{bio}[intel/2017a] dammit 0.3.2 /w Python 2.7.13 (REVIEW)

easybuild/easyconfigs/d/dammit/dammit-0.3.2-intel-2017a-Python-2.7.13.eb

@@ -0,0 +1,90 @@
+easyblock = 'Bundle'
+
+name = 'dammit'
+version = '0.3.2'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'http://www.camillescott.org/dammit/'
+description = """dammit is a simple de novo transcriptome annotator. It was born out of
+ the observations that annotation is mundane and annoying,
+ all the individual pieces of the process exist already, and the existing
+ solutions are overly complicated or rely on crappy non-free software."""
+
+toolchain = {'name': 'intel', 'version': '2017a'}
+
+# this is a bundle of Python packages
+exts_defaultclass = 'PythonPackage'
+
+dependencies = [
+    ('Python', '2.7.13'),
+    ('X11', '20170314'),
+    ('matplotlib', '2.0.2', '-Python-%(pyver)s-Qt-4.8.7'),
+    ('EMBOSS', '6.6.0', '-X11-20170314'),
+    ('HMMER', '3.1b2'),
+    ('Infernal', '1.1.2'),
+    ('BUSCO', '1.22', '-Python-%(pyver)s'),  # Exact version needed
+    ('LAST', '869'),
+    ('TransDecoder', '2.1.0', '-Perl-5.24.1'),
+    ('khmer', '2.1.1', '-Python-%(pyver)s'),
+    ('crb-blast', '0.6.9'),
+]
+
+exts_list = [
+    ('cloudpickle', '0.4.0', {
+        'source_urls': ['https://pypi.python.org/packages/source/c/cloudpickle'],
+        'checksums': ['5bb83eb466f0733dbd077e76cf1a15c404a94eb063cecc7049a1482fa1b11661'],
+    }),
+    ('pyinotify', '0.9.6', {
+        'source_urls': ['https://pypi.python.org/packages/source/p/pyinotify'],
+        'checksums': ['9c998a5d7606ca835065cdabc013ae6c66eb9ea76a00a1e3bc6e0cfe2b4f71f4'],
+    }),
+    ('configparser', '3.5.0', {
+        'source_urls': ['https://pypi.python.org/packages/source/c/configparser'],
+        'checksums': ['5308b47021bc2340965c371f0f058cc6971a04502638d4244225c49d80db273a'],
+    }),
+    ('doit', '0.29.0', {
+        'source_urls': ['https://pypi.python.org/packages/source/d/doit'],
+        'checksums': ['fcb479482644de3e83d6faed9b29373f1f38942b79b991a7432943a84416d5cd'],
+    }),
+    ('nose', '1.3.4', {
+        'source_urls': ['https://pypi.python.org/packages/source/n/nose'],
+        'checksums': ['76bc63a4e2d5e5a0df77ca7d18f0f56e2c46cfb62b71103ba92a92c79fab1e03'],
+    }),
+    ('nose-capturestderr', '1.0', {
+        'modulename': 'nose_capturestderr',
+        'source_urls': ['https://pypi.python.org/packages/source/n/nose-capturestderr'],
+        'checksums': ['8a05620bec5acaf006acfe59ad1225673350bba359e1b946ddba53206a3f8c98'],
+    }),
+    ('ficus', '0.3.3', {
+        'source_urls': ['https://pypi.python.org/packages/source/f/ficus'],
+        'checksums': ['7dbd69a4aceb0406e53cf8ede98c039a03110b7b8860b64356554caf537b9324'],
+    }),
+    ('numexpr', '2.6.2', {
+        'source_urls': ['https://pypi.python.org/packages/source/n/numexpr'],
+        'checksums': ['6ab8ff5c19e7f452966bf5a3220b845cf3244fe0b96544f7f9acedcc2db5c705'],
+    }),
+    (name, version, {
+        'patches': [
+            'dammit-0.3.2_nodocs.patch',
+            'dammit-0.3.2_py2busco.patch',
+        ],
+        'source_urls': ['https://pypi.python.org/packages/source/d/dammit'],
+        'checksums': [
+            '400bb9c6644c4edd5f7b8bf294c142e89baa148008b3aba39d2c5e89f99ff278',  # dammit-0.3.2.tar.gz
+            '79dc4da8a778d842f7614e287add044cc0a7138d5a43ec80b378ac715054ae3b',  # dammit-0.3.2_nodocs.patch
+            '44f867adbd2f2117c36695b4e8eb5c79d57fb8df7b5b9a5257a828ff977eaf6f',  # dammit-0.3.2_py2busco.diff
+        ],
+    }),
+]
+
+# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module
+full_sanity_check = True
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']}
+
+moduleclass = 'bio'

easybuild/easyconfigs/d/dammit/dammit-0.3.2_nodocs.patch

@@ -0,0 +1,24 @@
+# Do not install sphynx, as documantation is not made (not even the source bundled)
+# October 11th, 2017 by B. Hajgato (Free University Brussel - VUB) 
+--- dammit-0.3.2/setup.py.orig	2016-11-23 05:49:45.000000000 +0100
++++ dammit-0.3.2/setup.py	2017-10-11 22:28:09.104110519 +0200
+@@ -37,8 +37,6 @@
+                                 'pandas>=0.18.1',
+                                 'khmer>=2.0',
+                                 'doit==0.29.0',
+-                                'Sphinx>1.3.1',
+-                                'sphinx-rtd-theme>=0.1.9',
+                                 'nose==1.3.4',
+                                 'nose-capturestderr==1.0',
+                                 'ficus>=0.1',
+--- dammit-0.3.2/dammit.egg-info/requires.txt.orig	2016-11-23 05:51:53.000000000 +0100
++++ dammit-0.3.2/dammit.egg-info/requires.txt	2017-10-11 22:26:59.426080680 +0200
+@@ -2,8 +2,6 @@
+ pandas>=0.18.1
+ khmer>=2.0
+ doit==0.29.0
+-Sphinx>1.3.1
+-sphinx-rtd-theme>=0.1.9
+ nose==1.3.4
+ nose-capturestderr==1.0
+ ficus>=0.1

easybuild/easyconfigs/d/dammit/dammit-0.3.2_py2busco.patch

@@ -0,0 +1,13 @@
+# Use BUSCO with default Python instead of Python3
+# October 27th 2017 by B. Hajgato (Free Ubiveristy Brussel - VUB)
+--- dammit-0.3.2/dammit/tasks.py.orig	2016-11-23 05:04:29.000000000 +0100
++++ dammit-0.3.2/dammit/tasks.py	2017-10-27 13:47:22.687134646 +0200
+@@ -376,7 +376,7 @@
+     # BUSCO chokes on file paths as output names
+     output_name = os.path.basename(output_name)
+
+-    cmd = 'python3 {exc} -in {input_filename} -f -o {output_name} -l {busco_db_dir} '\
++    cmd = 'python {exc} -in {input_filename} -f -o {output_name} -l {busco_db_dir} '\
+             '-m {input_type} -c {n_threads}'.format(**locals())
+
+     return {'name': name,

easybuild/easyconfigs/l/LAST/LAST-869-intel-2017a.eb

@@ -0,0 +1,26 @@
+easyblock = 'ConfigureMake'
+
+name = 'LAST'
+version = '869'
+
+homepage = 'http://last.cbrc.jp/'
+description = "LAST finds similar regions between sequences."
+
+toolchain = {'name': 'intel', 'version': '2017a'}
+toolchainopts = {'cstd': 'c++11'}
+
+source_urls = ['http://last.cbrc.jp/']
+sources = ['last-%(version)s.zip']
+checksums = ['6371a6282bc1bb02a5e5013cc463625f2ce3e7746ff2ea0bdf9fe6b15605a67c']
+
+skipsteps = ['configure']
+
+buildopts = 'CC="$CC" CXX="$CXX" CFLAGS="$CFLAGS" CXXFLAGS="$CXXFLAGS -pthread -DHAS_CXX_THREADS"'
+installopts = 'prefix=%(installdir)s'
+
+sanity_check_paths = {
+    'files': ['bin/lastal', 'bin/lastdb'],
+    'dirs': [],
+}
+
+moduleclass = 'bio'

easybuild/easyconfigs/t/TransDecoder/TransDecoder-2.1.0-intel-2017a-Perl-5.24.1.eb

@@ -0,0 +1,29 @@
+easyblock = "PackedBinary"
+
+name = "TransDecoder"
+version = '2.1.0'
+versionsuffix = '-Perl-%(perlver)s'
+
+homepage = 'https://github.com/TransDecoder/TransDecoder/wiki'
+description = """TransDecoder identifies candidate coding regions within transcript sequences,
+ such as those generated by de novo RNA-Seq transcript assembly using Trinity,
+ or constructed based on RNA-Seq alignments to the genome using
+ Tophat and Cufflinks."""
+
+toolchain = {'name': 'intel', 'version': '2017a'}
+
+source_urls = ['https://github.com/TransDecoder/TransDecoder/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['681a8dd72e482cb322d74d8431ddcda61f25c53ad5453d0e22c02c92b2157b24']
+
+dependencies = [
+    ('Perl', '5.24.1'),
+    ('CD-HIT', '4.6.8'),
+]
+
+sanity_check_paths = {
+    'files': ['TransDecoder.LongOrfs', 'TransDecoder.Predict'],
+    'dirs': ['PerlLib', 'sample_data', 'util'],
+}
+
+moduleclass = 'bio'