From 9feb68eb0ef4c4582ba4e639416d66ea05d71af8 Mon Sep 17 00:00:00 2001
From: Balazs Hajgato <hajgato@vub.ac.be>
Date: Fri, 15 Sep 2017 09:58:44 +0200
Subject: [PATCH 01/13] {bio}[intel/2017a] dammit 0.3.2 /w Python 2.7.13
 (REVIEW)

---
 .../dammit-0.3.2-intel-2017a-Python-2.7.13.eb | 82 +++++++++++++++++++
 .../l/LAST/LAST-869-GCCcore-6.3.0.eb          | 42 ++++++++++
 .../l/LAST/LAST-869_makefile.patch            | 10 +++
 ...nsDecoder-2.1.0-intel-2017a-Perl-5.24.1.eb | 30 +++++++
 4 files changed, 164 insertions(+)
 create mode 100644 easybuild/easyconfigs/d/dammit/dammit-0.3.2-intel-2017a-Python-2.7.13.eb
 create mode 100644 easybuild/easyconfigs/l/LAST/LAST-869-GCCcore-6.3.0.eb
 create mode 100644 easybuild/easyconfigs/l/LAST/LAST-869_makefile.patch
 create mode 100644 easybuild/easyconfigs/t/TransDecoder/TransDecoder-2.1.0-intel-2017a-Perl-5.24.1.eb

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..3b03e53025c6
--- /dev/null
+++ b/easybuild/easyconfigs/d/dammit/dammit-0.3.2-intel-2017a-Python-2.7.13.eb
@@ -0,0 +1,82 @@
+easyblock = 'Bundle'
+
+name = 'dammit'
+version = '0.3.2'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'http://matplotlib.org'
+description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of
+ hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python
+ and ipython shell, web application servers, and six graphical user interface toolkits."""
+
+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', '-Ruby-2.3.4') 
+]
+
+
+exts_list = [
+    ('cloudpickle', '0.4.0', {
+        'source_urls': ['https://pypi.python.org/packages/source/c/cloudpickle'],
+        'checksums': ['5bb83eb466f0733dbd077e76cf1a15c404a94eb063cecc7049a1482fa1b11661'],
+
+    }),
+    ('pynotify', '0.1.1', {
+        'source_urls': ['https://pypi.python.org/packages/source/p/pynotify'],
+        'checksums': ['f14c485bd1bd861666e6fae94ef58b65b83b430a1617e226a6cef2120a911503'],
+    }),
+    # Exact version needed:
+    ('doit', '0.29.0', {
+        'source_urls': ['https://pypi.python.org/packages/source/d/doit'],
+        'checksums': ['fcb479482644de3e83d6faed9b29373f1f38942b79b991a7432943a84416d5cd'],
+    }),
+    # Exact version needed:
+    ('nose', '1.3.4', {
+        'source_urls': ['https://pypi.python.org/packages/source/n/nose'],
+        'checksums': ['76bc63a4e2d5e5a0df77ca7d18f0f56e2c46cfb62b71103ba92a92c79fab1e03'],
+    }),
+    # Exact version needed:
+    ('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, {
+        'source_urls': ['https://pypi.python.org/packages/source/d/dammit'],
+        'checksums': ['400bb9c6644c4edd5f7b8bf294c142e89baa148008b3aba39d2c5e89f99ff278'],
+    }),
+]
+
+# 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/l/LAST/LAST-869-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/LAST/LAST-869-GCCcore-6.3.0.eb
new file mode 100644
index 000000000000..13dd6d8343e5
--- /dev/null
+++ b/easybuild/easyconfigs/l/LAST/LAST-869-GCCcore-6.3.0.eb
@@ -0,0 +1,42 @@
+easyblock = 'MakeCp'
+
+name = 'LAST'
+version = '869'
+
+homepage = 'http://last.cbrc.jp/'
+description = """ LAST finds similar regions between sequences. The main technical innovation
+ is that LAST finds initial matches based on their multiplicity,
+ instead of using a fixed length (e.g. BLAST uses 11-mers)."""
+
+toolchain = {'name': 'GCCcore', 'version': '6.3.0'}
+toolchainopts = {'cstd': 'c++11', 'opt': True}
+
+source_urls = ['http://last.cbrc.jp/']
+sources = ['%(namelower)s-%(version)s.zip']
+
+patches = ['%(name)s-%(version)s_makefile.patch']
+
+checksums = ['6371a6282bc1bb02a5e5013cc463625f2ce3e7746ff2ea0bdf9fe6b15605a67c']
+
+list_of_executables = [
+    'fastq-interleave', 'last-dotplot', 'last-map-probs', 'last-postmask', 'last-train', 'maf-convert', 'maf-join',
+    'maf-sort', 'maf-swap', 'parallel-fasta', 'parallel-fastq',
+]
+
+files_to_copy = [
+    (['scripts/%s' % x for x in list_of_executables], "bin"),
+    'ChangeLog.txt',
+    'COPYING.txt',
+    'data',
+    'doc',
+    'examples',
+    'README.txt',
+    'src',
+]
+
+sanity_check_paths = {
+    'files': ["bin/%s" % x for x in list_of_executables],
+    'dirs': ['data', 'doc', 'examples', 'src'],
+}
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/l/LAST/LAST-869_makefile.patch b/easybuild/easyconfigs/l/LAST/LAST-869_makefile.patch
new file mode 100644
index 000000000000..02a3ccfa2ea0
--- /dev/null
+++ b/easybuild/easyconfigs/l/LAST/LAST-869_makefile.patch
@@ -0,0 +1,10 @@
+# Pick up EB CXXFLAGS
+# September 11th 2017 by B. Hajgato (Free Univeristy Brussels - VUB)
+--- last-869/makefile.orig	2016-12-13 07:22:11.000000000 +0100
++++ last-869/makefile	2017-09-11 14:14:17.989174000 +0200
+@@ -1,4 +1,4 @@
+-CXXFLAGS = -O3 -std=c++11 -pthread -DHAS_CXX_THREADS
++CXXFLAGS += -pthread -DHAS_CXX_THREADS
+ all:
+ 	@cd src && $(MAKE) CXXFLAGS="$(CXXFLAGS)"
+ 
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..bfecffdad2fc
--- /dev/null
+++ b/easybuild/easyconfigs/t/TransDecoder/TransDecoder-2.1.0-intel-2017a-Perl-5.24.1.eb
@@ -0,0 +1,30 @@
+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.%s' % x for x in ['Predict', 'LongOrfs']],
+    'dirs': ['PerlLib', 'sample_data', 'util'],
+}
+
+moduleclass = 'bio'

From 50873d6a9029a48fae4a06df9ae890b928dc839a Mon Sep 17 00:00:00 2001
From: Balazs Hajgato <hajgato@vub.ac.be>
Date: Fri, 15 Sep 2017 11:38:09 +0200
Subject: [PATCH 02/13] Down with PEP8\!

---
 .../d/dammit/dammit-0.3.2-intel-2017a-Python-2.7.13.eb        | 4 ++--
 easybuild/easyconfigs/l/LAST/LAST-869-GCCcore-6.3.0.eb        | 2 ++
 .../TransDecoder-2.1.0-intel-2017a-Perl-5.24.1.eb             | 2 +-
 3 files changed, 5 insertions(+), 3 deletions(-)

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
index 3b03e53025c6..720301d5d5e3 100644
--- 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
@@ -21,11 +21,11 @@ dependencies = [
     ('EMBOSS', '6.6.0', '-X11-20170314'),
     ('HMMER', '3.1b2'),
     ('Infernal', '1.1.2'),
-    ('BUSCO', '1.22', '-Python-%(pyver)s'), # Exact version needed
+    ('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', '-Ruby-2.3.4') 
+    ('crb-blast', '0.6.9', '-Ruby-2.3.4'),
 ]
 
 
diff --git a/easybuild/easyconfigs/l/LAST/LAST-869-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/LAST/LAST-869-GCCcore-6.3.0.eb
index 13dd6d8343e5..4ae647fa8184 100644
--- a/easybuild/easyconfigs/l/LAST/LAST-869-GCCcore-6.3.0.eb
+++ b/easybuild/easyconfigs/l/LAST/LAST-869-GCCcore-6.3.0.eb
@@ -18,6 +18,8 @@ patches = ['%(name)s-%(version)s_makefile.patch']
 
 checksums = ['6371a6282bc1bb02a5e5013cc463625f2ce3e7746ff2ea0bdf9fe6b15605a67c']
 
+builddependencies = [('binutils', '2.28')]
+
 list_of_executables = [
     'fastq-interleave', 'last-dotplot', 'last-map-probs', 'last-postmask', 'last-train', 'maf-convert', 'maf-join',
     'maf-sort', 'maf-swap', 'parallel-fasta', 'parallel-fastq',
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
index bfecffdad2fc..2a7396dd4a76 100644
--- 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
@@ -12,7 +12,7 @@ description = """TransDecoder identifies candidate coding regions within transcr
 
 toolchain = {'name': 'intel', 'version': '2017a'}
 
-source_urls = ['https://github.com/TransDecoder/TransDecoder/archive/'] 
+source_urls = ['https://github.com/TransDecoder/TransDecoder/archive/']
 sources = ['v%(version)s.tar.gz']
 
 checksums = ['681a8dd72e482cb322d74d8431ddcda61f25c53ad5453d0e22c02c92b2157b24']

From f723acfc9a0ecbd5b8aaf8c358415365d9134936 Mon Sep 17 00:00:00 2001
From: Balazs Hajgato <hajgato@vub.ac.be>
Date: Wed, 20 Sep 2017 16:58:24 +0200
Subject: [PATCH 03/13] style nosuffix last /w intel

---
 ...-2.7.13.eb => dammit-0.3.2-intel-2017a.eb} | 10 +++++-----
 ...Ccore-6.3.0.eb => LAST-869-intel-2017a.eb} |  9 ++++++---
 .../l/LAST/LAST-869_makefile.patch            | 19 +++++++++++++++++++
 3 files changed, 30 insertions(+), 8 deletions(-)
 rename easybuild/easyconfigs/d/dammit/{dammit-0.3.2-intel-2017a-Python-2.7.13.eb => dammit-0.3.2-intel-2017a.eb} (88%)
 rename easybuild/easyconfigs/l/LAST/{LAST-869-GCCcore-6.3.0.eb => LAST-869-intel-2017a.eb} (77%)

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.eb
similarity index 88%
rename from easybuild/easyconfigs/d/dammit/dammit-0.3.2-intel-2017a-Python-2.7.13.eb
rename to easybuild/easyconfigs/d/dammit/dammit-0.3.2-intel-2017a.eb
index 720301d5d5e3..a3ba1ef4834a 100644
--- 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.eb
@@ -4,10 +4,11 @@ name = 'dammit'
 version = '0.3.2'
 versionsuffix = '-Python-%(pyver)s'
 
-homepage = 'http://matplotlib.org'
-description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of
- hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python
- and ipython shell, web application servers, and six graphical user interface toolkits."""
+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'}
 
@@ -28,7 +29,6 @@ dependencies = [
     ('crb-blast', '0.6.9', '-Ruby-2.3.4'),
 ]
 
-
 exts_list = [
     ('cloudpickle', '0.4.0', {
         'source_urls': ['https://pypi.python.org/packages/source/c/cloudpickle'],
diff --git a/easybuild/easyconfigs/l/LAST/LAST-869-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/LAST/LAST-869-intel-2017a.eb
similarity index 77%
rename from easybuild/easyconfigs/l/LAST/LAST-869-GCCcore-6.3.0.eb
rename to easybuild/easyconfigs/l/LAST/LAST-869-intel-2017a.eb
index 4ae647fa8184..34394533d959 100644
--- a/easybuild/easyconfigs/l/LAST/LAST-869-GCCcore-6.3.0.eb
+++ b/easybuild/easyconfigs/l/LAST/LAST-869-intel-2017a.eb
@@ -8,7 +8,7 @@ description = """ LAST finds similar regions between sequences. The main technic
  is that LAST finds initial matches based on their multiplicity,
  instead of using a fixed length (e.g. BLAST uses 11-mers)."""
 
-toolchain = {'name': 'GCCcore', 'version': '6.3.0'}
+toolchain = {'name': 'intel', 'version': '2017a'}
 toolchainopts = {'cstd': 'c++11', 'opt': True}
 
 source_urls = ['http://last.cbrc.jp/']
@@ -16,9 +16,12 @@ sources = ['%(namelower)s-%(version)s.zip']
 
 patches = ['%(name)s-%(version)s_makefile.patch']
 
-checksums = ['6371a6282bc1bb02a5e5013cc463625f2ce3e7746ff2ea0bdf9fe6b15605a67c']
+checksums = [
+    '6371a6282bc1bb02a5e5013cc463625f2ce3e7746ff2ea0bdf9fe6b15605a67c',  # last-869.zip
+    'b7b697b048e22c913eb196449eb895fc70b22fb72db5cca1f8dc948cde164309',  # LAST-869_makefile.patch
+]
 
-builddependencies = [('binutils', '2.28')]
+builddependencies = [('binutils', '2.27')]
 
 list_of_executables = [
     'fastq-interleave', 'last-dotplot', 'last-map-probs', 'last-postmask', 'last-train', 'maf-convert', 'maf-join',
diff --git a/easybuild/easyconfigs/l/LAST/LAST-869_makefile.patch b/easybuild/easyconfigs/l/LAST/LAST-869_makefile.patch
index 02a3ccfa2ea0..54976cebe978 100644
--- a/easybuild/easyconfigs/l/LAST/LAST-869_makefile.patch
+++ b/easybuild/easyconfigs/l/LAST/LAST-869_makefile.patch
@@ -8,3 +8,22 @@
  all:
  	@cd src && $(MAKE) CXXFLAGS="$(CXXFLAGS)"
  
+--- last-869/src/makefile.orig	2017-06-02 12:27:21.000000000 +0200
++++ last-869/src/makefile	2017-09-20 16:49:03.731331507 +0200
+@@ -1,12 +1,11 @@
+-CXX = g++
+-CC  = gcc
++CXX ?= g++
++CC  ?= gcc
+ 
+-CXXFLAGS = -O3 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef	\
+--Wcast-align -pedantic -g -std=c++11 -pthread -DHAS_CXX_THREADS
++CXXFLAGS += -pthread -DHAS_CXX_THREADS
+ # -Wconversion
+ # -fomit-frame-pointer ?
+ 
+-CFLAGS = -Wall -O2
++CFLAGS ?= -Wall -O2
+ 
+ alpObj = alp/sls_alignment_evaluer.o alp/sls_pvalues.o		\
+ alp/sls_alp_sim.o alp/sls_alp_regression.o alp/sls_alp_data.o	\

From 876a259fccb7e50403a8e974001c6f88d87a2c5a Mon Sep 17 00:00:00 2001
From: Balazs Hajgato <hajgato@vub.ac.be>
Date: Wed, 20 Sep 2017 17:00:40 +0200
Subject: [PATCH 04/13] python suffix

---
 ...2-intel-2017a.eb => dammit-0.3.2-intel-2017a-Python-2.7.13.eb} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename easybuild/easyconfigs/d/dammit/{dammit-0.3.2-intel-2017a.eb => dammit-0.3.2-intel-2017a-Python-2.7.13.eb} (100%)

diff --git a/easybuild/easyconfigs/d/dammit/dammit-0.3.2-intel-2017a.eb b/easybuild/easyconfigs/d/dammit/dammit-0.3.2-intel-2017a-Python-2.7.13.eb
similarity index 100%
rename from easybuild/easyconfigs/d/dammit/dammit-0.3.2-intel-2017a.eb
rename to easybuild/easyconfigs/d/dammit/dammit-0.3.2-intel-2017a-Python-2.7.13.eb

From 70dbcaedf3fd5525edad4ef90c44455b7abe9c54 Mon Sep 17 00:00:00 2001
From: Balazs Hajgato <hajgato@vub.ac.be>
Date: Wed, 11 Oct 2017 22:48:20 +0200
Subject: [PATCH 05/13] pynotify-> pyinotify, do not install spinx, add
 configparse

---
 .../dammit-0.3.2-intel-2017a-Python-2.7.13.eb | 50 +++++++++++++------
 .../d/dammit/dammit-0.3.2_nodocs.patch        | 24 +++++++++
 2 files changed, 59 insertions(+), 15 deletions(-)
 create mode 100644 easybuild/easyconfigs/d/dammit/dammit-0.3.2_nodocs.patch

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
index a3ba1ef4834a..f0ff1bcffe21 100644
--- 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
@@ -32,40 +32,60 @@ dependencies = [
 exts_list = [
     ('cloudpickle', '0.4.0', {
         'source_urls': ['https://pypi.python.org/packages/source/c/cloudpickle'],
-        'checksums': ['5bb83eb466f0733dbd077e76cf1a15c404a94eb063cecc7049a1482fa1b11661'],
-
+        'checksums': [
+            '5bb83eb466f0733dbd077e76cf1a15c404a94eb063cecc7049a1482fa1b11661',  # cloudpickle-0.4.0.tar.gz
+        ],
+    }),
+    ('pyinotify', '0.9.6', {
+        'source_urls': ['https://pypi.python.org/packages/source/p/pyinotify'],
+        'checksums': [
+            '9c998a5d7606ca835065cdabc013ae6c66eb9ea76a00a1e3bc6e0cfe2b4f71f4',  # pyinotify-0.9.6.tar.gz
+        ],
     }),
-    ('pynotify', '0.1.1', {
-        'source_urls': ['https://pypi.python.org/packages/source/p/pynotify'],
-        'checksums': ['f14c485bd1bd861666e6fae94ef58b65b83b430a1617e226a6cef2120a911503'],
+    ('configparser', '3.5.0', {
+        'source_urls': ['https://pypi.python.org/packages/source/c/configparser'],
+        'checksums': [
+            '5308b47021bc2340965c371f0f058cc6971a04502638d4244225c49d80db273a',  # configparser-3.5.0.tar.gz
+        ],
     }),
-    # Exact version needed:
     ('doit', '0.29.0', {
         'source_urls': ['https://pypi.python.org/packages/source/d/doit'],
-        'checksums': ['fcb479482644de3e83d6faed9b29373f1f38942b79b991a7432943a84416d5cd'],
+        'checksums': [
+            'fcb479482644de3e83d6faed9b29373f1f38942b79b991a7432943a84416d5cd',  # doit-0.29.0.tar.gz
+        ],
     }),
-    # Exact version needed:
     ('nose', '1.3.4', {
         'source_urls': ['https://pypi.python.org/packages/source/n/nose'],
-        'checksums': ['76bc63a4e2d5e5a0df77ca7d18f0f56e2c46cfb62b71103ba92a92c79fab1e03'],
+        'checksums': [
+            '76bc63a4e2d5e5a0df77ca7d18f0f56e2c46cfb62b71103ba92a92c79fab1e03',  # nose-1.3.4.tar.gz
+        ],
     }),
-    # Exact version needed:
     ('nose-capturestderr', '1.0', {
         'modulename': 'nose_capturestderr',
         'source_urls': ['https://pypi.python.org/packages/source/n/nose-capturestderr'],
-        'checksums': ['8a05620bec5acaf006acfe59ad1225673350bba359e1b946ddba53206a3f8c98'],
+        'checksums': [
+            '8a05620bec5acaf006acfe59ad1225673350bba359e1b946ddba53206a3f8c98',  # nose-capturestderr-1.0.tar.gz
+        ],
     }),
     ('ficus', '0.3.3', {
         'source_urls': ['https://pypi.python.org/packages/source/f/ficus'],
-        'checksums': ['7dbd69a4aceb0406e53cf8ede98c039a03110b7b8860b64356554caf537b9324'],
+        'checksums': [
+            '7dbd69a4aceb0406e53cf8ede98c039a03110b7b8860b64356554caf537b9324',  # ficus-0.3.3.tar.gz
+        ],
     }),
     ('numexpr', '2.6.2', {
         'source_urls': ['https://pypi.python.org/packages/source/n/numexpr'],
-        'checksums': ['6ab8ff5c19e7f452966bf5a3220b845cf3244fe0b96544f7f9acedcc2db5c705'],
+        'checksums': [
+            '6ab8ff5c19e7f452966bf5a3220b845cf3244fe0b96544f7f9acedcc2db5c705',  # numexpr-2.6.2.tar.gz
+        ],
     }),
-    (name, version, {
+    ('dammit', '0.3.2', {
+        'patches': ['dammit-0.3.2_nodocs.patch'],
         'source_urls': ['https://pypi.python.org/packages/source/d/dammit'],
-        'checksums': ['400bb9c6644c4edd5f7b8bf294c142e89baa148008b3aba39d2c5e89f99ff278'],
+        'checksums': [
+            '400bb9c6644c4edd5f7b8bf294c142e89baa148008b3aba39d2c5e89f99ff278',  # dammit-0.3.2.tar.gz
+            '79dc4da8a778d842f7614e287add044cc0a7138d5a43ec80b378ac715054ae3b',  # dammit-0.3.2_nodocs.patch
+        ],
     }),
 ]
 
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

From 45776fd102609753d4f6aa95d03c93c5a5c468c5 Mon Sep 17 00:00:00 2001
From: Balazs Hajgato <hajgato@vub.ac.be>
Date: Thu, 26 Oct 2017 09:09:28 +0200
Subject: [PATCH 06/13] Change to Python 3.6.1

---
 ...ython-2.7.13.eb => dammit-0.3.2-intel-2017a-Python-3.6.1.eb} | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)
 rename easybuild/easyconfigs/d/dammit/{dammit-0.3.2-intel-2017a-Python-2.7.13.eb => dammit-0.3.2-intel-2017a-Python-3.6.1.eb} (99%)

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-3.6.1.eb
similarity index 99%
rename from easybuild/easyconfigs/d/dammit/dammit-0.3.2-intel-2017a-Python-2.7.13.eb
rename to easybuild/easyconfigs/d/dammit/dammit-0.3.2-intel-2017a-Python-3.6.1.eb
index f0ff1bcffe21..9926f608b641 100644
--- 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-3.6.1.eb
@@ -16,7 +16,7 @@ toolchain = {'name': 'intel', 'version': '2017a'}
 exts_defaultclass = 'PythonPackage'
 
 dependencies = [
-    ('Python', '2.7.13'),
+    ('Python', '3.6.1'),
     ('X11', '20170314'),
     ('matplotlib', '2.0.2', '-Python-%(pyver)s-Qt-4.8.7'),
     ('EMBOSS', '6.6.0', '-X11-20170314'),

From 2c99053870ed1291952c3c0c7e617791d96f80d7 Mon Sep 17 00:00:00 2001
From: Balazs Hajgato <hajgato@vub.ac.be>
Date: Thu, 26 Oct 2017 11:28:23 +0200
Subject: [PATCH 07/13] intermezzo

---
 .../dammit-0.3.2-intel-2017a-Python-3.6.1.eb  |  2 +-
 .../khmer-2.1.1-intel-2017a-Python-3.6.1.eb   | 51 +++++++++++++++++++
 2 files changed, 52 insertions(+), 1 deletion(-)
 create mode 100644 easybuild/easyconfigs/k/khmer/khmer-2.1.1-intel-2017a-Python-3.6.1.eb

diff --git a/easybuild/easyconfigs/d/dammit/dammit-0.3.2-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/d/dammit/dammit-0.3.2-intel-2017a-Python-3.6.1.eb
index 9926f608b641..56eb3b2a2933 100644
--- a/easybuild/easyconfigs/d/dammit/dammit-0.3.2-intel-2017a-Python-3.6.1.eb
+++ b/easybuild/easyconfigs/d/dammit/dammit-0.3.2-intel-2017a-Python-3.6.1.eb
@@ -18,7 +18,7 @@ exts_defaultclass = 'PythonPackage'
 dependencies = [
     ('Python', '3.6.1'),
     ('X11', '20170314'),
-    ('matplotlib', '2.0.2', '-Python-%(pyver)s-Qt-4.8.7'),
+    ('matplotlib', '2.0.2', '-Python-%(pyver)s-libpng-1.6.29'),
     ('EMBOSS', '6.6.0', '-X11-20170314'),
     ('HMMER', '3.1b2'),
     ('Infernal', '1.1.2'),
diff --git a/easybuild/easyconfigs/k/khmer/khmer-2.1.1-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/k/khmer/khmer-2.1.1-intel-2017a-Python-3.6.1.eb
new file mode 100644
index 000000000000..1e5df10ab286
--- /dev/null
+++ b/easybuild/easyconfigs/k/khmer/khmer-2.1.1-intel-2017a-Python-3.6.1.eb
@@ -0,0 +1,51 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Pablo Escobar Lopez
+# Swiss Institute of Bioinformatics
+# Biozentrum - University of Basel
+# 1.4.1 modified by:
+# Adam Huffman
+# The Francis Crick Institute
+
+easyblock = "Bundle"
+
+name = 'khmer'
+version = '2.1.1'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://github.com/ged-lab/khmer/'
+description = """ In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more """
+
+toolchain = {'name': 'intel', 'version': '2017a'}
+
+# this is a bundle of Python packages
+exts_defaultclass = 'PythonPackage'
+
+dependencies = [
+    ('Python', '3.6.1'),
+]
+
+exts_list = [
+    ('bz2file', '0.98', {
+        'source_urls': ['https://pypi.python.org/packages/source/b/bz2file'],
+        'checksums': ['64c1f811e31556ba9931953c8ec7b397488726c63e09a4c67004f43bdd28da88'],
+    }),
+    ('screed', '1.0', {
+        'source_urls': ['https://pypi.python.org/packages/source/s/screed'],
+        'checksums': ['5db69f8c413a984ade62eb8344a6eb2be26555d74be86d38512673c1cf621b91'],
+    }),
+    ('khmer', '2.1.1', {
+        'source_urls': ['https://github.com/ged-lab/khmer/archive/'],
+        'source_tmpl': 'v%(version)s.tar.gz',
+        'checksums': ['39981730c2e08ee183c5ce6ce80cfe2bd6d813cfa37b9ae1f7be0dd1a01dae85'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ["bin/%s" % x for x in ["count-median.py", "extract-long-sequences.py", "filter-abund.py",
+                                     "load-into-counting.py", "sample-reads-randomly.py"]],
+    'dirs': ["lib/python%(pyshortver)s/site-packages/khmer-%(version)s-py%(pyshortver)s-linux-x86_64.egg"],
+}
+
+modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']}
+
+moduleclass = 'bio'

From f8ee921cb5d74d082fc24deed50cbc586f02d3d0 Mon Sep 17 00:00:00 2001
From: Balazs Hajgato <hajgato@vub.ac.be>
Date: Fri, 27 Oct 2017 14:08:20 +0200
Subject: [PATCH 08/13] Use BUSCO w/Python2

---
 ...dammit-0.3.2-intel-2017a-Python-2.7.13.eb} | 41 ++++++-------------
 .../d/dammit/dammit-0.3.2_py2busco.diff       | 13 ++++++
 2 files changed, 26 insertions(+), 28 deletions(-)
 rename easybuild/easyconfigs/d/dammit/{dammit-0.3.2-intel-2017a-Python-3.6.1.eb => dammit-0.3.2-intel-2017a-Python-2.7.13.eb} (66%)
 create mode 100644 easybuild/easyconfigs/d/dammit/dammit-0.3.2_py2busco.diff

diff --git a/easybuild/easyconfigs/d/dammit/dammit-0.3.2-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/d/dammit/dammit-0.3.2-intel-2017a-Python-2.7.13.eb
similarity index 66%
rename from easybuild/easyconfigs/d/dammit/dammit-0.3.2-intel-2017a-Python-3.6.1.eb
rename to easybuild/easyconfigs/d/dammit/dammit-0.3.2-intel-2017a-Python-2.7.13.eb
index 56eb3b2a2933..8fe1d1792217 100644
--- a/easybuild/easyconfigs/d/dammit/dammit-0.3.2-intel-2017a-Python-3.6.1.eb
+++ b/easybuild/easyconfigs/d/dammit/dammit-0.3.2-intel-2017a-Python-2.7.13.eb
@@ -16,9 +16,9 @@ toolchain = {'name': 'intel', 'version': '2017a'}
 exts_defaultclass = 'PythonPackage'
 
 dependencies = [
-    ('Python', '3.6.1'),
+    ('Python', '2.7.13'),
     ('X11', '20170314'),
-    ('matplotlib', '2.0.2', '-Python-%(pyver)s-libpng-1.6.29'),
+    ('matplotlib', '2.0.2', '-Python-%(pyver)s-Qt-4.8.7'),
     ('EMBOSS', '6.6.0', '-X11-20170314'),
     ('HMMER', '3.1b2'),
     ('Infernal', '1.1.2'),
@@ -32,59 +32,44 @@ dependencies = [
 exts_list = [
     ('cloudpickle', '0.4.0', {
         'source_urls': ['https://pypi.python.org/packages/source/c/cloudpickle'],
-        'checksums': [
-            '5bb83eb466f0733dbd077e76cf1a15c404a94eb063cecc7049a1482fa1b11661',  # cloudpickle-0.4.0.tar.gz
-        ],
+        'checksums': ['5bb83eb466f0733dbd077e76cf1a15c404a94eb063cecc7049a1482fa1b11661'],
     }),
     ('pyinotify', '0.9.6', {
         'source_urls': ['https://pypi.python.org/packages/source/p/pyinotify'],
-        'checksums': [
-            '9c998a5d7606ca835065cdabc013ae6c66eb9ea76a00a1e3bc6e0cfe2b4f71f4',  # pyinotify-0.9.6.tar.gz
-        ],
+        'checksums': ['9c998a5d7606ca835065cdabc013ae6c66eb9ea76a00a1e3bc6e0cfe2b4f71f4'],
     }),
     ('configparser', '3.5.0', {
         'source_urls': ['https://pypi.python.org/packages/source/c/configparser'],
-        'checksums': [
-            '5308b47021bc2340965c371f0f058cc6971a04502638d4244225c49d80db273a',  # configparser-3.5.0.tar.gz
-        ],
+        'checksums': ['5308b47021bc2340965c371f0f058cc6971a04502638d4244225c49d80db273a'],
     }),
     ('doit', '0.29.0', {
         'source_urls': ['https://pypi.python.org/packages/source/d/doit'],
-        'checksums': [
-            'fcb479482644de3e83d6faed9b29373f1f38942b79b991a7432943a84416d5cd',  # doit-0.29.0.tar.gz
-        ],
+        'checksums': ['fcb479482644de3e83d6faed9b29373f1f38942b79b991a7432943a84416d5cd'],
     }),
     ('nose', '1.3.4', {
         'source_urls': ['https://pypi.python.org/packages/source/n/nose'],
-        'checksums': [
-            '76bc63a4e2d5e5a0df77ca7d18f0f56e2c46cfb62b71103ba92a92c79fab1e03',  # nose-1.3.4.tar.gz
-        ],
+        'checksums': ['76bc63a4e2d5e5a0df77ca7d18f0f56e2c46cfb62b71103ba92a92c79fab1e03'],
     }),
     ('nose-capturestderr', '1.0', {
         'modulename': 'nose_capturestderr',
         'source_urls': ['https://pypi.python.org/packages/source/n/nose-capturestderr'],
-        'checksums': [
-            '8a05620bec5acaf006acfe59ad1225673350bba359e1b946ddba53206a3f8c98',  # nose-capturestderr-1.0.tar.gz
-        ],
+        'checksums': ['8a05620bec5acaf006acfe59ad1225673350bba359e1b946ddba53206a3f8c98'],
     }),
     ('ficus', '0.3.3', {
         'source_urls': ['https://pypi.python.org/packages/source/f/ficus'],
-        'checksums': [
-            '7dbd69a4aceb0406e53cf8ede98c039a03110b7b8860b64356554caf537b9324',  # ficus-0.3.3.tar.gz
-        ],
+        'checksums': ['7dbd69a4aceb0406e53cf8ede98c039a03110b7b8860b64356554caf537b9324'],
     }),
     ('numexpr', '2.6.2', {
         'source_urls': ['https://pypi.python.org/packages/source/n/numexpr'],
-        'checksums': [
-            '6ab8ff5c19e7f452966bf5a3220b845cf3244fe0b96544f7f9acedcc2db5c705',  # numexpr-2.6.2.tar.gz
-        ],
+        'checksums': ['6ab8ff5c19e7f452966bf5a3220b845cf3244fe0b96544f7f9acedcc2db5c705'],
     }),
-    ('dammit', '0.3.2', {
-        'patches': ['dammit-0.3.2_nodocs.patch'],
+    (name, version, {
+        'patches': ['dammit-0.3.2_nodocs.patch', 'dammit-0.3.2_py2busco.diff'],
         '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
         ],
     }),
 ]
diff --git a/easybuild/easyconfigs/d/dammit/dammit-0.3.2_py2busco.diff b/easybuild/easyconfigs/d/dammit/dammit-0.3.2_py2busco.diff
new file mode 100644
index 000000000000..18c0bc5c7f73
--- /dev/null
+++ b/easybuild/easyconfigs/d/dammit/dammit-0.3.2_py2busco.diff
@@ -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,

From 83f80e25fd63d639d4b9b17ee8751760d36519dc Mon Sep 17 00:00:00 2001
From: Balazs Hajgato <hajgato@vub.ac.be>
Date: Fri, 27 Oct 2017 14:10:40 +0200
Subject: [PATCH 09/13] remove khmer w/Python3

---
 .../khmer-2.1.1-intel-2017a-Python-3.6.1.eb   | 51 -------------------
 1 file changed, 51 deletions(-)
 delete mode 100644 easybuild/easyconfigs/k/khmer/khmer-2.1.1-intel-2017a-Python-3.6.1.eb

diff --git a/easybuild/easyconfigs/k/khmer/khmer-2.1.1-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/k/khmer/khmer-2.1.1-intel-2017a-Python-3.6.1.eb
deleted file mode 100644
index 1e5df10ab286..000000000000
--- a/easybuild/easyconfigs/k/khmer/khmer-2.1.1-intel-2017a-Python-3.6.1.eb
+++ /dev/null
@@ -1,51 +0,0 @@
-# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
-# Author: Pablo Escobar Lopez
-# Swiss Institute of Bioinformatics
-# Biozentrum - University of Basel
-# 1.4.1 modified by:
-# Adam Huffman
-# The Francis Crick Institute
-
-easyblock = "Bundle"
-
-name = 'khmer'
-version = '2.1.1'
-versionsuffix = '-Python-%(pyver)s'
-
-homepage = 'https://github.com/ged-lab/khmer/'
-description = """ In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more """
-
-toolchain = {'name': 'intel', 'version': '2017a'}
-
-# this is a bundle of Python packages
-exts_defaultclass = 'PythonPackage'
-
-dependencies = [
-    ('Python', '3.6.1'),
-]
-
-exts_list = [
-    ('bz2file', '0.98', {
-        'source_urls': ['https://pypi.python.org/packages/source/b/bz2file'],
-        'checksums': ['64c1f811e31556ba9931953c8ec7b397488726c63e09a4c67004f43bdd28da88'],
-    }),
-    ('screed', '1.0', {
-        'source_urls': ['https://pypi.python.org/packages/source/s/screed'],
-        'checksums': ['5db69f8c413a984ade62eb8344a6eb2be26555d74be86d38512673c1cf621b91'],
-    }),
-    ('khmer', '2.1.1', {
-        'source_urls': ['https://github.com/ged-lab/khmer/archive/'],
-        'source_tmpl': 'v%(version)s.tar.gz',
-        'checksums': ['39981730c2e08ee183c5ce6ce80cfe2bd6d813cfa37b9ae1f7be0dd1a01dae85'],
-    }),
-]
-
-sanity_check_paths = {
-    'files': ["bin/%s" % x for x in ["count-median.py", "extract-long-sequences.py", "filter-abund.py",
-                                     "load-into-counting.py", "sample-reads-randomly.py"]],
-    'dirs': ["lib/python%(pyshortver)s/site-packages/khmer-%(version)s-py%(pyshortver)s-linux-x86_64.egg"],
-}
-
-modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']}
-
-moduleclass = 'bio'

From d86505c27c443581496d4a13245314b84c25b74f Mon Sep 17 00:00:00 2001
From: Balazs Hajgato <hajgato@vub.ac.be>
Date: Wed, 8 Nov 2017 11:53:06 +0100
Subject: [PATCH 10/13] copy LAST binary files to bin as well

---
 easybuild/easyconfigs/l/LAST/LAST-869-intel-2017a.eb | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/easybuild/easyconfigs/l/LAST/LAST-869-intel-2017a.eb b/easybuild/easyconfigs/l/LAST/LAST-869-intel-2017a.eb
index 34394533d959..db6e3740d13f 100644
--- a/easybuild/easyconfigs/l/LAST/LAST-869-intel-2017a.eb
+++ b/easybuild/easyconfigs/l/LAST/LAST-869-intel-2017a.eb
@@ -23,13 +23,18 @@ checksums = [
 
 builddependencies = [('binutils', '2.27')]
 
-list_of_executables = [
+list_of_scripts = [
     'fastq-interleave', 'last-dotplot', 'last-map-probs', 'last-postmask', 'last-train', 'maf-convert', 'maf-join',
     'maf-sort', 'maf-swap', 'parallel-fasta', 'parallel-fastq',
 ]
 
+list_of_executables = [
+    'lastal', 'lastal8', 'lastdb', 'lastdb8', 'last-merge-batches', 'last-pair-probs', 'last-split', 'last-split8',
+]
+
 files_to_copy = [
-    (['scripts/%s' % x for x in list_of_executables], "bin"),
+    (['src/%s' % x for x in list_of_executables], "bin"),
+    (['scripts/%s' % x for x in list_of_scripts], "bin"),
     'ChangeLog.txt',
     'COPYING.txt',
     'data',
@@ -40,7 +45,7 @@ files_to_copy = [
 ]
 
 sanity_check_paths = {
-    'files': ["bin/%s" % x for x in list_of_executables],
+    'files': ["bin/%s" % x for x in list_of_executables + list_of_scripts],
     'dirs': ['data', 'doc', 'examples', 'src'],
 }
 

From fc8e8ed53948440bf0526bf402855ffab863ac68 Mon Sep 17 00:00:00 2001
From: Balazs Hajgato <hajgato@vub.ac.be>
Date: Wed, 27 Dec 2017 19:24:02 +0100
Subject: [PATCH 11/13] crb-blast without ruby suffix

---
 .../d/dammit/dammit-0.3.2-intel-2017a-Python-2.7.13.eb          | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

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
index 8fe1d1792217..51ce51b3bbb9 100644
--- 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
@@ -26,7 +26,7 @@ dependencies = [
     ('LAST', '869'),
     ('TransDecoder', '2.1.0', '-Perl-5.24.1'),
     ('khmer', '2.1.1', '-Python-%(pyver)s'),
-    ('crb-blast', '0.6.9', '-Ruby-2.3.4'),
+    ('crb-blast', '0.6.9'),
 ]
 
 exts_list = [

From 369c915715575e7081e7e2ca471c1309aafbc9c3 Mon Sep 17 00:00:00 2001
From: Balazs Hajgato <hajgato@vub.ac.be>
Date: Sat, 30 Dec 2017 16:02:34 +0100
Subject: [PATCH 12/13] Comments implemented

---
 .../d/dammit/dammit-0.3.2-intel-2017a-Python-2.7.13.eb       | 5 ++++-
 ...ammit-0.3.2_py2busco.diff => dammit-0.3.2_py2busco.patch} | 0
 easybuild/easyconfigs/l/LAST/LAST-869-intel-2017a.eb         | 4 ----
 .../TransDecoder-2.1.0-intel-2017a-Perl-5.24.1.eb            | 3 +--
 4 files changed, 5 insertions(+), 7 deletions(-)
 rename easybuild/easyconfigs/d/dammit/{dammit-0.3.2_py2busco.diff => dammit-0.3.2_py2busco.patch} (100%)

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
index 51ce51b3bbb9..13200b3bb164 100644
--- 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
@@ -64,7 +64,10 @@ exts_list = [
         'checksums': ['6ab8ff5c19e7f452966bf5a3220b845cf3244fe0b96544f7f9acedcc2db5c705'],
     }),
     (name, version, {
-        'patches': ['dammit-0.3.2_nodocs.patch', 'dammit-0.3.2_py2busco.diff'],
+        '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
diff --git a/easybuild/easyconfigs/d/dammit/dammit-0.3.2_py2busco.diff b/easybuild/easyconfigs/d/dammit/dammit-0.3.2_py2busco.patch
similarity index 100%
rename from easybuild/easyconfigs/d/dammit/dammit-0.3.2_py2busco.diff
rename to easybuild/easyconfigs/d/dammit/dammit-0.3.2_py2busco.patch
diff --git a/easybuild/easyconfigs/l/LAST/LAST-869-intel-2017a.eb b/easybuild/easyconfigs/l/LAST/LAST-869-intel-2017a.eb
index db6e3740d13f..2ae51e8fe11e 100644
--- a/easybuild/easyconfigs/l/LAST/LAST-869-intel-2017a.eb
+++ b/easybuild/easyconfigs/l/LAST/LAST-869-intel-2017a.eb
@@ -13,16 +13,12 @@ toolchainopts = {'cstd': 'c++11', 'opt': True}
 
 source_urls = ['http://last.cbrc.jp/']
 sources = ['%(namelower)s-%(version)s.zip']
-
 patches = ['%(name)s-%(version)s_makefile.patch']
-
 checksums = [
     '6371a6282bc1bb02a5e5013cc463625f2ce3e7746ff2ea0bdf9fe6b15605a67c',  # last-869.zip
     'b7b697b048e22c913eb196449eb895fc70b22fb72db5cca1f8dc948cde164309',  # LAST-869_makefile.patch
 ]
 
-builddependencies = [('binutils', '2.27')]
-
 list_of_scripts = [
     'fastq-interleave', 'last-dotplot', 'last-map-probs', 'last-postmask', 'last-train', 'maf-convert', 'maf-join',
     'maf-sort', 'maf-swap', 'parallel-fasta', 'parallel-fastq',
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
index 2a7396dd4a76..e4d2fdc6f094 100644
--- 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
@@ -14,7 +14,6 @@ toolchain = {'name': 'intel', 'version': '2017a'}
 
 source_urls = ['https://github.com/TransDecoder/TransDecoder/archive/']
 sources = ['v%(version)s.tar.gz']
-
 checksums = ['681a8dd72e482cb322d74d8431ddcda61f25c53ad5453d0e22c02c92b2157b24']
 
 dependencies = [
@@ -23,7 +22,7 @@ dependencies = [
 ]
 
 sanity_check_paths = {
-    'files': ['TransDecoder.%s' % x for x in ['Predict', 'LongOrfs']],
+    'files': ['TransDecoder.LongOrfs', 'TransDecoder.Predict'],
     'dirs': ['PerlLib', 'sample_data', 'util'],
 }
 

From 957090e57598a362bbca2246d11c669fd6e2c86a Mon Sep 17 00:00:00 2001
From: Balazs Hajgato <hajgato@vub.ac.be>
Date: Sat, 30 Dec 2017 19:57:19 +0100
Subject: [PATCH 13/13] change LATS to ConfigureMake

---
 .../l/LAST/LAST-869-intel-2017a.eb            | 46 +++++--------------
 .../l/LAST/LAST-869_makefile.patch            | 29 ------------
 2 files changed, 12 insertions(+), 63 deletions(-)
 delete mode 100644 easybuild/easyconfigs/l/LAST/LAST-869_makefile.patch

diff --git a/easybuild/easyconfigs/l/LAST/LAST-869-intel-2017a.eb b/easybuild/easyconfigs/l/LAST/LAST-869-intel-2017a.eb
index 2ae51e8fe11e..f16714bf12e5 100644
--- a/easybuild/easyconfigs/l/LAST/LAST-869-intel-2017a.eb
+++ b/easybuild/easyconfigs/l/LAST/LAST-869-intel-2017a.eb
@@ -1,48 +1,26 @@
-easyblock = 'MakeCp'
+easyblock = 'ConfigureMake'
 
 name = 'LAST'
 version = '869'
 
 homepage = 'http://last.cbrc.jp/'
-description = """ LAST finds similar regions between sequences. The main technical innovation
- is that LAST finds initial matches based on their multiplicity,
- instead of using a fixed length (e.g. BLAST uses 11-mers)."""
+description = "LAST finds similar regions between sequences."
 
 toolchain = {'name': 'intel', 'version': '2017a'}
-toolchainopts = {'cstd': 'c++11', 'opt': True}
+toolchainopts = {'cstd': 'c++11'}
 
 source_urls = ['http://last.cbrc.jp/']
-sources = ['%(namelower)s-%(version)s.zip']
-patches = ['%(name)s-%(version)s_makefile.patch']
-checksums = [
-    '6371a6282bc1bb02a5e5013cc463625f2ce3e7746ff2ea0bdf9fe6b15605a67c',  # last-869.zip
-    'b7b697b048e22c913eb196449eb895fc70b22fb72db5cca1f8dc948cde164309',  # LAST-869_makefile.patch
-]
-
-list_of_scripts = [
-    'fastq-interleave', 'last-dotplot', 'last-map-probs', 'last-postmask', 'last-train', 'maf-convert', 'maf-join',
-    'maf-sort', 'maf-swap', 'parallel-fasta', 'parallel-fastq',
-]
-
-list_of_executables = [
-    'lastal', 'lastal8', 'lastdb', 'lastdb8', 'last-merge-batches', 'last-pair-probs', 'last-split', 'last-split8',
-]
-
-files_to_copy = [
-    (['src/%s' % x for x in list_of_executables], "bin"),
-    (['scripts/%s' % x for x in list_of_scripts], "bin"),
-    'ChangeLog.txt',
-    'COPYING.txt',
-    'data',
-    'doc',
-    'examples',
-    'README.txt',
-    'src',
-]
+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/%s" % x for x in list_of_executables + list_of_scripts],
-    'dirs': ['data', 'doc', 'examples', 'src'],
+    'files': ['bin/lastal', 'bin/lastdb'],
+    'dirs': [],
 }
 
 moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/l/LAST/LAST-869_makefile.patch b/easybuild/easyconfigs/l/LAST/LAST-869_makefile.patch
deleted file mode 100644
index 54976cebe978..000000000000
--- a/easybuild/easyconfigs/l/LAST/LAST-869_makefile.patch
+++ /dev/null
@@ -1,29 +0,0 @@
-# Pick up EB CXXFLAGS
-# September 11th 2017 by B. Hajgato (Free Univeristy Brussels - VUB)
---- last-869/makefile.orig	2016-12-13 07:22:11.000000000 +0100
-+++ last-869/makefile	2017-09-11 14:14:17.989174000 +0200
-@@ -1,4 +1,4 @@
--CXXFLAGS = -O3 -std=c++11 -pthread -DHAS_CXX_THREADS
-+CXXFLAGS += -pthread -DHAS_CXX_THREADS
- all:
- 	@cd src && $(MAKE) CXXFLAGS="$(CXXFLAGS)"
- 
---- last-869/src/makefile.orig	2017-06-02 12:27:21.000000000 +0200
-+++ last-869/src/makefile	2017-09-20 16:49:03.731331507 +0200
-@@ -1,12 +1,11 @@
--CXX = g++
--CC  = gcc
-+CXX ?= g++
-+CC  ?= gcc
- 
--CXXFLAGS = -O3 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef	\
---Wcast-align -pedantic -g -std=c++11 -pthread -DHAS_CXX_THREADS
-+CXXFLAGS += -pthread -DHAS_CXX_THREADS
- # -Wconversion
- # -fomit-frame-pointer ?
- 
--CFLAGS = -Wall -O2
-+CFLAGS ?= -Wall -O2
- 
- alpObj = alp/sls_alignment_evaluer.o alp/sls_pvalues.o		\
- alp/sls_alp_sim.o alp/sls_alp_regression.o alp/sls_alp_data.o	\