progress on #224 Transrate

224_Transrate/Transrate-1.0.3-GCC-12.3.0.eb

@@ -21,6 +21,8 @@ builddependencies = [
 dependencies = [
     ('Ruby', '3.3.0'),
     ('crb-blast', '0.6.9'),
+    ('colorize', '0.7.7'),
+    ('yell', '2.2.2'),
 ]
 
 preinstallopts = """sed -i "s/'yell', '~> 2.0',/'yell',/g" transrate.gemspec && """

224_Transrate/Transrate-1.0.3-GCC-12.3.0.eb.Components

@@ -0,0 +1,75 @@
+easyblock = 'Bundle'
+
+name = 'Transrate'
+version = '1.0.3'
+
+homepage = 'https://hibberdlab.com/transrate'
+description = """Transrate is software for de-novo transcriptome assembly quality analysis.
+ It examines your assembly in detail and compares it to experimental evidence such as the sequencing reads,
+ reporting quality scores for contigs and assemblies. This allows you to choose between assemblers and parameters,
+ filter out the bad contigs from an assembly, and help decide when to stop trying to improve the assembly."""
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+dependencies = [
+    ('Ruby', '3.3.0'),
+]
+
+default_easyblock = 'RubyGem'
+
+default_component_specs = {
+    'source_urls': ['https://rubygems.org/downloads/'],
+    'sources': ['%(name)s-%(version)s.gem'],
+}
+
+components = [
+    ('colorize', '0.7.7', {
+        'checksums': ['d6ab95a5fcdea3c36c3327d38c1e79e2950ee1788506d8489ae35db330937a99'],
+    }),
+    ('facade', '1.2.1', {
+        'checksums': ['0764de5519088227675a2a67da23322500c3c507b89486d91296e031d87d036e'],
+    }),
+    ('pathname2', '1.8.4', {
+        'checksums': ['1711264f3f7c1b380f96e1f0383b135d9703488f7b1acf66346a176efc257b7a'],
+    }),
+    ('fixwhich', '1.0.2', {
+        'checksums': ['c6a8f796a7eb60ffbc29f0d2af85461761a36c2864d25e445ff18bfbd1657078'],
+    }),
+    ('bindeps', '1.2.1', {
+        'checksums': ['3c11d75aa722bed67246852bb430a182361a128910d384b664b91f3e65bc34b5'],
+    }),
+    ('yell', '2.2.2', {
+        'checksums': ['1d166f3cc3b6dc49a59778ea7156ed6d8de794c15106d48ffd6cbb061b9b26bc'],
+    }),
+    ('bio', '1.6.0.pre.20181210', {
+        'checksums': ['c4114aeb99b012f90660b92ead4ca88c1578fd58252ed3ec46eb45dc4a2c6cc9'],
+    }),
+    ('threach', '0.2.0', {
+        'checksums': ['432cbf3569bf9b09e26f93d0959fd6fb911c71e790e8a4cc4d1110e139a2ffca'],
+    }),
+    ('trollop', '2.9.10', {
+        'checksums': ['ceca2d91f349163d6ee3e792d356d4ded7472e6da31ac6dcc5956d1b03607bf7'],
+    }),
+    ('crb-blast', '0.6.9', {
+        'checksums': ['69c346e7d83efe9b9a383a39b57e7cce186a82b7074f275b14906f8f05678e3e'],
+    }),
+    ('%(namelower)', version, {
+        'preinstallopts': """sed -i "s/'yell', '~> 2.0',/'yell',/g" transrate.gemspec && """,
+        'checksums': ['2ccb101cfab5a33586ea9e62af2b2f14caf6bc016724d1fef796b427e39fe100'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/%(namelower)s'],
+    'dirs': ['gems/%(namelower)s-%(version)s'],
+}
+
+sanity_check_commands = ["%(namelower)s --help"]
+
+modextrapaths = {'GEM_PATH': ['']}
+
+moduleclass = 'bio'

224_Transrate/colorize-0.7.7-GCC-12.3.0.eb

@@ -0,0 +1,31 @@
+easyblock = 'RubyGem'
+
+name = 'colorize'
+version = '0.7.7'
+
+homepage = 'https://github.com/fazibear/colorize'
+description = """Ruby gem for colorizing text using ANSI escape sequences.
+Extends String class or add a ColorizedString with methods to set the text color, background color and text effects."""
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+
+source_urls = ['https://rubygems.org/downloads/']
+sources = ['%(name)s-%(version)s.gem']
+checksums = ['d6ab95a5fcdea3c36c3327d38c1e79e2950ee1788506d8489ae35db330937a99']
+
+gem_file = '%(name)s-%(version)s.gem'
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+dependencies = [
+    ('Ruby', '3.3.0'),
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['gems/%(namelower)s-%(version)s'],
+}
+
+moduleclass = 'lib'

224_Transrate/crb-blast-0.6.9-GCC-12.3.0.eb

@@ -24,9 +24,6 @@ exts_default_options = {
 exts_defaultclass = 'RubyGem'
 
 exts_list = [
-    ('colorize', '0.7.7', {  # extra
-        'checksums': ['d6ab95a5fcdea3c36c3327d38c1e79e2950ee1788506d8489ae35db330937a99'],
-    }),
     ('facade', '1.2.1', {
         'checksums': ['0764de5519088227675a2a67da23322500c3c507b89486d91296e031d87d036e'],
     }),
@@ -36,15 +33,9 @@ exts_list = [
     ('fixwhich', '1.0.2', {
         'checksums': ['c6a8f796a7eb60ffbc29f0d2af85461761a36c2864d25e445ff18bfbd1657078'],
     }),
-    ('bindeps', '1.2.1', {  # extra
+    ('bindeps', '1.2.1', {
         'checksums': ['3c11d75aa722bed67246852bb430a182361a128910d384b664b91f3e65bc34b5'],
     }),
-    ('yell', '2.2.2', {  # extra
-        'checksums': ['1d166f3cc3b6dc49a59778ea7156ed6d8de794c15106d48ffd6cbb061b9b26bc'],
-    }),
-    # ('yell', '2.0.7', {  # extra  # TODO latest required version possible
-    #     'checksums': ['2b6ed2f855cdab139d70b6b6dc58e34155c80e150d4a5f0da2d97e3d060d78d4'],
-    # }),
     ('bio', '1.6.0.pre.20181210', {
         'checksums': ['c4114aeb99b012f90660b92ead4ca88c1578fd58252ed3ec46eb45dc4a2c6cc9'],
     }),

224_Transrate/rubygem.py

@@ -65,58 +65,52 @@ def run(self):
 
         self.ext_src = self.src
         self.log.debug("Installing Ruby gem %s version %s." % (self.name, self.version))
-        self.extract_step()
-        self.configure_step()
         self.install_step()
 
     def extract_step(self):
         """Skip extraction of .gem files, which are installed as downloaded"""
-        if not self.is_extension:
-            if len(self.src) > 1:
-                raise EasyBuildError(f"Don't know how to handle Ruby gems with multiple sources. {str(self.src)} len {type(self.src)}")
+        if len(self.src) > 1:
+            raise EasyBuildError("Don't know how to handle Ruby gems with multiple sources.")
+        else:
+            src = self.src[0]
+            if src['path'].endswith('.gem'):
+                copy_file(src['path'], self.builddir)
+                self.ext_src = src['name']
+                # set final path since it can't be determined from unpacked sources (used for guessing start_dir)
+                src['finalpath'] = self.builddir
             else:
-                src = self.src[0]
-                if src['path'].endswith('.gem'):
-                    copy_file(src['path'], self.builddir)
-                    self.ext_src = src['name']
-                    # set final path since it can't be determined from unpacked sources (used for guessing start_dir)
-                    src['finalpath'] = self.builddir
-                else:
-                    # unpack zipped gems, use specified path to gem file
-                    super(RubyGem, self).extract_step()
+                # unpack zipped gems, use specified path to gem file
+                super(RubyGem, self).extract_step()
 
     def configure_step(self):
         """No separate configuration for Ruby Gems."""
         pass
 
     def build_step(self):
-        if not self.is_extension:
-            src = self.src[0]
-            if src['path'].endswith('.gem'):
-                pass
-            if self.cfg['gem_file']:
-                self.ext_src = os.path.join(src['finalpath'], self.cfg['gem_file'])
-                if not os.path.exists(self.ext_src):
-                    raise EasyBuildError("Gem file not found at %s", self.ext_src)
+        src = self.src[0]
+        if self.cfg['gem_file']:
+            self.ext_src = os.path.join(src['finalpath'], self.cfg['gem_file'])
+            if not os.path.exists(self.ext_src):
+                raise EasyBuildError("Gem file not found at %s", self.ext_src)
+        else:
+            gemfile = "%s.gem" % self.name
+            gemfile_lower = "%s.gem" % self.name.lower()
+            if os.path.exists(gemfile):
+                self.ext_src = os.path.join(src['finalpath'], gemfile)
+            elif os.path.exists(gemfile_lower):
+                self.ext_src = os.path.join(src['finalpath'], gemfile_lower)
             else:
-                gemfile = "%s.gem" % self.name
-                gemfile_lower = "%s.gem" % self.name.lower()
-                if os.path.exists(gemfile):
-                    self.ext_src = os.path.join(src['finalpath'], gemfile)
-                elif os.path.exists(gemfile_lower):
-                    self.ext_src = os.path.join(src['finalpath'], gemfile_lower)
+                gemspec = "%s.gemspec" % self.name
+                gemspec_lower = "%s.gemspec" % self.name.lower()
+                if os.path.exists(gemspec):
+                    run_cmd("gem build %s -o %s.gem" % (gemspec, self.name))
+                    self.ext_src = "%s.gem" % self.name
+                elif os.path.exists(gemspec_lower):
+                    run_cmd("gem build %s -o %s.gem" % (gemspec_lower, self.name.lower()))
+                    self.ext_src = "%s.gem" % self.name.lower()
                 else:
-                    gemspec = "%s.gemspec" % self.name
-                    gemspec_lower = "%s.gemspec" % self.name.lower()
-                    if os.path.exists(gemspec):
-                        run_cmd("gem build %s -o %s.gem" % (gemspec, self.name))
-                        self.ext_src = "%s.gem" % self.name
-                    elif os.path.exists(gemspec_lower):
-                        run_cmd("gem build %s -o %s.gem" % (gemspec_lower, self.name.lower()))
-                        self.ext_src = "%s.gem" % self.name.lower()
-                    else:
-                        raise EasyBuildError("No gem_file specified and no"
-                            " %s.gemspec or %s.gemspec found." % (self.name, self.name.lower()))
+                    raise EasyBuildError("No gem_file specified and no"
+                                         " %s.gemspec or %s.gemspec found." % (self.name, self.name.lower()))
 
     def test_step(self):
         """No separate (standard) test procedure for Ruby Gems."""

224_Transrate/yell-2.2.2-GCC-12.3.0.eb

@@ -0,0 +1,30 @@
+easyblock = 'RubyGem'
+
+name = 'yell'
+version = '2.2.2'
+
+homepage = 'https://github.com/rudionrails/yell'
+description = """Yell - Your Extensible Logging Library is a comprehensive logging replacement for Ruby."""
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+
+source_urls = ['https://rubygems.org/downloads/']
+sources = ['%(name)s-%(version)s.gem']
+checksums = ['1d166f3cc3b6dc49a59778ea7156ed6d8de794c15106d48ffd6cbb061b9b26bc']
+
+gem_file = '%(name)s-%(version)s.gem'
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+dependencies = [
+    ('Ruby', '3.3.0'),
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['gems/%(namelower)s-%(version)s'],
+}
+
+moduleclass = 'lib'