemoryStatusEx(&status); | ||
| - return (size_t) status.ullTotalPhys; | ||
| - | ||
| -#elif defined(__unix__) || defined(__unix) || defined(unix) \ | ||
| - || (defined(__APPLE__) && defined(__MACH__)) | ||
| - /* UNIX variants. ------------------------------------------- */ | ||
| - /* Prefer sysctl() over sysconf() except sysctl() HW_REALMEM and HW_PHYSMEM | ||
| - */ | ||
| - | ||
| -#if defined(CTL_HW) && (defined(HW_MEMSIZE) || defined(HW_PHYSMEM64)) | ||
| - int mib[2]; | ||
| - mib[0] = CTL_HW; | ||
| -#if defined(HW_MEMSIZE) | ||
| - mib[1] = HW_MEMSIZE; /* OSX. --------------------- */ | ||
| -#elif defined(HW_PHYSMEM64) | ||
| - mib[1] = HW_PHYSMEM64; /* NetBSD, OpenBSD. --------- */ | ||
| -#endif | ||
| - int64_t size = 0; /* 64-bit */ | ||
| - size_t len = sizeof(size); | ||
| - if (sysctl(mib, 2, &size, &len, NULL, 0) == 0) return (size_t) size; | ||
| - return 0L; /* Failed? */ | ||
| - | ||
| -#elif defined(_SC_AIX_REALMEM) | ||
| - /* AIX. ----------------------------------------------------- */ | ||
| - return (size_t) sysconf(_SC_AIX_REALMEM) * (size_t) 1024L; | ||
| - | ||
| -#elif defined(_SC_PHYS_PAGES) && defined(_SC_PAGESIZE) | ||
| - /* FreeBSD, Linux, OpenBSD, and Solaris. -------------------- */ | ||
| - return (size_t) sysconf(_SC_PHYS_PAGES) * (size_t) sysconf(_SC_PAGESIZE); | ||
| - | ||
| -#elif defined(_SC_PHYS_PAGES) && defined(_SC_PAGE_SIZE) | ||
| - /* Legacy. -------------------------------------------------- */ | ||
| - return (size_t) sysconf(_SC_PHYS_PAGES) * (size_t) sysconf(_SC_PAGE_SIZE); | ||
| - | ||
| -#elif defined(CTL_HW) && (defined(HW_PHYSMEM) || defined(HW_REALMEM)) | ||
| - /* DragonFly BSD, FreeBSD, NetBSD, OpenBSD, and OSX. -------- */ | ||
| - int mib[2]; | ||
| - mib[0] = CTL_HW; | ||
| -#if defined(HW_REALMEM) | ||
| - mib[1] = HW_REALMEM; /* FreeBSD. ----------------- */ | ||
| -#elif defined(HW_PYSMEM) | ||
| - mib[1] = HW_PHYSMEM; /* Others. ------------------ */ | ||
| -#endif | ||
| - unsigned int size = 0; /* 32-bit */ | ||
| - size_t len = sizeof(size); | ||
| - if (sysctl(mib, 2, &size, &len, NULL, 0) == 0) return (size_t) size; | ||
| - return 0L; /* Failed? */ | ||
| -#endif /* sysctl and sysconf variants */ | ||
| - | ||
| -#else | ||
| - return 0L; /* Unknown OS. */ | ||
| -#endif | ||
| } | ||
|
|
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| -inline unsigned long long remain_memory(const double& adjFactor = 0.8) | ||
| -{ | ||
| - return (misc::getMemorySize() * adjFactor - getCurrentRSS()); | ||
| -} | ||
| -} |