Building on M1 Mac from source

[jonathan-bravo]

This took me almost all night to figure out so I just wanted to post this as info for anyone else trying to do this.

Use homebrew to install the required libraries

brew install xz zlib bzip2 icu4c
brew link icu4c --force

• cd EpansionHunterDenovo direcotry
• mkdir build
• cd into the build directory
• run cmake ../source

Modify the line in ExpansionHunterDenovo/source/thirdparty/catch2/catch.hpp:

change line 6014 from:

#define CATCH_TRAP() __asm__("int $3\n" : : ) /* NOLINT */

To:

#if defined(__i386__) || defined(__x86_64__)
    #define CATCH_TRAP() __asm__("int $3\n" : : ) /* NOLINT */
#elif defined(__aarch64__)
    #define CATCH_TRAP()  __asm__(".inst 0xd4200000")
#endif

Modify the line in build/thirdparty/htslib-1.9-source/cram/cram_io.c

changed the #include <lzma.h> to #include "/opt/homebrew/opt/xz/include/lzma.h"

THEN in the build directory you can run make and the build should complete!

[BenjaminDEMAILLE]

Thanks a lot

[BenjaminDEMAILLE]

This took me almost all night to figure out so I just wanted to post this as info for anyone else trying to do this.

Use homebrew to install the required libraries

brew install xz zlib bzip2 icu4c brew link icu4c --force

• cd EpansionHunterDenovo direcotry
• mkdir build
• cd into the build directory
• run cmake ../source

Modify the line in ExpansionHunterDenovo/source/thirdparty/catch2/catch.hpp:

change line 6014 from:

#define CATCH_TRAP() __asm__("int $3\n" : : ) /* NOLINT */

To:

#if defined(__i386__) || defined(__x86_64__)
    #define CATCH_TRAP() __asm__("int $3\n" : : ) /* NOLINT */
#elif defined(__aarch64__)
    #define CATCH_TRAP()  __asm__(".inst 0xd4200000")
#endif

Modify the line in build/thirdparty/htslib-1.9-source/cram/cram_io.c

changed the #include <lzma.h> to #include "/opt/homebrew/opt/xz/include/lzma.h"

THEN in the build directory you can run make and the build should complete!

Hi

I tried but got :

benjamin@MacBook-Pro-de-Benjamin build % cmake ../source
CMake Deprecation Warning at thirdparty/boost-cmake-1.67.0/CMakeLists.txt:1 (cmake_minimum_required):
  Compatibility with CMake < 3.10 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value.  Or, use the <min>...<max> syntax
  to tell CMake that the project requires at least <min> but has been updated
  to work with policies introduced by <max> or earlier.


CMake Warning (dev) at thirdparty/boost-cmake-1.67.0/CMakeLists.txt:7 (set):
  implicitly converting 'DIRECTORY' to 'STRING' type.
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Downloading Boost from https://dl.bintray.com/boostorg/release/1.67.0/source/boost_1_67_0.tar.bz2
-- [download 0% complete]
CMake Error at thirdparty/boost-cmake-1.67.0/cmake/Modules/DownloadBoost.cmake:66 (file):
  file DOWNLOAD cannot compute hash on failed download

    status: [22;"HTTP response code said error"]
Call Stack (most recent call first):
  thirdparty/boost-cmake-1.67.0/CMakeLists.txt:11 (include)


CMake Error at thirdparty/boost-cmake-1.67.0/cmake/Modules/DownloadBoost.cmake:76 (message):
  Download failed.  Status: 22 "HTTP response code said error"

  Log: Host dl.bintray.com:443 was resolved.

  IPv6: (none)

  IPv4: 18.214.194.113, 3.95.117.170, 18.232.172.199

    Trying 18.214.194.113:443...

  Connected to dl.bintray.com (18.214.194.113) port 443

  ALPN: curl offers http/1.1

  (304) (OUT), TLS handshake, Client hello (1):

  [312 bytes data]

   CAfile: /etc/ssl/cert.pem
   CApath: none

  (304) (IN), TLS handshake, Server hello (2):

  [108 bytes data]

  TLSv1.2 (IN), TLS handshake, Certificate (11):

  [3680 bytes data]

  TLSv1.2 (IN), TLS handshake, Server key exchange (12):

  [300 bytes data]

  TLSv1.2 (IN), TLS handshake, Server finished (14):

  [4 bytes data]

  TLSv1.2 (OUT), TLS handshake, Client key exchange (16):

  [37 bytes data]

  TLSv1.2 (OUT), TLS change cipher, Change cipher spec (1):

  [1 bytes data]

  TLSv1.2 (OUT), TLS handshake, Finished (20):

  [16 bytes data]

  TLSv1.2 (IN), TLS change cipher, Change cipher spec (1):

  [1 bytes data]

  TLSv1.2 (IN), TLS handshake, Finished (20):

  [16 bytes data]

  SSL connection using TLSv1.2 / ECDHE-RSA-AES256-GCM-SHA384 / [blank] /
  UNDEF

  ALPN: server accepted http/1.1

  Server certificate:

   subject: CN=*.bintray.com
   start date: Nov 14 00:00:00 2024 GMT
   expire date: Nov  8 23:59:59 2025 GMT
   subjectAltName: host "dl.bintray.com" matched cert's "*.bintray.com"
   issuer: C=US; O=DigiCert Inc; OU=www.digicert.com; CN=GeoTrust TLS RSA CA G1
   SSL certificate verify ok.

  using HTTP/1.x

  GET /boostorg/release/1.67.0/source/boost_1_67_0.tar.bz2 HTTP/1.1

  Host: dl.bintray.com

  User-Agent: curl/8.7.1

  Accept: */*

  

  Request completely sent off

  HTTP/1.1 404 Not Found

  Date: Sun, 05 Jan 2025 09:18:55 GMT

  Content-Type: text/html

  Content-Length: 146

  Connection: keep-alive

  Strict-Transport-Security: max-age=31536000; includeSubDomains

  

  The requested URL returned error: 404

  Closing connection

  TLSv1.2 (OUT), TLS alert, close notify (256):

  [2 bytes data]

Call Stack (most recent call first):
  thirdparty/boost-cmake-1.67.0/CMakeLists.txt:11 (include)


-- Configuring incomplete, errors occurred!
benjamin@MacBook-Pro-de-Benjamin build % 

at = run cmake ../source
Can you help me ?