diff --git a/easybuild/easyconfigs/d/dammit/dammit-0.3.2-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/d/dammit/dammit-0.3.2-intel-2017a-Python-2.7.13.eb new file mode 100644 index 000000000000..13200b3bb164 --- /dev/null +++ b/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' diff --git a/easybuild/easyconfigs/d/dammit/dammit-0.3.2_nodocs.patch b/easybuild/easyconfigs/d/dammit/dammit-0.3.2_nodocs.patch new file mode 100644 index 000000000000..eb2ab6a2426d --- /dev/null +++ b/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 diff --git a/easybuild/easyconfigs/d/dammit/dammit-0.3.2_py2busco.patch b/easybuild/easyconfigs/d/dammit/dammit-0.3.2_py2busco.patch new file mode 100644 index 000000000000..18c0bc5c7f73 --- /dev/null +++ b/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, diff --git a/easybuild/easyconfigs/l/LAST/LAST-869-intel-2017a.eb b/easybuild/easyconfigs/l/LAST/LAST-869-intel-2017a.eb new file mode 100644 index 000000000000..f16714bf12e5 --- /dev/null +++ b/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' diff --git a/easybuild/easyconfigs/t/TransDecoder/TransDecoder-2.1.0-intel-2017a-Perl-5.24.1.eb b/easybuild/easyconfigs/t/TransDecoder/TransDecoder-2.1.0-intel-2017a-Perl-5.24.1.eb new file mode 100644 index 000000000000..e4d2fdc6f094 --- /dev/null +++ b/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'