salmon: add v1.4.0 (#22201)

devendored (most) dependencies, added missing dependencies.
added resources and bypassed external fetching.

var/spack/repos/builtin/packages/libdivsufsort/package.py

@@ -14,3 +14,7 @@ class Libdivsufsort(CMakePackage):
     url      = "https://github.com/y-256/libdivsufsort/archive/2.0.1.tar.gz"
 
     version('2.0.1', sha256='9164cb6044dcb6e430555721e3318d5a8f38871c2da9fd9256665746a69351e0')
+
+    def cmake_args(self):
+        args = ['-DBUILD_DIVSUFSORT64=ON']
+        return args

var/spack/repos/builtin/packages/salmon/package.py

@@ -3,8 +3,6 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-from spack import *
-
 
 class Salmon(CMakePackage):
     """Salmon is a tool for quantifying the expression of transcripts using
@@ -13,22 +11,75 @@ class Salmon(CMakePackage):
     homepage = "http://combine-lab.github.io/salmon/"
     url      = "https://github.com/COMBINE-lab/salmon/archive/v0.8.2.tar.gz"
 
+    version('1.4.0', sha256='6d3e25387450710f0aa779a1e9aaa9b4dec842324ff8551d66962d7c7606e71d')
     version('0.14.1', sha256='05289170e69b5f291a8403b40d6b9bff54cc38825e9f721c210192b51a19273e')
     version('0.12.0', sha256='91ebd1efc5b0b4c12ec6babecf3c0b79f7102e42b8895ca07c8c8fea869fefa3')
     version('0.9.1', sha256='3a32c28d217f8f0af411c77c04144b1fa4e6fd3c2f676661cc875123e4f53520')
     version('0.8.2', sha256='299168e873e71e9b07d63a84ae0b0c41b0876d1ad1d434b326a5be2dce7c4b91')
 
-    depends_on('tbb')
-    depends_on('boost@:1.66.0')
+    variant('build_type', default='RELEASE',
+            description='CMake build type',
+            values=('DEBUG', 'RELEASE'))
 
+    depends_on('tbb')
+    depends_on('boost@:1.66.0', when='@:0.14.1')
+    depends_on('boost@1.72.0', when='@1.4.0')
+    depends_on('cereal')
+    depends_on('jemalloc')
+    depends_on('xz')
+    depends_on('zlib')
+    depends_on('bzip2')
+    depends_on('libdivsufsort')
+    depends_on('staden-io-lib~curl')
+    depends_on('libgff')
+    depends_on('pkgconfig')
     depends_on('curl', when='@0.14.1:')
 
     conflicts('%gcc@:5.1', when='@0.14.1:')
 
+    resources = [
+        ('1.4.0', 'pufferfish', '059207e8d3134060ed70595e53f4189954c9e5edfaa6361b46304f55d1b71bc7'),
+        ('0.14.1', 'RapMap', 'fabac2f360513b803aa3567415eddcd97261ab8a23d4f600af5f98ee8ffd944b'),
+        ('0.12.0', 'RapMap', '05102c0bbc8a0c0056a01cd0e8788fa5b504aee58ac226ab8c0e3ffec8019790'),
+        ('0.9.1', 'RapMap', '8975e5a1ed61ed9354ba776272927545f417ecdce95823e71ba1e7b61de7d380'),
+        ('0.8.2', 'RapMap', '1691f4bca2b604f05f36772ae45faf0842ab4809843df770bd10366a5cfd6822'),
+    ]
+
+    for ver, repo, checksum in resources:
+        resource(name='rapmap',
+                 url='https://github.com/COMBINE-lab/{0}/archive/salmon-v{1}.zip'.format(repo, ver),
+                 sha256=checksum,
+                 placement='external',
+                 expand=False,
+                 when='@{0}'.format(ver))
+
     def patch(self):
         # remove static linking to libstdc++
         filter_file('-static-libstdc++', '', 'CMakeLists.txt', string=True)
+        if self.spec.satisfies('@0.8.2:0.9.1'):
+            filter_file('${FAST_MALLOC_LIB}',
+                        '${FAST_MALLOC_LIB}\n'
+                        '${CMAKE_DL_LIBS}',
+                        'src/CMakeLists.txt',
+                        string=True)
+
+        if self.spec.satisfies('@:0.14.1'):
+            filter_file('curl -k.*',
+                        '',
+                        'scripts/fetchRapMap.sh')
+            symlink('./salmon-v{0}.zip'.format(self.version),
+                    './external/rapmap.zip')
+
+        if self.spec.satisfies('@1.4.0:'):
+            filter_file('curl -k.*',
+                        '',
+                        'scripts/fetchPufferfish.sh')
+            symlink('./salmon-v{0}.zip'.format(self.version),
+                    './external/pufferfish.zip')
 
     def cmake_args(self):
-        args = ['-DBOOST_ROOT=%s' % self.spec['boost'].prefix]
+        args = [
+            '-DBOOST_ROOT=%s' % self.spec['boost'].prefix,
+        ]
+
         return args

var/spack/repos/builtin/packages/staden-io-lib/package.py

@@ -15,4 +15,15 @@ class StadenIoLib(AutotoolsPackage):
 
     version('1.14.8', sha256='3bd560309fd6d70b14bbb8230e1baf8706b804eb6201220bb6c3d6db72003d1b')
 
+    variant('curl', default=False, description='Build with curl support')
+
     depends_on('zlib')
+    depends_on('curl', when='+curl')
+
+    def configure_args(self):
+        args = []
+
+        if self.spec.satisfies('~curl'):
+            args.append('--without-libcurl')
+
+        return args