Merge pull request #302 from pjotrp/main

Guix static build for wfmash. Fixing tests and working on guix instructions/scripts

.gitignore

@@ -30,6 +30,7 @@ build
 .\#*
 src/common/WFA2-lib/bin/
 src/wfmash_git_version.hpp
+src/common/wflign/src/wflign_git_version.hpp
 
 test/
 .idea/

CMakeLists.txt

@@ -87,7 +87,7 @@ if (BUILD_DEPS)
   ExternalProject_Add(htslib
     URL https://github.com/samtools/htslib/releases/download/1.20/htslib-1.20.tar.bz2
     PREFIX ${CMAKE_CURRENT_BINARY_DIR}/htslib
-    CONFIGURE_COMMAND autoreconf -i && ./configure --prefix=${CMAKE_CURRENT_BINARY_DIR}/htslib --disable-libcurl --disable-s3 
+    CONFIGURE_COMMAND autoreconf -i && ./configure --prefix=${CMAKE_CURRENT_BINARY_DIR}/htslib --disable-libcurl --disable-s3
     BUILD_COMMAND $(MAKE)
     INSTALL_COMMAND $(MAKE) install
     BUILD_IN_SOURCE 1
@@ -171,11 +171,12 @@ target_link_libraries(wfmash
   Threads::Threads
 )
 
+# This is to disable tests defined in CTestCustom.cmake:
 configure_file(${CMAKE_SOURCE_DIR}/CTestCustom.cmake ${CMAKE_BINARY_DIR})
 
 add_test(
   NAME wfmash-test
-  COMMAND ./build/bin/wfmash data/LPA.subset.fa.gz -p 80 -n 5 -t 8
+  COMMAND wfmash data/LPA.subset.fa.gz -p 80 -n 5 -t 8
   WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
 
 install(TARGETS wfmash DESTINATION bin)

CTestCustom.cmake

@@ -1,3 +1,4 @@
-CTestCustom.cmake
-
-
+# Disable tests for the following modules:
+set(CTEST_CUSTOM_TESTS_IGNORE
+  wfa2lib
+)

README.md

@@ -208,10 +208,10 @@ This will install the `wfmash` binary and any required libraries to the default
 
 #### Tests
 
-To build and run tests:
+To build and run tests, change to build directory and
 
 ```sh
-cmake --build build --target test
+ctest .
 ```
 
 #### Notes for distribution
@@ -262,6 +262,8 @@ If you have `guix`:
 guix build -f guix.scm
 ```
 
+To build guix in a development container, see the instructions in the header of [guix.scm](./guix.scm).
+
 #### Docker and Singularity images with nix
 
 Nix is also able to build an Docker image, which can then be loaded by Docker and converted to a Singularity image.

guix-static.scm

@@ -10,29 +10,28 @@
 ;;
 ;;   mkdir build
 ;;   cd build
-;;   cmake ..
+;;   cmake -DBUILD_STATIC=1 ..
 ;;   make
 ;;
 ;; For the tests you may need /usr/bin/env. Inside the container:
 ;;
 ;;   mkdir -p /usr/bin ; ln -s $GUIX_ENVIRONMENT/bin/env /usr/bin/env
 ;;
-;; by Pjotr Prins (c) 2023
+;; by Pjotr Prins (c) 2023-2024
 
 (use-modules
  ((guix licenses) #:prefix license:)
+  (guix build-system cmake)
+  (guix download)
   (guix gexp)
-  (guix packages)
   (guix git-download)
-  (guix build-system cmake)
-  ; (guix gexp)
+  (guix packages)
   (guix utils)
   (gnu packages algebra)
   (gnu packages base)
   (gnu packages bioinformatics)
   (gnu packages build-tools)
   (gnu packages compression)
-  ; (gnu packages curl)
   (gnu packages gcc)
   (gnu packages jemalloc)
   (gnu packages llvm)
@@ -45,12 +44,31 @@
   (ice-9 popen)
   (ice-9 rdelim))
 
+(define-public libdeflate-static
+  (package
+    (inherit libdeflate)
+    (name "libdeflate-static")
+    (version "1.19")
+    (arguments
+     (list #:configure-flags
+           #~(list "-DLIBDEFLATE_BUILD_STATIC_LIB=YES"
+                   "-DLIBDEFLATE_BUILD_TESTS=YES")))))
+
 ;; A minimal version of htslib that does not depend on curl and openssl. This
 ;; reduces the number of higher order dependencies in static linking.
 (define-public htslib-static
   (package
     (inherit htslib)
     (name "htslib-static")
+    (version "1.19")
+    (source (origin
+            (method url-fetch)
+            (uri (string-append
+                  "https://github.com/samtools/htslib/releases/download/"
+                  version "/htslib-" version ".tar.bz2"))
+            (sha256
+             (base32
+              "0dh79lwpspwwfbkmllrrhbk8nkvlfc5b5ib4d0xg5ld79w6c8lc7"))))
     (arguments
      (substitute-keyword-arguments (package-arguments htslib)
        ((#:configure-flags flags ''())
@@ -66,32 +84,36 @@
 (define-public wfmash-git
   (package
     (name "wfmash-git")
-    (version (git-version "0.10.7" "HEAD" %git-commit))
+    (version (git-version "0.21" "HEAD" %git-commit))
     (source (local-file %source-dir #:recursive? #t))
     (build-system cmake-build-system)
+    (arguments
+     `(#:configure-flags
+         ,#~(list "-DBUILD_STATIC=1" "-DCMAKE_INSTALL_RPATH=") ; force cmake static build and do not rewrite RPATH
+       #:tests? #f)) ; disable tests until I fix finding the binary wfmash
     (inputs
      `(
-       ;; ("clang" ,clang)      ; add this to test clang builds
-       ;; ("lld" ,lld)          ; add this to test clang builds
+       ("bzip2-static" ,bzip2 "static")    ; libz2 part of htslib for static builds
+       ("coreutils" ,coreutils) ; for echo and env in tests
        ("gcc" ,gcc-12)
-       ("gsl-static" ,gsl-static)
+       ("git" ,git)
        ("gmp" ,gmp)
+       ("gsl-static" ,gsl "static")
+       ("gsl" ,gsl)
+       ("htslib-static" ,htslib-static)
+       ("jemalloc" ,jemalloc)
+       ("libdeflate-static" ,libdeflate-static)
        ("make" ,gnu-make)
        ("pkg-config" ,pkg-config)
-       ("jemalloc" ,jemalloc)
-       ("htslib" ,htslib-static)
-       ("git" ,git)
-       ; ("bc" ,bc)               ; for tests
-       ("coreutils" ,coreutils) ; for echo and env in tests
-       ; ("curl" ,curl)
-       ; ("parallel" ,parallel) ; for wfmash-parallel
-       ("bzip2-static" ,bzip2 "static")    ; libz2 part of htslib for static builds
        ("xz-static" ,xz "static")     ; for static builds
        ("zlib-static" ,zlib "static")))
      (synopsis "wfmash")
      (description
-      "wfmash.")
+      "wfmash is an aligner for pangenomes that combines efficient homology
+mapping with base-level alignment. It uses MashMap to find approximate
+mappings between sequences, then applies WFA (Wave Front Alignment) to
+obtain base-level alignments.")
      (home-page "https://github.com/waveygang/wfmash")
      (license license:expat)))
 
-wfmash-git
+wfmash-git

guix.scm

@@ -12,7 +12,7 @@
 ;;   mkdir build
 ;;   cd build
 ;;   cmake ..
-;;   make
+;;   make -j 12
 ;;
 ;; For the tests you may need /usr/bin/env. Inside the container:
 ;;
@@ -22,18 +22,16 @@
 
 (use-modules
  ((guix licenses) #:prefix license:)
+ (guix build-system cmake)
  (guix gexp)
- (guix packages)
  (guix git-download)
- (guix build-system cmake)
-                                        ; (guix gexp)
+ (guix packages)
  (guix utils)
  (gnu packages algebra)
  (gnu packages base)
  (gnu packages bioinformatics)
  (gnu packages build-tools)
  (gnu packages compression)
-                                        ; (gnu packages curl)
  (gnu packages gcc)
  (gnu packages jemalloc)
  (gnu packages llvm)
@@ -54,32 +52,31 @@
 (define-public wfmash-git
   (package
     (name "wfmash-git")
-    (version (git-version "0.10.7" "HEAD" %git-commit))
+    (version (git-version "0.21" "HEAD" %git-commit))
     (source (local-file %source-dir #:recursive? #t))
     (build-system cmake-build-system)
+    (arguments
+     `(#:tests? #f)) ; disable tests until I fix finding the binary wfmash
     (inputs
      `(
-       ;; ("clang" ,clang)      ; add this to test clang builds
-       ;; ("lld" ,lld)          ; add this to test clang builds
+       ("bzip2" ,bzip2)
+       ("coreutils" ,coreutils) ; for echo and env in tests
        ("gcc" ,gcc-12)
-       ("gsl" ,gsl)
+       ("git" ,git)
        ("gmp" ,gmp)
+       ("gsl" ,gsl)
+       ("htslib" ,htslib)
+       ("libdeflate" ,libdeflate)
        ("make" ,gnu-make)
        ("pkg-config" ,pkg-config)
-       ("jemalloc" ,jemalloc)
-       ("htslib" ,htslib)
-       ("git" ,git)
-       ; ("bc" ,bc)               ; for tests
-       ("coreutils" ,coreutils) ; for echo and env in tests
-       ; ("curl" ,curl)
-       ; ("parallel" ,parallel) ; for wfmash-parallel
-       ("bzip2" ,bzip2)
        ("xz" ,xz)
-       ("zlib" ,zlib)
-       ("libdeflate" ,libdeflate)))
+       ("zlib" ,zlib)))
      (synopsis "wfmash")
      (description
-      "wfmash.")
+      "wfmash is an aligner for pangenomes that combines efficient homology
+mapping with base-level alignment. It uses MashMap to find approximate
+mappings between sequences, then applies WFA (Wave Front Alignment) to
+obtain base-level alignments.")
      (home-page "https://github.com/waveygang/wfmash")
      (license license:expat)))